OCS Study 

•

MMS 2001-070 

Methods for Performing Monitoring, 

Impact, and Ecological Studies on 

Rocky Shores 

Final Technical Summary 

Final Study Report 

U.S. Department of the Interior 

Minerals Management Service

Pacific OCS Region 

 
Final Technical Summary – Murray et al. 

2
3

Methods for Performing Monitoring, 

Impact, and Ecological Studies on 

Rocky Shores 

Final Technical Summary 

Final Study Report 

Authors 

Steven N. Murray 

Richard F. Ambrose 

Principal Investigators 

and 

Megan N. Dethier

Prepared under MMS Cooperative 

Agreement No. 14-35-0001-30761 

by 

Southern California Educational Initiative 

Marine Science Institute 

University of California 

Santa Barbara, CA 93106 

U.S. Department of the Interior 

Minerals Management Service Camarillo

Pacific OCS Region March 2002
Final Technical Summary – Murray et al. 

4

Disclaimer 

This report has been reviewed by the Pacific Outer Continental Shelf Region, Minerals 

Management Service, U.S. Department of the Interior and approved for publication. The 

opinions, findings, conclusions, or recommendations in this report are those of the author, and do 

not necessarily reflect the views and policies of the Minerals Management Service. Mention of 

trade names or commercial products does not constitute an endorsement or recommendation for 

use. This report has not been edited for conformity with Minerals Management Service editorial 

standards. 

Availability of Report

Extra copies of the report may be obtained from: 

U.S. Dept. of the Interior 

Minerals Management Service 

Pacific OCS Region 

770 Paseo Camarillo 

Camarillo, CA 93010 

Phone: 805-389-7621 

A PDF file of this report is available at: 

http://www.coastalresearchcenter.ucsb.edu/SCEI/ 

Suggested Citation 

The suggested citation for this report is: 

Murray, Steven N., Ambrose, Richard F., and Megan N. Dethier. Methods for Performing 

Monitoring, Impact, and Ecological Studies on Rocky Shores. MMS OCS Study 2001-070. 

Coastal Research Center, Marine Science Institute, University of California, Santa Barbara, 

California. MMS Cooperative Agreement Number 14-35-0001-30761. 217 pages. 
5

TABLE OF CONTENTS

FINAL TECHNICAL SUMMARY 1 

FINAL STUDY REPORT: Methods for Performing Monitoring, 

Impact, and Ecological Studies on Rocky Shores

by S.N. Murray, R.F. Ambrose, and M.N. Dethier 3 

 Acknowledgements 3 

 About the Authors 5 

 Foreward 7 

 

Chapter 1. Designing Rocky Intertidal Monitoring and Impact 

 Field Studies: A Brief Overview by Steven N. Murray 8-21 

 

 Introduction 9 

 Design Elements for Rocky Intertidal Field Studies 10 

 Study Types and Goals 11 

 Study Designs 12 

 One-Time or “One-Off” Baseline Studies 13 

 Impact Studies 13 

 Monitoring Programs 17 

 Literature Cited 19 

Chapter 2. Site Classification and Selection

 by Megan N. Dethier 22-47 

 Introduction 23 

 Classifying Shorelines 24 

 Geophysical Features 25 

 Wave Energy 25 

 Aspect and Slope 28 

 Topographical Heterogeneity and Rock Type 28 

 Sand Burial and Scour 29 

 Salinity 30 

 Human Disturbance 30 

 Mapping Methods 31 

 Habitat Types 33 

 Methods for Site Selection 36 

 Monitoring Studies 36 

 Impact Studies 39 

 Numbers of Sampling Sites 40 

 Summary 41 

 Literature Cited 42 

 
Final Technical Summary – Murray et al. 

6

 

Chapter 3. Biological Units

by Megan N. Dethier 48-73 

 Introduction 49 

 Species-Level Sampling 49 

 Down-a-Level: Individual-Based Sampling 55 

 Up-a-Level: Supra-Species Sampling 56 

 Higher Taxonomic Categories 57 

 Functional Groups 58 

 Community-Level Metrics 60 

 Summary 66 

 Literature Cited 67 

 

Chapter 4. Sampling Design

 by Richard F. Ambrose 74-97 

 

 Introduction 75 

 Statistical Considerations 75 

 Assumptions 75 

 Statistical Power 77 

 Location of Sampling Units 79 

 Distribution of Sampling Effort 79 

 Establishing Sample Locations 79 

 Random 79 

 Systematic 81 

 Targeted 82 

 Stratification 82 

 Comparison of Approaches 85 

 One-Time (“One-Off”) versus Repeated Assessments 86 

 Fixed Plots 87 

 Comparison of Fixed versus Non-fixed Plots 89 

 Number of Samples: How Many is Enough? 90 

 Impact Assessment 93 

 Summary 94 

 Literature Cited 95 

 
7

Chapter 5. Transects, Quadrats, and Other Sampling Units

 by Richard F. Ambrose 98-122 

 Introduction 99 

 Quadrat or Plot-Based Methods 99 

 Line Transects 100 

 Plots or Quadrats 104 

 Comparing Transects and Quadrats 107 

 Size of Sampling Units 108 

 Plotless Designs 110 

 Distance Sampling Methods 111 

 Timed Search 113 

 Special Habitats 114 

 Tidepools 115 

 Boulderfields 115 

 Summary 118 

 Literature Cited 119 

Chapter 6. Quantifying Abundance: Density and Cover

 by Steven N. Murray 123-154 

 

 Introduction 124 

 Rapid Surveys 124 

 Plotless and Line Transect Methods 128 

 Plot or Quadrat-Based Methods 130 

 Density 130 

 Cover 132 

 Field Methods: Visual Scanning 136 

 Field Methods: Point Contacts 137 

 Photographic Sampling 140 

 35-mm Photographic Sampling 141 

 Video Sampling 145 

 Laboratory Assessment of Photographic Samples 146 

 Summary 148 

 Literature Cited 150 

 
Final Technical Summary – Murray et al. 

8

Chapter 7. Quantifying Abundance: Biomass

 by Steven N. Murray 155-169 

 Introduction 156 

 Harvesting Procedures 159 

 Biomass Determination 163 

 Wet Biomass 163 

 Dry Biomass 164 

 Ash-Free Dry Biomass 165 

 Summary 167 

 Literature Cited 167 

Chapter 8. Individual-Based Parameters: Age-Determination, 

 Growth Rates, Size Structure, and Reproduction

 By Steven N. Murray 170-206 

 Introduction 171 

 Seaweeds 173 

 Growth Rates and Age Determination 173 

 Growth Rates 173 

 Age Determination 174 

 Population Size Structure 176 

 Sex or Phase Ratios 178 

 Reproductive Output 179 

 Macroinvertebrates 182 

 Growth Rates 182 

 Marking Animals with Tags 183 

 Measuring Growth 185 

 Age Determination 187 

 Annuli and Growth Rings 187 

 Age Calculation from Growth Rates 188 

 Population Size Structure 189 

 Size-Frequency Profiles 189 

 Growth Rates from Size-Frequency Profiles 191 

 Reproductive Condition and Output 193 

 Summary 197 

 Literature Cited 199 

Subject Index 207 

Taxonomic Index 216 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

1

FINAL TECHNICAL SUMMARY 

STUDY TITLE: Methods for Performing Monitoring, Impact, and Ecological Studies on 

Rocky Shores 

REPORT TITLE: Methods for Performing Monitoring, Impact, and Ecological Studies on 

Rocky Shores 

CONTRACT NUMBER: 14-35-0001-30761 

SPONSORING OCS REGION: Pacific 

APPLICABLE PLANNING AREA: Pacific Coast of North America including Alaska; Other 

areas where rocky shores occur 

FISCAL YEAR OF PROJECT FUNDING: FY 96 

COMPLETION DATE OF REPORT: March 2002 

COSTS: FY 96 - $43,825 (CSUF) and $58,108 (UCLA), FY 97 – no cost, FY 98 – no cost, FY 

99 – no cost, FY 00 – no cost, FY 01 – no cost 

CUMULATIVE PROJECT COST: $101,933 

PROJECT MANAGER: Steven N. Murray 

AFFILIATION: California State University, Fullerton 

ADDRESS: Department of Biological Sciences, California State University, 800 North State 

College Blvd., Fullerton, CA 92834-6850 

PRINCIPAL INVESTIGATORS: 1

Steven N. Murray and 2Richard F. Ambrose 

ADDRESSES: 1

Department of Biological Sciences, California State University, 800 North 

State College Blvd., Fullerton, CA 92834-6850; 2

Department of Environmental Health Sciences, 

University of California, Box 951772, Los Angeles, CA 90095-1772

KEY WORDS: Rocky Intertidal; Monitoring Studies; Impact Studies; Benthic Sampling 

Programs, Benthic Study Designs; Site Selection; Marine Invertebrates, Seaweeds, Seagrasses 

BACKGROUND: This book describes and discusses methods and approaches for performing 

monitoring, impact, and ecological studies of rocky intertidal populations and communities. 

Emphasis is placed on intertidal macroinvertebrates, seaweeds, and seagrasses. Developing 

effective sampling procedures to detect ecologically meaningful changes in population and 

community parameters is often challenging in rocky intertidal habitats. This project grew out of 
Final Technical Summary – Murray et al. 

2

discussions held at a workshop on rocky intertidal monitoring programs and a symposium on this 

topic convened at an annual meeting of the Southern California Academy of Sciences. The 

contents and organization of this book were developed by the three authors (Steven N. Murray, 

Richard F. Ambrose, and Megan N. Dethier), who individually authored its chapters. 

OBJECTIVES: The objectives of this volume are to provide descriptions and analyses of 

methods and approaches for sampling rocky intertidal macroinvertebrate and macrophyte 

populations and communities. Emphasis has been placed on procedures used in monitoring and 

impact studies. A goal of this work is to identify sampling issues and concerns and to facilitate 

decision-making for parties involved in developing rocky intertidal sampling programs. 

DESCRIPTION: This volume attempts to improve understanding of the various approaches 

used in executing rocky intertidal sampling programs. Included are discussions of the principles 

of designing effective monitoring and impact studies, site selection, the taxonomic or other 

biological units chosen for sampling, sampling layouts and designs, the use of transects, 

quadrats, and other sampling units, methods for quantifying species abundances, and methods for 

determining growth rates, age, population size structure, and reproductive condition. The volume 

consists of a total of eight chapters, and includes besides the volume cover, eight chapter cover 

photos, 52 photos and figures, and 11 tables. The volume also contains a taxonomic and subject 

index. 

SIGNIFICANT CONCLUSIONS: The discussions of sampling and study approaches represent 

key contributions to the literature available to individuals interested in designing, executing, and 

evaluating rocky intertidal sampling programs. The various methods and techniques are 

described and sufficiently evaluated for readers to determine the best approaches to meet the 

goals of their specific studies. 

STUDY RESULTS: Methods and approaches for selecting sites, determining the biological 

units to be studied, developing field sampling layouts and designs, identifying appropriate 

sampling units and sample numbers, quantifying species abundances, and determining growth 

rates, age, population size structure, and reproductive condition are described and evaluated. The 

volume summarizes various methods and approaches commonly used in intertidal sampling 

programs and discusses their efficacy. In addition to contributing to on-going academic 

discussions of sampling methodologies, this volume also provides a practical guide to parties 

interested in designing cost-effective and scientifically sound monitoring and impact studies. 

STUDY PRODUCT: 

Murray, S.N., R.F. Ambrose, and M.N. Dethier. 2002. Methods for Performing Monitoring, 

Impact, and Ecological Studies on Rocky Shores. Technical Report prepared for the U. S. 

Department of Interior, Minerals Management Service, Pacific OCS Region, Camarillo, 

California. OCS Study MMS 2001-070. MMS Cooperative Agreement No. 14-35-0001-

30761. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

3

FINAL STUDY REPORT 

Acknowledgements 

Putting together this book proved to be a much longer and more difficult task than originally 

envisioned, and we would not have been able to complete this project without the contributions, 

assistance, and patience of many individuals. 

First, our thanks go to Fred Piltz, Mary Elaine Dunaway, and Maurice Hill of the Minerals 

Management Service (Pacific Region) of the U. S. Department of Interior for their assistance and 

support throughout this project. It is clearly to their credit that Fred, Mary Elaine, Maurice, and 

others at MMS recognize that strong and well thought out study and sampling programs cannot 

be taken for granted, particularly in variable rocky intertidal habitats. We thank Mary Elaine for 

her support, encouragement, and patience throughout this project. 

Funds to organize and develop this handbook were provided by MMS through the Southern 

California Educational Initiative (SCEI) program (MMS Agreement No. 14-35-0001-30761) 

administered by the Marine Science Institute (MSI) of the University of California, Santa 

Barbara. We are grateful for the patience and interest in this project displayed by Russ Schmitt, 

Director of the SCEI program, and very much appreciate the excellent administrative support 

provided by Bonnie Williamson of the MSI who served as SCEI Program Manager. 

Mary Elaine Dunaway and Maurice Hill from MMS, John Tarpley and Rob Ricker from the 

Office of Spill Prevention and Response (OSPR) unit of the California Department of Fish and 

Game, and John Cubit from NOAA’s Natural Resources Damage Assessment (NRDA) Division 

provided guidance and direction at the initial stages of developing this handbook, with the hope 

that multiple needs could be met by a single product. We are grateful for the guidance, criticism, 

and insight provided by Mary Elaine, Maurice, John, Rob, and John. Their reviews of earlier 

drafts of this handbook are much appreciated. 

Peer-reviews of the chapters contained in this handbook were carried out by several individuals 

besides our MMS, OSPR and NOAA colleagues. Specifically, we would like to thank Gray 

Williams, Susan Brawley, Roger Seapy, the late Mia Tegner, Pete Raimondi, Jack Engle, Helen 

Berry, and Lucinda Tear for reviewing whole or sections of handbook chapters. Numerous other 

individuals were also contacted for advice and discussion during development of this work. We 

are grateful for their comments and insight and the many constructive suggestions made by our 

reviewers. The assistance of our reviewers and colleagues clearly made the final draft of this 

book a better product. We take responsibility for any remaining mistakes, errors, or inaccuracies, 

and appreciate the efforts of our reviewers to keep us on the right path. 

Finally, we would like to thank Esther Scale for clerical support, Kelly Donovan for assistance 

with most of the line-art, and Janine Kido and Jayson Smith for their comments and support 

during various stages of this project. SNM would like to acknowledge Phyllis Grifman of the 

University of Southern California Sea Grant Program for encouraging work on this handbook, 
Final Study Report – Murray et al. 

4

and the National Sea Grant Program and the California State Resources Agency (NOAA Grant 

NA46RG0472 to the USC Sea Grant Program) for funding studies on rocky intertidal systems 

that contributed greatly to the development of the discussions in Chapters 1, 6, 7, and 8 of the 

handbook. SNM would also like to thank C. Eugene Jones (Chairperson) and the Department of 

Biological Science at California State University, Fullerton, for support and assistance during the 

development and completion of this project. RFA would like to acknowledge the California 

Coastal Commission for funding studies that contributed to the discussions in Chapters 4 and 5.

MND gratefully acknowledges helpful discussions and input from Carl Schoch and Lucinda 

Tear, and support from the Friday Harbor Laboratories during the writing of Chapters 2 and 3. 

The views, opinions, and conclusions in this book are solely those of the authors and do not 

necessarily reflect the views or official policies, either expressed or implied, of MMS, OSPR, 

NOAA or any other Federal, State, or local government or governmental agency of the United 

States. Mention of trade names or commercial products does not constitute an endorsement or 

recommendation for use. This contribution has been reviewed by the Pacific Outer Continental 

Shelf Region, Minerals Management Service, U. S. Department of the Interior and approved for 

publication. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

5

About The Authors 

Dr. Steven N. Murray 

Department of Biological Science 

California State University, Fullerton 

Fullerton, California, USA 

Steve Murray is a Professor of Biology at California State University, Fullerton. He received his 

B. A. and M. A. degrees from UC Santa Barbara in 1966 and 1968, and his Ph.D. at the 

University of California, Irvine in 1971. For his dissertation work, he studied the reproduction 

and life histories of red seaweeds under the mentorship of Peter Dixon. He has been studying 

coastal communities and processes for more than 30 years as a faculty member at California 

State University, Fullerton. Steve has published on topics such as marine herbivory, 

biogeography, human impacts on coastal populations and communities, genetic structure of 

coastal populations, and the physiological ecology and reproductive biology of seaweeds. Most 

of his research has been performed in temperate Californian waters. His recent research has 

focused on determining long-term changes in species distributions and abundances, productivity, 

and food web structure in rocky intertidal communities over a period of shifts in oceanographic 

climate and increasing urbanization. His research has included evaluation of the success of 

coastal reserves in protecting rocky intertidal populations and communities receiving high 

amounts of human use. This research has involved assessments of the abundances and structures 

of extracted and trampled populations in and outside of longstanding coastal reserves. He is also 

participating in a regional program designed to monitor temporal changes in rocky intertidal 

populations and communities over regional spatial scales. Recently, he initiated studies of exotic, 

aquarium-traded seaweeds to determine their potential for invading temperate California waters. 

Dr. Richard F. Ambrose 

Department of Environmental Health Sciences 

University of California, Los Angeles 

Los Angeles, California, USA 

Rich Ambrose is Professor in the Department of Environmental Health Sciences and Director of 

the Environmental Science and Engineering Program at the University of California, Los 

Angeles. He received his B.S. in Biological Sciences from UC Irvine in 1975 and his Ph.D. in 

Marine Ecology from UCLA in 1982. After conducting postdoctoral research at Simon Fraser 

University in Vancouver, British Columbia, he spent seven years at the Marine Science Institute 

at UC Santa Barbara, before coming to UCLA in 1992. His research focuses on the ecological 

aspects of environmental problems, particularly in coastal environments, and he has worked in 

intertidal, subtidal and wetland habitats. His current research on environmental issues centers on 

the restoration of degraded coastal habitats, especially wetlands, and ecological monitoring and 

assessment. He is currently working on several tidal wetland restoration projects in California. 

Other research projects include monitoring change in rocky intertidal habitats (with a particular 

focus on being able to detect effects of oil spills) using a network of monitoring sites throughout 

southern California, assessing the nature of human activities in rocky intertidal habitats and 
Final Study Report – Murray et al. 

6

determining ways to restore degraded intertidal communities, assessing the impacts of 

contaminants on coastal wetland species, developing performance standards for determining the 

success of habitat restoration projects, understanding the dynamics of sea urchin-dominated 

rocky reefs, and evaluating alternatives for managing watershed-level ecological problems. 

Dr. Megan N. Dethier 

Friday Harbor Laboratories and 

Department of Zoology 

University of Washington 

Friday Harbor, Washington, USA 

Megan Dethier grew up spending summers on the shores of New England and was thus preadapted to become a marine biologist. She did her undergraduate work at Carleton College in 

Minnesota, despite the apparent lack of ocean there, and then did her Ph.D. work under Bob 

Paine at the University of Washington, near a real ocean. Her dissertation revolved around the 

community ecology of intertidal pools. Since completing graduate work she has been in 

residence at the Friday Harbor Laboratories and is a Research Associate Professor in the Zoology 

Department at University of Washington. She has thus worked on shoreline ecology of the 

Pacific Northwest for over 25 years, first exclusively on rocky shores but now also in mud, 

gravel, and salt marsh habitats. She designed a marine habitat classification system for 

Washington State, and has helped the National Park Service and various Washington state 

agencies design shoreline mapping and monitoring programs. Her current research efforts 

include: 1) investigating the linkage between physical features of shoreline habitats and their 

biota; 2) studying the plant/herbivore ecology and ecophysiology of an intertidal seaweed; and 

3) investigating interactions between native salt marsh communities and an invasive cordgrass in 

Puget Sound. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

7

Foreward 

The purpose of this handbook is to provide interested investigators with the information needed 

to determine the methods and procedures for carrying out key elements of a rocky intertidal 

field-sampling program. Critical discussions and evaluations of the various elements of an 

effective rocky intertidal field-sampling program are provided in the ensuing chapters. The 

handbook has been written for research and agency scientists, agency managers, and students 

who might benefit from consolidated discussions and reviews of important sampling issues and 

field procedures for designing and evaluating field monitoring and impact studies performed on 

rocky intertidal macroinvertebrates, seaweeds, and seagrasses. Emphasis has been placed on 

describing and discussing options for field methods and procedures with a focus on their use in 

monitoring programs and impact studies. Users are required to formulate their own study goals 

and study designs. Clearly, any effective study program must have clear goals and objectives and 

invoke robust study designs. 

In this handbook, we have attempted to break down the decision-making process into its various 

elements so investigators can become aware of the advantages and disadvantages of choosing a 

particular method or approach and can consider trade-offs between time and cost and the value 

of the collected data. No handbook can serve as a menu of fixed procedures for sampling 

complex rocky intertidal environments. Spatial variability and different site histories mean that 

the methods and procedures that best match study goals at one site may not be optimal at another 

site where habitat topography and the distributions and abundances of targeted species vary. For 

example, the size and number of sampling units required to effectively determine the abundances 

of a dense barnacle population at one site might differ from those selected to optimally sample 

the same species at another site where densities are much lower and the habitat is more 

topographically heterogeneous. For these reasons, it is impossible to prescribe standard protocols 

or procedures that can be used effectively to sample rocky intertidal organisms under all 

encountered conditions. Instead, sound scientific studies can only be designed following careful 

consideration of each element of the field-sampling program. This requires that investigators 

have sufficient information to select procedures that best address study goals and questions given 

consideration of tidal schedules and available resources. In the following chapters, we 

sequentially present discussions of factors involved in site selection (Chapter 2), the biological 

units to be sampled (Chapter 3), field sampling layouts and designs (Chapter 4), selection of 

sampling units (Chapter 5), non-destructive (Chapter 6) and destructive (Chapter 7) methods of 

quantifying abundance, and methods for measuring age, growth rates, size structure and 

reproductive condition intertidal organisms (Chapter 8). 
Final Study Report – Murray et al. 

8

Chapter 1. 

Designing Rocky Intertidal Monitoring and Impact 

Field Studies: a Brief Overview 

By 

Steven N. Murray 

 Victoria Street Beach, Laguna Beach, California 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

9

Introduction 

Field sampling programs provide the information needed to determine the status and dynamics of 

populations and communities and thus are the foundation for many kinds of research, including 

impact and monitoring studies. Certain habitat types present more formidable challenges 

compared with others when it comes to designing and performing field studies. The rocky 

intertidal zone is one of these habitat types. Basic descriptions of the natural history and abiotic 

and biotic patterns and processes that characterize rocky intertidal environments will not be 

addressed here. The interested reader can find such discussions in many sources, including, for 

example, Lewis (1964), Stephenson and Stephenson (1972), Carefoot (1977), Kozloff(1983), 

Ricketts et al. (1985), Raffaelli and Hawkins (1996), Knox (2000), and Menge and Branch 

(2000). The unique features of rocky intertidal environments need to be understood in order to 

select the most appropriate field procedures for sampling rocky intertidal organisms. 

The physical and biological complexity of most rocky shores results in high variability in almost 

any measured parameter, even over very short vertical and horizontal scales. The sources of this 

variability must be taken into account when designing and performing field sampling programs 

in rocky intertidal habitats. 

Unlike terrestrial habitats, the intertidal zone is accessible for most studies only during limited 

periods when the tide is low. These periods will vary daily in both tidal magnitude and the time 

of day when they occur. Hence, intertidal investigators must develop work calendars and plans 

dictated by the tides, and be prepared to perform fieldwork during almost any hour of the day 

depending on tidal schedules. In addition, daily fieldwork must be performed efficiently in order 

to complete sampling programs during the few hours when the tide is out and the shore is 

accessible. 

Although environmental conditions are usually quite constant in most marine habitats, the 

intertidal zone experiences large changes over the daily tidal cycle, with higher shore elevations 

receiving longer periods of emersion and exposure to physically-harsh conditions. This creates a 

strong vertical gradient in stressful physical conditions running up and down the shore, which 

contributes to the well-known zonation patterns displayed by rocky intertidal organisms. Rocky 

shores also show horizontal gradients of exposure to wave action and, if near freshwater inputs, 

salinity. In addition, rocky shores vary over horizontal scales in substratum type and topography. 

Some shores are dominated by expansive flattened benches, others by steeply sloped vertical 

stacks, while others consist mostly of boulders and rocks that can vary in size from centimeters 

(shingles, cobbles, and small boulders) to meters (large boulders). Crevices, channels, and pools 

typically break up even the most flattened rocky intertidal benches. Thus, almost all rocky 

intertidal habitats appear as a heterogeneous mosaic of microhabitat types resulting in a 

landscape that varies greatly even over very short vertical and horizontal distances. 
Final Study Report – Murray et al. 

10

Rocky intertidal habitats are perhaps best known for the rich variety of organisms that they 

support. Although fishes and other mobile organisms play a role during periods of tidal 

immersion, slow-moving and sessile invertebrates, seaweeds, and seagrasses dominate the 

intertidal landscape during periods of low tide, when rocky intertidal habitats can most easily be 

accessed. Historically, it is this rich and diverse assemblage of benthic invertebrates and marine 

plants, distributed over short expanses of variable shoreline, that has attracted the public, 

educators, and members of the scientific community to engage in exploration and study in the 

rocky intertidal zone. The strong vertical and horizontal gradients in environmental conditions 

affect the distributions and abundances of these organisms and contribute to community 

structures that vary with vertical shore position, from sheltered to exposed conditions, across 

salinity gradients, and with substrate type and configuration. Because of the high phyletic 

diversity encountered on most rocky shores, investigators performing community—level studies 

must have extensive and broad taxonomic expertise. 

Species distributions and abundances not only vary over spatial scales but also can show 

considerable temporal variation over time scales ranging from years to decades, even in the 

absence of major disturbances. Knowledge of the historical patterns of physical and biological 

disturbance, recruitment, and other processes that might drive temporal variation in rocky 

intertidal populations and communities is almost never available. This means that habitat 

histories can vary considerably over spatial scales ranging from kilometers to meters, and 

significantly influence species distributions, abundances, and population structures. 

Most methods and procedures for designing and performing field sampling programs can be 

readily transferred among habitat types. For example, there is a long history of testing and 

evaluating field procedures for sampling vegetation and animals in terrestrial environments, and 

many of these procedures have been adopted to sample rocky intertidal organisms. However, the 

high spatial variability in both abiotic and biotic features typically encountered in rocky intertidal 

sampling programs usually exceeds variability at the physical and biological scales addressed by 

most terrestrial sampling programs. Established methods and procedures need to be carefully 

analyzed and selected so as take into account the high “noise to signal” ratios almost surely to be 

encountered in rocky intertidal habitats when performing quantitative sampling programs. For 

these reasons, much discussion of rocky intertidal sampling approaches and methodologies 

continues to take place. The purpose of this handbook is to provide interested investigators with 

the information needed to determine the most appropriate methods and procedures for carrying 

out key elements of a rocky intertidal field-sampling program. 

Design Elements for Rocky Intertidal Field Studies 

The steps in designing a field sampling program include: 1) identifying the study goals including 

the questions to be answered by the study or the hypotheses to be tested, and 2) developing an 

effective and statistically powerful study design. These steps will be followed by determining 

study sites, the biological units to be sampled, the sampling design, layout, and units to be 

employed, and the type of data to be obtained (Fig. 1-1). 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

11

Identifying study goals and developing effective and appropriate study designs will be discussed 

only briefly here. Emphasis in this handbook is placed on the methods and procedures for 

carrying out field monitoring, impact, or other ecological studies once the goals and overall 

design have been determined. 

Fig. 1-1. Decision—tree for designing rocky intertidal sampling programs. The goals of most 

monitoring or impact sampling programs will focus on either specific sites and habitat types or 

biological units. Decision flow in these studies should be dictated by program goals. Selection of 

sampling units and sampling design or layout should be selected in coordination to match 

biological units and the types of data (population-based or individual-based parameters) to be 

collected. 
Final Study Report – Murray et al. 

12

Study Types and Goals 

The specific goals and objectives of field studies must be identified and will dictate the overall 

study design and elements of the field-sampling program. Maher et al. (1994) stress the need for 

clearly stating the problem of concern or reason for sampling, and identifying the study 

objectives which can then be stated as testable hypotheses. Most ecology texts outline the basic 

elements of developing study questions or hypotheses; Kingsford and Battershill (1998) provide 

a particularly good discussion of procedures for establishing field studies. Field studies can 

generally be classified into four general categories (Kingsford et al. 1998). These are: 1) baseline 

studies, 2) impact studies, 3) monitoring studies, and 4) patterns and processes (ecological) 

studies. Using their definitions as a foundation, these study types are defined herein as follows. 

Baseline studies are considered to have the goal of determining the present status of biological 

conditions, for example species abundances or community composition. These often are referred 

to as one-time or “one-off” studies because they are planned to be executed at only a single point 

in time. The goals of impact studies include determining and relating biological changes to a 

particular known perturbation, such as a sewage outfall or an oil spill, and also measuring the 

spatial and temporal scales of detected changes. Monitoring studies focus on the following 

biological parameters through time, usually with the objective of detecting changes in measured 

parameters due to existing or future threats from human activities. Studies of patterns and 

processes are types of ecological field assessments that describe species distributions and 

abundances (patterns) with the intent of determining the factors that cause them (processes) 

(Kingsford et al. 1998). Process studies generally involve both descriptive and experimental 

approaches. Although many of the same considerations apply to the actual execution of patterns 

and processes studies, emphasis in this handbook is placed on rocky intertidal baseline, impact, 

and monitoring field studies. Discussions of patterns and processes studies can be found in 

Underwood (1993a, 1997) and many other sources and will not be covered here. 

Study Designs 

Once study goals are clearly identified, the next step in developing a field-sampling program is 

to determine an effective study design. The specifics of this design will vary with the study type 

and goals, but also will be dictated by circumstances such as the availability of suitable study 

areas and available resources. Regardless of the goals of the field study, Kingsford and 

Battershill (1998) describe considerations that should be incorporated into the study design. 

These include: 1) the need for controls in both space and time, 2) pre-determination of the 

methods of data analysis required to answer study questions, 3) replication of every level of 

sampling, 4) the use of multiple locations for sampling, 5) potential effects of existing variation 

over short temporal and small spatial scales, 6) insurance that independent and replicate samples 

are to be taken, 7) depending on the design, that sampling is done randomly (preferably) or 

haphazardly, and 8) that quantitative results can be expressed with a measure of statistical 

variability. Most rocky intertidal field sampling programs will address questions that focus either 

on study sites or on biological units (e.g., targeted populations or communities) depending on 

study goals. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

13

One-Time or “One-Off” Baseline Studies. These studies are generally performed to obtain 

information about the present status of populations or communities. Because by definition, they 

are not replicated in time, they will be of only limited value. Results can be used to evaluate the 

“health” of an intertidal habitat in the absence of historical data by comparing measured 

parameters with information obtained in the literature or from other study areas. Data also can be 

used to produce a record of baseline conditions prior to proceeding with, for example, a coastal 

development or establishment of a marine protected area, and to predict the impact of such 

activities (e.g., risk assessment sensu Suter 1993). However, one-time baseline studies in rocky 

intertidal habitats will only useful at detecting the grossest changes in populations and 

communities (Hawkins and Hartnoll 1983), or where the biological outcomes of identified 

stressors or events are well understood. Another implicit goal of one-time studies is often to 

establish a baseline for the biological populations or communities against which change can be 

measured at some unknown future time. The lack of replication through time in one-off studies 

means that there is no chance of quantifying natural variability in biological parameters, and thus 

to distinguish future changes resulting from a particular event or stressor from those reflecting 

natural temporal variation. Baseline data, however, might allow retrospective risk assessment. If 

the potential for future re-sampling is envisioned, specific site locations (e.g., transect heads or 

reference points) should be thoroughly documented to allow relocation, and robust and 

repeatable sampling procedures should be employed when performing a one-time study. 

Kingsford and Battershill (1998) also emphasize the advantages of sampling multiple locations 

within the defined study area when performing one-time baseline studies. 

Impact Studies. Impact studies are designed to determine the changes brought about by a 

perturbation or stressor by comparing the status of natural or unimpacted biological or other 

measured parameters with their status under impacted conditions. Impact study designs have 

received much attention, since Green’s (1979) pivotal treatment of impact sampling designs and 

statistical methods. Excellent discussions of the advantages and disadvantages of various impact 

study designs can be found in Stewart-Oaten et al. (1986), Underwood (1991, 1992, 1993b, 

1994), Osenberg and Schmitt (1996), Osenberg et al. (1996), Stewart-Oaten (1996), Ellis and 

Schneider (1997), Kingsford and Battershill (1998), and Kingsford (1998). Researchers 

interested in determining impacts of human activities or natural events on rocky intertidal 

populations and communities should become well informed about the advantages and 

disadvantages of the various impact study models before designing a field sampling program. 

Several models generally are used in performing field studies of impacts (Fig. 1-2). 

Unfortunately, choice of models is often dictated by circumstances such as the availability of 

sites, funding levels, and timing, instead of selecting the most ecologically robust study design. 

The most robust models, particularly for sampling rocky intertidal environments that show high 

biological variation in both space and time, require the collection of data prior to the onset of an 

impact. This means that a commitment of funds and implementation of a scientifically sound 

study design must proceed well in advance of an impact, events that can only occur in the case of 

planned coastal developments or activities. For unplanned impacts, such as a major oil spill, 

robust before-impact data sets will almost always be absent unless commitment has been made to 

carry out a long-term and scientifically-sound, regional monitoring program. In Southeastern 

Alaska, the lack of robust data sets prior to the Exxon Valdez oil spill was identified as a major 

problem for designing effective post-spill impact studies (Paine et al. 1996). 
Final Study Report – Murray et al. 

14

Fig. 1-2. Selected models for performing impact studies. Rectangles represent sites and 

individual sites are numbered; degree of shading represents magnitude of impact. A. Gradient 

design where sites are distributed at various distances from a central impact site creating a 

gradient of control and impact conditions. B. Before-After design where the same site is studied 

both before and after an impact; C. Control-Impact design where data are collected at a single 

point in time from impact site or sites and compared with data collected from control site or 

sites; D. BACI design where data are collected from both control and impact sites both before 

and after an impact; E. BACIPS design where data are collected on multiple occasions (here 5 

times) from control and impact sites both before and after an impact; and, F. Asymmetrical 

BACI design where data are collected on multiple occasions (here 5 times) both before and after 

an impact usually from one impact and multiple (here 4) control sites. These different study 

designs have advantages and disadvantages and require different statistical methods for 

analyzing the collected data. However, all designs require decisions on site selection, biological 

units, the sampling units to be employed, the design for locating sampling units, and the type of 

data to be taken. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

15

Gradient models (Fig. 1-2A), where sampling is done at intervals distributed at variable 

distances from the source of impact, have long been used to detect changes in biological 

parameters. Gradient Impact Designs are particularly useful where a stressor or disturbance 

attenuates with distance from a point source whereas other designs are more appropriate 

where impacts have distinct boundaries and control and impact sites can be identified (Ellis 

and Schneider 1997). Examples where gradient designs are appropriate include cases where 

an impact is due to discharge of a sewage effluent or an oil drilling operation. In these cases, 

field study sites can be set up in a grid both within and at various distances from the point 

source of the impact. Analyses of quantitative data collected in such a gradient design can be 

carried out by regression or Analysis of Covariance (ANCOVA) or by using multivariate 

techniques. A Gradient Sampling Design was found to be more powerful than other design 

alternatives in detecting certain effects of oil drilling operations in the Ekofisk oil field in the 

North Sea (Ellis and Schneider 1997). 

Several impact study designs are appropriate where distinct control and impact conditions 

can be determined in time or space. One such model (Fig. 1-2B) involves collecting data at a 

single site both before and after an impact. Impact determination is based on finding 

significant statistical differences between parameters measured before and after the impact. 

This Before-After Design avoids problems of spatial variation, an important consideration in 

rocky intertidal sampling programs, by restricting sampling to the same site, with samples 

being taken at one or more times prior and one or more times after an impact. Although 

eliminating the potentially confounding effects of spatial variation, this impact study design 

is seriously flawed by its failure to separate natural temporal variability from effects due to 

the impact. In other words, this design cannot eliminate the possibility that detected changes 

have resulted from other regional events (e.g., increased sea temperatures) instead of the 

impacting agent. 

Another often-used model in impact studies is the Control-Impact Design (Fig. 1-2C), where 

studies are performed at one or more control and one or more impact sites. This is a 

commonly used study design, probably because it does not depend on before-impact data, 

which usually are unavailable. Although accounting for temporal variability by sampling 

both control and impact sites at essentially the same time, this design is unable to separate 

natural spatial variability from effects due to the activity (see Chapter 2). The design is based 

on the assumption that control and impact sites are identical except for the impact, an 

occurrence that is highly unlikely particularly in complex and dynamic rocky intertidal 

habitats. Greater ability to statistically discriminate impacts from natural spatial variation 

among study sites can be obtained by replicating control and impact sites. For example, 

nested Analysis of Variance (ANOVA) can be used in selected cases to discriminate among 
Final Study Report – Murray et al. 

16

impacted and control (unimpacted) sites (McKone and Lively 1993). However, in rocky 

intertidal and other spatially variable habitats, differences within replicated site parameters 

often swamp differences between control and impact site groups for all but the largest impact 

effects. In most cases, i.e., point source discharges from a sewage or power plant outfall, 

impacted sites cannot be replicated leaving a choice of comparing one or more control sites 

with a single impacted site. 

A fourth design addresses the problems of spatial and temporal variation by combining the two 

designs into a single design — what Green (1979) referred to as the Before-After-ControlImpact or BACI Design (Fig. 1-2D). There are several ways to employ this type of design 

depending on the number of sampling periods and sites to be sampled. In the simplest case, one 

control and one impacted site are sampled one time before and one time after the impact. As 

described by Osenberg and Schmitt (1996), impact determination is then based on the 

“interaction between Time and Location effects, using variability among samples taken within a 

site (on a single date) as the error term”. Unfortunately, as illustrated by Osenberg and Schmitt 

(1996), successful use of this design depends on the variables measured at the control and impact 

sites following the same trajectories through time; a significant interaction only shows that the 

measured variables did not track one another before and after the impact. As pointed out by 

Hurlbert (1984), this circumstance may or may not be attributable to the impact perturbation. 

To correct deficiencies in the BACI Design, Stewart-Oaten et al. (1986) argued for a design 

based on comparisons of a time series of differences between control and impact sites taken 

before and after an impact. This design (Fig. 1-2E) has been referred to as the Before-AfterControl-Impact Paired Series or BACIPS Design (sensu Osenberg and Schmitt 1996). Impact 

determination in this design is based on statistical comparison of the before differences with the 

after differences for the variables measured at the two sites. The assumption in this analysis is 

that each difference in the before period is an independent estimate of the natural spatial 

variation between the control and the to-be-impacted sites. As discussed by Osenberg and 

Schmitt (1996), this design also has limitations, including that it lacks spatial replication 

(Underwood 1994), but these are clearly understood and have been delineated by Stewart-Oaten 

et al. (1986) and Stewart-Oaten (1996). In the latter contribution, Stewart-Oaten discusses 

additional analysis options that strengthen the efficacy of the BACIPS Design. 

Underwood (1991, 1992, 1994) discusses an impact study design that overcomes deficiencies in 

the previous BACI based models, including the BACIPS model. This is the Asymmetrical 

Before-After-Control-Impact or BACI Design (Fig. 1-2F). In this design, multiple controls and 

a single impacted site are studied both before and after an impact. In this design, impact 

determination is made by observing statistical differences between changes at multiple (and 

presumably variable) control sites and the impacted site using ANOVA. The use of multiple 

controls overcomes several problems with BACI designs, including the problem of spatialtemporal interactions in BACIPS designs. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

17

Monitoring Programs. Monitoring programs by definition involve the repeated sampling of 

measured parameters over time. Monitoring programs in aquatic environments have focused on 

chemical, physical, and biological parameters, and have addressed goals as diverse as detecting 

microbial contamination of beaches, determining the concentrations of potentially harmful 

materials in fish, and learning whether the effects of discharged sewage are creating biological 

changes across the sea floor. Rocky intertidal habitats are important candidates for establishing 

effective monitoring programs because of their high public visibility and value, and their 

potential to undergo degradation from human activities. 

Karr and Chu (1997) recently reviewed the history of monitoring programs in aquatic systems 

and emphasized the need for measurement and assessment endpoints that are explicitly 

biological. Various descriptions of the goals of biological monitoring programs have been 

produced but most concern identifying the presence or effects of an existing or potential human 

activity on a biological system. For example, the goal of biological monitoring is described, in 

the narrow sense, by Stevens (1994) as “tracking a particular environmental entity through time, 

observing its condition, and the change of its condition in response to a well defined stimulus”. 

Kingsford and Battershill (1998), describe an ideal monitoring program as involving “sampling 

in time with adequate replication to detect variation over a temporal range from short and long 

time periods, done at more than one location”. As pointed out by Kingsford et al (1998), 

monitoring studies require repeated sampling through time and should be designed so that the 

sampling program is able to detect predetermined levels of change in monitored parameters. 

Field biological monitoring programs usually have concentrated on population-based abundance 

parameters such as population density as the biological signal to be monitored (Green 1979, 

Underwood 1991, 1994). Often only a few key species or “indicator organisms”, which have 

characteristics that make them suitable for detecting impacts (Jones and Kaly 1996), have been 

targeted for biological monitoring given funding limitations and the logistic inability to study all 

biological components of any system. However, multimetric indices (e.g., diversity indices; 

index of biological integrity (IBI)), which require data on multiple taxa and biological 

conditions, also are often recommended and commonly used to monitor the status of biological 

systems (Karr and Chu 1997; see Chapter 3). 

Despite different views on the goals of biological monitoring programs and approaches in their 

execution, several common requirements for effective field monitoring programs appear to 

emerge: 1) the biological monitoring program must be carried out over long periods and 

designed so as to account for natural variability in the biological system, 2) the program must be 

designed using the best available ecological concepts, study designs, and principles; 3) the data 

must be collected in a consistent and well documented manner to achieve required continuity and 

reliability; 4) the program should be designed so that the detection of change and impacts can be 

statistically based. 
Final Study Report – Murray et al. 

18

Fig. 1-3. Overview of monitoring programs. A. Program involves only a single study site in the 

area of interest. B. Program involves several study sites in the area of interest. C. Program is 

part of a regional monitoring program. Only the third approach allows changes at study sites in 

the area of interest to be placed in the context of regional changes in rocky intertidal populations 

and communities. 

The most formidable challenge for any successful field-monitoring program is to design an 

approach that can separate effects of human perturbations from those occurring naturally in the 

biological system. Natural variability is particularly high in rocky intertidal and other marine 

systems, and most unsuccessful monitoring programs are plagued by the inability to separate all 

but the very largest impacts from the subtler and constantly on-going changes that take place due 

to natural processes. In order to understand natural variability in complex rocky intertidal 

systems, a regional approach is clearly required. For example (as illustrated in Figs. 1-3A,B), a 

single agency or entity interested in monitoring the biological condition of a small section of 

rocky coastline cannot separate changes due to natural regional processes, such as fluctuations in 

oceanographic climate, from those caused by local human activities. A much broader regional 

approach (Fig. 1-3C) is required to meet the need for data from multiple sites (Kingsford and 

Battershill 1998). One such approach is that employed in a California rocky intertidal monitoring 

program being carried out under the leadership of the Minerals Management Service (Ambrose 

et al. 1995, Raimondi et al. 1999). Funding for broad regional approaches, however, is difficult 

to maintain over the time scales required to obtain understanding of natural cycles in marine 

biological systems, and almost always must involve coordinated efforts by multiple parties and 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

19

agencies. Southward (1995) argues that to be effective, program lengths need to cover the life 

spans of the dominant organisms in the system and the cycling periods of important 

environmental factors, which amounted to periods of 11 to 45 years in the English Channel. 

Timely and coherent ecological information collected over regional and national scales is an 

integral part of the Environmental Monitoring and Assessment (EMAP) program initiated by the 

U. S. Environmental Protection Agency (Stevens 1994). 

Literature Cited 

Ambrose, R. F., J. M. Engle, P. T. Raimondi, M. Wilson, and J. A. Altstatt. 1995. Rocky 

intertidal and subtidal resources: Santa Barbara County mainland. Report to the Minerals 

Management Service. Pacific OCS Region. OCS Study MMS 95-0067. 

Carefoot, T. 1977. Pacific seashores. A guide to intertidal ecology. University of Washington 

Press, Seattle, Washington, USA. 

Ellis, J. I. and D. C. Schneider. 1997. Evaluation of a gradient sampling design for environmental 

impact assessment. Environ. Mon. Assessment 48: 157-172. 

Green, R. H. 1979. Sampling design and statistical methods for environmental biologists. John 

Wiley and Sons, Inc. New York, New York, USA. 

Hawkins, S. J. and R. G. Hartnoll. 1983. Changes in a rocky shore community: an evaluation of 

monitoring. Mar. Environ. Res. 9: 131-181. 

Hurlbert, S. J. 1984. Pseudoreplication and the design of ecological field experiments. Ecol. 

Monogr. 54: 187-211. 

Jones, G. P. and U. L. Kaly. 1996. Criteria for selecting marine organisms in biomonitoring 

studies. Pages 29-48 in R. J. Schmitt and C. W. Osenberg, editors. Detecting ecological 

impacts: concepts and applications in coastal habitats. Academic Press, New York, New 

York, USA. 

Karr, J. R. and E. W. Chu. 1997. Biological monitoring: essential foundation for ecological risk 

assessment. Hum. Ecol. Risk Assessment 3: 993-1004. 

Kingsford, M. J. 1998. Analytical aspects of sampling design. Pages 49-83 in M. Kingsford and 

C. Battershill, editors. Studying temperate marine environments. A handbook for 

ecologists. Canterbury University Press, Christchurch, New Zealand. 

Kingsford, M. J. 1998. Procedures for establishing a study. Pages 29-48 in M. Kingsford and C. 

Battershill, editors. Studying temperate marine environments. A handbook for ecologists. 

Canterbury University Press, Christchurch, New Zealand. 
Final Study Report – Murray et al. 

20

Kingsford, M. J., C. N. Battershill, and K. Walls. 1998. Introduction to ecological assessments. 

Pages 17-28 in M. Kingsford and C. Battershill, editors. Studying temperate marine 

environments. A handbook for ecologists. Canterbury University Press, Christchurch, 

New Zealand. 

Knox, G. A. 2000. The ecology of seashores. CRC Press, Boca Raton, Florida, USA. 

Kozloff, E. N. 1983. Seashore life of the northern Pacific coast. An illustrated guide to northern 

California, Oregon, Washington, and British Columbia. University of Washington Press, 

Seattle, Washington, USA. 

Lewis, J. R. 1964. Ecology of rocky shores. English Universities Press, London, UK. 

Maher, W. A., P. W. Cullen, and R. H. Norris. 1994. Framework for designing sampling 

programs. Environ. Mon. Assessment 30: 139-162. 

McKone, M. J. and C. M. Lively. 1993. Statistical analysis of experiments conducted at multiple 

sites. Oikos 67: 184-186. 

Menge, B. A. and G. Branch. 2000. Rocky intertidal communities. Pages 221-251 in M. D. 

Bertness, S. D. Gaines, and M. E. Hay, editors. Marine community ecology. Sinauer 

Associates, Inc., Sunderland, Massachusetts, USA. 

Osenberg, C. W. and R. J. Schmitt. 1996. Detecting ecological impacts caused by human 

activities. Pages 3-16 in R. J. Schmitt and C. W. Osenberg, editors. Detecting ecological 

impacts: concepts and applications in coastal habitats. Academic Press, New York, New 

York, USA. 

Osenberg, C. W., R. J. Schmitt, S. J. Holbrook, K. Abu-Saba, and A. R. Flegal. 1996. Detection 

of environmental impacts: natural variability, effect size, and power analysis. Pages 83-

107 in R. J. Schmitt and C. W. Osenberg, editors. Detecting ecological impacts: concepts 

and applications in coastal habitats. Academic Press, New York, New York, USA. 

Paine, R. T., J. L. Ruesink, A. Sun, E. L. Soulanilee, M. J. Wonham, C. D. G. Harley, D. R. 

Brumbaugh, and D. L. Secord. 1996. Trouble on oiled waters: lessons from the Exxon 

Valdez oil spill. Ann. Rev. Ecol. Syst. 27: 197-235. 

Raffaelli, D. and S. Hawkins. 1996. Intertidal ecology. Chapman and Hall, London, UK. 

Raimondi, P. T., R. F. Ambrose, J. M. Engle, S. N. Murray, and M. Wilson. 1999. Monitoring of 

rocky intertidal resources along the central and southern California mainland. 3-year 

report for San Luis Obispo, Santa Barbara, and Orange Counties (Fall 1995 - Spring 

1998). U. S. Department of Interior, Minerals Management Service, Pacific OCS Region, 

Technical Report MMS 99-0032. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

21

Ricketts, E. F., J. Calvin, J. W. Hedgpeth, and D. W. Phillips. 1985. Between Pacific Tides, fifth 

edition. Stanford University Press, Stanford, California, USA. 

Southward, A. J. 1995. The importance of long time-series in understanding the variability of 

natural systems. Helgolander Meeresunters. 49: 329—333. 

Stephenson, T. A. and A. Stephenson. 1972. Life between tidemarks on rocky shores. W. H. 

Freeman, San Francisco, California, USA. 

Stewart-Oaten, A. 1996. Problems in the analysis of environmental monitoring data. Pages 109-

131 in R. J. Schmitt and C. W. Osenberg, editors. Detecting ecological impacts: concepts 

and applications in coastal habitats. Academic Press, New York, New York, USA. 

Stewart-Oaten, A., W. W. Murdoch, and K. R. Parker. 1986. Environmental impact assessment: 

“pseudoreplication” in time? Ecology 67: 929-940. 

Stevens, D. L. Jr. 1994. Implementation of national monitoring program. J. Environ. Monitoring 

42: 1-29. 

Suter, G. W., editor. 1993. Ecological risk assessment. Lewis Publishers, Boca Raton, Florida, 

USA. 

Underwood, A. J. 1991. Beyond BACI: experimental designs for detecting human environmental 

impacts on temporal variations in natural populations. Aust. J. Mar. Freshwat. Res. 42: 

569-587. 

Underwood, A. J. 1992. Beyond BACI: the detection of environmental impacts on populations in 

the real, but variable world. J. Exp. Mar. Biol. Ecol. 161: 145-178. 

Underwood, A. J. 1993a. Field experiments in intertidal ecology. Proc. 2nd Int. Temperate Reef 

Symp., pp. 7-13. 

Underwood, A. J. 1993b. The mechanics of spatially replicated sampling programmes to detect 

environmental impacts in a variable world. Aust. J. Ecol. 18: 99-116. 

Underwood, A. J. 1994. On beyond BACI: sampling designs that might reliably detect 

environmental disturbances. Ecol. Appl. 4: 3-15. 

Underwood, A. J. 1997. Experiments in ecology: their logical design and interpretation using 

analysis of variance. Cambridge University Press, Cambridge, UK. 
Final Study Report – Murray et al. 

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Chapter 2. 

Site Classification and Selection 

By 

Megan N. Dethier 

 Outer Coast, Washington
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

23

Introduction 

For any intertidal sampling program, site selection probably has the greatest influence on the 

overall program design. As discussed in later chapters, the answer to “where to sample?” 

depends on the program goals. Is the goal to characterize the health of an entire coastline or to 

determine the impact of pollutants at a specific site? Do we need to infer from our data how a 

population is changing 100 km up the coast, or simply how many species were at a site before oil 

hit it? Are we trying to detect impacts on all intertidal substratum types or only on flat rocky 

benches? Unless sampling is intentionally confined to one location, and site comparisons are not 

needed, site selection is an important decision—one upon which all conclusions obtained from 

the sampling program will be based. If sites to be compared (e.g., control sites vs. impact sites, 

or multiple sites along a gradient of anthropogenic influence) are not physically similar, then 

physical differences can confound any conclusions about what might cause or correlate with any 

detected differences or trends. 

 

Fig. 2-1. A 

recommended 

approach for site 

selection for 

comparative studies

of control and 

impacted study 

areas.
Final Study Report – Murray et al. 

24

This chapter discusses procedures for site selection (Fig. 2-1), including methods of classifying 

shorelines to avoid confounding problems resulting from differences in geophysical site 

characteristics. The utility of shoreline habitat maps and the pros and cons of sampling particular 

microhabitats on rocky shores also will be reviewed. Additionally, how sites should be selected 

based on program goals, and how these goals will differ depending on the objectives of the 

sampling program are discussed. Finally, the key role of replicating sites in developing robust 

study designs is addressed. 

Classifying Shorelines 

Intertidal ecologists have long noted that factors such as wave exposure, amount of shade, and 

even rock type can affect species distributions and abundances. These physical features provide 

the backdrop against which biological interactions occur; and, the presence or absence of a 

particular species in a community depends on having an appropriate physical environment. To 

select ecologically comparable sites (and thus avoid confounding influences during data 

analyses), we must control for these variables as thoroughly as possible. For example, Schoch 

and Dethier (1996) found that within a 5 km stretch of Washington shoreline, there were 

significant differences in community composition between rocky sites varying only in relatively 

subtle physical characteristics, especially slope. Site selection thus must begin by classifying 

potential study sites according to features important to the structure and dynamics of rocky shore 

communities. 

Table 2-1. Geophysical variables to consider when choosing sites for monitoring or impact 

assessment study programs. For details see Schoch and Dethier (1996). 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

25

Geophysical Features 

When are sites similar enough to allow valid comparisons between their biota? No one would 

compare a sand beach with a mud flat, but all rocky shores are not the same and comparing sites 

with different wave exposures, rock types, proximities to a river, or aspects can be very 

misleading. Table 2-1 offers a minimal checklist of physical factors important to rocky shore 

community structures. Screening for these factors during the early stages of study design should 

be part of any sound site-selection procedure. Besides the actual substratum type (e.g., rock vs. 

gravel), the most important attribute affecting intertidal community structure at landscape-level 

scales is probably wave energy. The other factors listed in Table 2-1 are probably of secondary 

importance, although research elucidating their relative roles in influencing community structure 

is lacking. At larger spatial scales, factors such as tidal range and regional climate probably also 

lead to the differentiation of intertidal communities. At smaller-than-landscape scales — for 

example, where substrata and wave energy are fairly homogeneous (e.g., exposed rocky shores) 

— other factors such as surface roughness and human disturbance gain importance. Of course, 

the list in Table 2-1 is not exhaustive; for instance, Menge et al. (1997) recently demonstrated 

that the degree of nearshore upwelling may have significant background effects on intertidal 

community structure, such that otherwise-similar rocky shores develop different patterns of 

species composition and abundance. In addition, any comparison of biota among sites or among 

times must carefully control for tidal height, since emersion time strongly affects the biota. 

Actual (as opposed to predicted) emersion time will be affected by wave run-up as discussed 

below. When comparing sites with different tidal ranges (as seen, for example, in NOAA tide 

tables), it may be useful to sample each site at a local datum (e.g., Mean Lower Low Water or 

Mean Sea Level) to compensate for these differences. 

Wave Energy. Wave energy is manifested in various ways. For example, wave velocity can tear 

organisms off rocks, or roll the substratum if particles are of critical rolling diameter, whereas 

wave run-up affects the vertical elevation of the community by reducing desiccation stress at 

higher tidal heights. Measuring wave exposure is one of the most difficult yet most important 

tasks for classifying rocky shores. 

There are three general procedures for measuring and expressing the degree of wave exposure 

experienced by a rocky shore: 1) estimating cumulative water motion or maximum wave force 

directly, using some kind of gauge, meter, or dissolution module (Fig. 2-2) (e.g., Denny 1985,

Bell and Denny 1994, Raffaelli and Hawkins 1996, Castilla et al. 1998); 2) calculating wave 

energy based on other measured parameters (e.g., Denny 1995; Table 2-2); and 3) estimating 

wave energy indirectly, using biological or physical indicators. Wave exposure also is often 

reported based on qualitative estimates that may be assigned to a numerical scale (e.g., 1 for 

extremely strong wave exposure and 5 for essentially no wave exposure). Direct measurements 

should be taken over a long time period (e.g., multi-seasonal) and under a range of conditions to 

best integrate the wave energies experienced by a site. Sites being matched for comparative 

study should have their wave energies quantified simultaneously to control for temporal variation 

in measured parameters. 
Final Study Report – Murray et al. 

26

Fig. 2-2. A. Wave force meters as designed by Bell and Denny (1994) and B. dissolution modules 

or clod cards similar to the model designed by Doty (1971). 

Table 2-2. Wave parameters derived for calculating the surf similarity index from Schoch and 

Dethier 1997. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

27

Indirect measurements include biotic indicators, such as the presence of indicator species, the 

width of the intertidal zone, the height of the splash or other distinct zones above low water, and 

physical indicators, such as the fetch or distances traveled by waves prior to reaching the site. 

Maximum fetch, for example, is often used in such indirect estimates of wave exposure because 

this is the longest distance over which waves travel to the site unimpeded by a landmass. Wave 

statistics also can be estimated using graphs published in the Shore Protection Manual (CERC 

1984). Table 2-2 provides an example of this indirect approach using the graphs for a large 

coastline with a broad range of energy levels. If investigators are interested only in relatively 

quiet bays or in summertime (non-stormy) conditions, then categories encompassing a narrow 

range of low wave energies could be used to form such site groups. 

Nearshore water depth, which affects the wave energy delivered to a rocky shore, also can be 

used to indirectly estimate wave exposure. Depth profiles usually can be adequately determined 

from detailed marine charts for the region near a study site. However, the scale over which the 

chart provides depth information must match the project’s scale. Sites where the ocean bottom 

drops off steeply near the shore, or where a deep submarine canyon approaches the coast, will 

receive greater wave forces than sites with long, shallow seaward approaches. Nearshore 

topography also can focus or diffuse waves; waves will refract and focus their energy on 

headlands, for example, while embayments will receive more diffuse and reduced wave energy 

(Fig. 2-3). 

Fig. 2-3. Types of coastline (Fig. 2-3A) and patterns of wave refraction showing convergence of 

wave energy on rocky headlands (Fig. 2-3B). Site a = protected outer coast; Sites b = exposed 

headlands; Site c = embayment. (Redrawn from Ricketts et al.1985.) 
Final Study Report – Murray et al. 

28

Aspect and Slope. The aspect, or primary compass direction of a site, is important in terms of 

both wave and sun exposure. If a beach is oriented in the direction facing prevailing swell 

patterns or large seasonal storms, considerable disturbance can be expected for communities 

occupying that face. Similar levels of disturbance, however, may not characterize communities 

facing other directions. In the Northern Hemisphere, shores facing to the south receive more 

direct sunlight and experience different desiccation and temperature extremes than north-facing 

shores. Site aspect can be determined readily from a detailed map or from on-the-ground 

surveys. Areas that comprise a rocky headland (Fig. 2-3) present more complexity compared 

with longshore habitats and should probably be considered at least two sites with different 

aspects — for example, a north-facing site as well as a south-facing site — because of their 

multiple faces with respect to sea and sun conditions. 

Slope is important because of its effects on both the dissipation of wave-energy and on insolation 

patterns. Steep shores will reflect waves. Low shore angles will dissipate wave energy, and 

intermediate angles will be the most disturbed by wave action because the wave energy will be 

expended suddenly on the beach face. Thus, shore slope may have a greater effect on the wave 

energy organisms experience than the run-up or maximum fetch over which waves travel before 

breaking on the shore. A high-shore area bordered by a long, flat, mid-shore bench will 

effectively experience less wave exposure than one with a steep mid- and low-shore region. 

Slope also may affect whether or not spilled oil will strand on a shore and, if oil deposition 

occurs, influence its pattern of distribution. The slope of a shore can be measured directly with 

an inclinometer or estimated from knowledge of tidal amplitude and the width of the intertidal 

zone; the latter information can be obtained from aerial photographs or videos taken at low tide. 

Topographical Heterogeneity and Rock Type. Topographical heterogeneity or roughness of 

rock surfaces creates turbulence that can dissipate wave energy (thus providing sheltered 

microhabitats) and possibly enhance nutrient/food and waste exchange. Topographical 

heterogeneity can be important on several spatial scales and influence species diversity and 

abundance (Archambault and Bourget 1996). Large (site)-scale roughness, for example, the 

relative abundance of topographic features such as crevices, pools, and hummocks, affects local 

distributional patterns by providing a variety of microhabitats for sessile and mobile organisms. 

This feature is perhaps best quantified on a subjective scale, e.g., a score of 1 for a site comprised 

of relatively unbroken, even bedrock, and 5 for a site where numerous features make the surface 

very irregular on a scale of meters. On a less coarse scale, variations in substratum topography 

can be measured using a transect tape and chain (Luckhurst and Luckhurst 1978). To apply this 

method, the chain is laid out along the bottom contours while the transect tape is pulled taut to 

measure the linear distance between the start and finishing points. The ratio of the surface 

distance (determined by the chain) to the linear distance (determined by the transect tape) is used 

as a measure of substratum rugosity. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

29

Surface roughness also can be described on a much smaller scale, where it relates closely to the 

type of rock, e.g. the fine crystalline texture of a rocky surface, or the abundance of tiny cracks 

and pores in vesicular volcanic rock. The importance of this textural roughness is not well 

known, but roughness could increase water retention and provide refugia for newly settled 

benthic recruits (Littler 1980), or serve to hold contaminants such as oil on the shore. Often 

surface roughness is quantified using a profile-gauge where the linear distances that randomly or 

regularly arranged rods are dropped perpendicular to the substratum from a level, horizontal 

frame or Plexiglas (Perspex) board (Fig. 2-4) are used to calculate a topographic index reflecting 

substratum microrelief (Underwood and Chapman 1989). Unfortunately, little research has been 

done on the effects of physical and chemical differences among rock types on rocky shore 

communities, although there is evidence that some organisms recruit or survive differentially on 

different substratum types (e.g., Stephenson 1961, Raimondi 1988, Lohse 1993). The tendency 

of some rock types to readily erode (e.g., sandstone) or fracture (e.g., some metamorphics) may 

also affect the development and persistence of sessile organisms on rocky shores. 

Fig. 2-4. A form of profile 

gauge for measuring 

topographic heterogeneity. 

An array of regularly 

spaced rods are dropped 

perpendicularly from the 

leveled platform and the 

distance to the substratum 

is measured. These data 

can be used to calculate a 

topographic index using 

procedures described by 

Underwood and Chapman 

(1989). 

Sand Burial and Scour. The frequency and magnitude of sand burial or scour is an important 

variable influencing the structure and organization of rocky shore communities. For example, 

sand affects the distribution and abundances of rocky intertidal populations along much of the 

southern California mainland coastline (Murray and Bray 1993) where the upper parts of shores 

are frequently covered and uncovered by sand (Littler et al. 1991). Sand-scoured rocky sites 

differ from those lacking sand influence, both in species composition and in the abundances and 

dynamics of resident populations. Three categories of macrophytes described by Littler et al. 

(1983) are found in abundance on southern California rocky shores that receive high levels of 

sand influence (Murray and Bray 1993): 1) opportunistic seaweeds that rapidly colonize 

disturbed substrata, 2) resistant macrophytes that tolerate sand abrasion and burial, and 3) “sand 

loving” or psammophytic algae that for unknown reasons are best represented in sand-influenced 

communities. 
Final Study Report – Murray et al. 

30

As with wave exposure, quantification of sand scour and sand burial is very difficult to perform. 

Researchers have used sediment traps (Airoldi and Cinelli 1997, Airoldi and Virgilio 1998) and 

abrasion rates of concrete blocks (Craik 1980) to measure sand influence. More common 

approaches are to make repeated measurements of the depth of sand at site reference stations or 

to rank sites in terms of sand exposure based on qualitative observations (e.g., 0 indicating no 

sand, 10 indicating frequent burial under thick sand). However, none of these approaches seems 

to fully reflect the role played by sand movements on rocky shore populations. Instead of sand, 

the degree or frequency of ice or driftwood scour or longshore ice flow may be important on 

some rocky shores and play a role in study-site selection (e.g., Dayton 1971, Wethey 1985, 

Kiirikki 1996, Pugh and Davenport 1997, McCook and Chapman 1997). 

Salinity. Salinity generally varies little along the open coast and is not considered to be an 

important factor in structuring rocky intertidal communities; however, salinity can be a very 

important factor in determining species distributions and abundances in estuarine situations or 

near the mouths of coastal rivers (reviewed in Ardisson and Bourget 1997, Witman and Grange 

1998). Sites near river mouths, or even openings of smaller streams, can be affected not only by 

variations in salinity but also by the sediment load and contaminants brought down to the shore 

from coastal watersheds. In addition, evaporation and rainfall can cause salinity to vary 

considerably on high-shore rock or pools, especially in wave-protected areas. Salinity can be 

measured directly at sites using a refractometer or portable conductivity meter; both types of 

devices are subject to calibration errors and should be checked for accuracy against known 

standards. As with wave action and other features of the physical environment that can vary 

considerably over short temporal scales, where salinity may be an important environmental 

factor measurements should be performed at study sites at approximately the same time and the 

same depth to optimize site comparisons. 

Human Disturbance. Lastly, human disturbance (e.g., trampling, collecting, and tidepool 

exploring) may seriously alter the biota of heavily-used rocky shores (Murray et al. 1999), such 

that even physically matched sites will have different community structures and dynamics if 

levels of human disturbance differ. Sites subjected to high levels of visitor foot traffic (Brosnan 

and Crumrine 1994) and exploratory activities (Addessi 1995) may show reduced abundances of 

vulnerable species and increased abundances of disturbance-resistant and opportunistic taxa. 

Collecting of organisms for human consumption, fish bait, or other purposes can cause exploited 

species to exhibit reduced densities and altered population size structures at heavily impacted 

sites (Griffiths and Branch 1997). There is an increasing effort in marine parks to gather data on 

levels of human impact. If available, such data could be used to create a ranking of this variable 

when popular sites are needed for a monitoring or impact-detection program. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

31

Mapping Methods 

If all shorelines worldwide were mapped with detailed information on the geophysical 

characteristic just described, it would be relatively simple to begin a study by identifying a pool 

of sites that meet targeted criteria. Because such maps do not exist for most areas, however, the 

alternatives are either to map the section of coastline under consideration and then identify 

potential study sites, or to choose a range of potential sites in the region, then screen them out 

according to selected criteria. Choosing between these options is likely to depend on funding and 

the time available before the study is to be initiated because it takes time and fiscal resources to 

develop useful maps. 

Mapping can be done at a wide variety of scales depending on the level of resolution needed for 

the study, the size and complexity of the shorelines being mapped, and available funds and 

equipment. Maps of an entire coastline designed to display the overall abundance of rock and 

sand, for instance, could probably be prepared using coarse-scale data such as aerial photographs 

(e.g., with color infrared photography) or satellite images. A central repository of maps, aerial 

photographs, videos, and other information providing data on shoreline geophysical 

characteristics would be of substantial value for first-cut site-selection decisions. This would be 

particularly true in the event of an oil spill because it is unlikely that time would be available to 

gather and analyze the geophysical information needed to set up intertidal study sites during the 

short period that spilled oil is at sea. Unfortunately, central repositories generally do not exist 

and investigators must usually gather their own geophysical data from a variety of sources in 

preparing for study site selection. 

Information on the physical features of shorelines has sometimes been taken from Environmental 

Sensitivity Maps (e.g., RPI 1990), but these are generally out of date, sometimes inaccurate, and 

often not of high enough resolution to inform site selection. Such qualitative maps, if used as the 

sole information source for selecting similar sites, are likely to lead to later problems in data 

analysis and interpretation because the degree of variability inherent in some of the categories 

(e.g., wave-cut platforms and exposed pier structures) means that the biota are likely to be 

similarly variable. If the geophysical and biotic characteristics of the sites selected for study vary 

greatly, then the ability to detect spatial or temporal differences in species distributions and 

abundances will be greatly weakened by the loss of statistical power that comes with high 

variance (see Chapter 4). 

Helicopter overflights supplemented with photographs and videos offer finer-resolution data 

(e.g., the ability to distinguish different types of unconsolidated beaches). This method was used 

to map the geophysical features of much of the Washington and British Columbia shoreline 

(Harper et al. 1991, Howes et al. 1994) and the coarse-scale physical features and biotic 

assemblages of intertidal habitats (Fig. 2-5) throughout southern California (Littler and Littler 
Final Study Report – Murray et al. 

32

Fig. 2-5. Example of a section of the coastline on San Nicolas Island in southern California 

categorized by Littler and Littler (1987) using helicopter overflights. (Redrawn from Littler and 

Littler 1987). 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

33

1987). The finest-resolution data come from trained observers boating closely or walking along 

the shoreline, gathering quantitative information on the physical characteristics described earlier 

(Schoch 1996), or from periodic helicopter landings for ground-truthing site characteristics 

viewed from the air (Littler and Littler 1987). If physical factors during such surveys are 

measured quantitatively (i.e., using categorical or continuous data), it is easier to avoid the error 

of assuming that sites are similar when they may have an accumulation of small but significant 

differences. If data are entered eventually into a digital mapping format such as a Geographical 

Information System, then many attributes can be included and used for site screening. Practically 

speaking, sites smaller than 10 or even 100 m in the longshore direction will be too small to be 

resolved when viewing a regional map. A useful approach for informing site selection is to map 

at scales greater than 10 m, seeking to compare beach segments that are physically homogeneous 

at this level of resolution. 

One system for gathering quantitative geophysical information is the SCALE (Shoreline 

Classification and Landscape Extrapolation) model (Fig. 2-6), which is designed to define 

shorelines precisely enough that the biota on statistically similar shores should be very similar 

(Schoch and Dethier, in prep.). This model was designed for shorelines characterized by a broad 

range of wave energies and substratum types, and for addressing questions involving change 

detection at the scale of species populations and sites. If shorelines are classified into 

geophysically homogeneous beaches, then each beach should in theory have relatively 

homogeneous biota presuming similar disturbance histories (Schoch and Dethier 1996). Such 

homogeneous beach groupings can serve as high-resolution mapping units for informing study 

site selection. The concept of using geophysical characteristics to predict potential biotic 

communities should hold for any coastal region. Of course, ecological history (e.g., exposure to 

disturbance events, past recruitment success) and biotic interactions (e.g., level of predation) will 

affect the current status of rocky intertidal populations and communities, resulting in biotic 

variation among sites that cannot be predicted by models built solely upon geophysical site 

features. We can never entirely remove these sources of variability, but choosing geographically 

close and physically similar sites will reduce their influence on collected data. 

Habitat Types 

Once shoreline classification has been done, the specific habitat types to be sampled must be 

determined. While this handbook focuses on rocky shores, even within this broad habitat type 

there are numerous decisions to be made about the specific features of the habitats selected for 

study. This is because rocky intertidal habitats are highly variable, and can be differentiated 

based on wave exposure, slope (e.g., steep versus flat benches), topographical heterogeneity, 

substratum composition and nature (e.g., bedrock versus boulder fields), and even the presence 

and frequency of microhabitats such as tidepools and crevices (Fig. 2-7). For each of these 

variable habitat types, sampling could be performed either across all tidal elevations from the 

high tideline to the lower limits of the intertidal zone, or only at selected tidal heights. On the 

other hand, sampling might be focused on biotically generated habitats such as surfgrass 

(Phyllospadix spp.) or mussel (Mytilus spp.) beds. 
Final Study Report – Murray et al. 

34

Given that rocky shores come in many forms, how should investigators target habitats for study? 

Due to logistical constraints, it will almost always be impossible to effectively sample all 

habitats. If the goal of the study is to select habitat types for a comprehensive monitoring 

program, then key questions might be what shoreline/habitat types are of greatest concern or 

interest, and what types are most at risk? Habitats of greatest concern might be those with the 

highest biodiversity, or those able to support populations of a particular species (such as 

abalone), or simply those most common along a coastline; this decision is value-based. Habitats 

most at risk might be flat rocky benches because they readily collect oil and often receive the 

greatest intensity of human visitation, or protected shores where pollutants may be more 

persistent. This decision must be based on the goals of the study program, for example, the 

likelihood of site exposure to current or future environmental stressors. Impact detection 

programs may justifiably focus on a constrained subset of habitat types. For example, if oil from 

a spill comes ashore only in the high zone, there will be limited utility in sampling biota 

occupying the diverse and complex low intertidal zone.

Fig 2-6. A SCALE map of a section of a Pacific Northwest shoreline showing key 

geophysical features of nearshore habitats. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

35

Fig. 2-7. Examples of various rocky intertidal habitat types. A. Strong wave exposure 

at Botany Beach, Vancouver Island, British Columbia; B. Topographically 

heterogeneous habitat at Torch Bay, Alaska; C. Broken bedrock and topographically 

heterogeneous habitat at Dana Point in southern California; D. Sand-influenced 

rocky intertidal habitat at Crystal Cove in southern California. 

Researchers may choose to target unusual habitat types because of their special value or 

vulnerability. Boulder fields, for example, contain a variety of microhabitats including the 

undersides of rocks and the sediment beneath them, as well as the more obvious visible (tops and 

sides) rock surfaces. Given that this habitat type is common in some coastal regions, is used by 

humans, is biologically diverse, and is likely to retain oil following a spill, it is probably an 

important one to sample for both monitoring and oil-impact assessment purposes. Tidepools 

often are a focus of public interest given that they have aesthetic appeal, may contain subtidal 

species that only rarely occur in intertidal habitats, and tend to be very accessible. However, 

because each tidepool is physically and biotically unique, information gained from studying one 

pool is unlikely to apply (at least quantitatively) to other pools. This uniqueness makes tidepools 

less useful as a focus of a comparative sampling program. Marking individual pools and 

quantifying their biota through time may provide information about changes that occur in that 

particular pool (e.g., from being visited by too many school children), but this approach cannot 
Final Study Report – Murray et al. 

36

be used to detect broad regional trends in pool biota. However, studies of the impact of oil, for 

example, in a few pools at one site may provide some indication of possible impacts in nearby 

pools and be useful for impact assessment. 

Structure-forming biota, such as mussels, surfgrass, and some tubeworms, may be a worthwhile 

focus of sampling because these bioengineered habitats are diverse and particularly vulnerable to 

some kinds of impact. For example, if an oil spill or other form of disturbance kills or reduces 

the abundance of the key structure-forming species, the entire habitat with its associated biota 

will be impacted. In addition, because these biotically-structured beds often are long-lived, their 

destruction is of particular concern. Chapters 4 and 5 discuss unique problems involved in 

sampling some of these habitat types. 

Methods for Site Selection 

Regardless of the program goals, it is important to consider geophysical features if a study is 

being designed to compare populations or communities among sites. Beyond this general caveat, 

methods of site selection will differ depending on the question being asked. In this section, I 

discuss site selection considerations for designing resource monitoring and impact determination 

studies. 

Monitoring Studies 

The ultimate goal of site selection for resource monitoring is to obtain data of long duration and 

low noise-to-signal ratio (i.e., low temporal and spatial variability relative to the effect or trend 

being quantified), so that we can detect biological patterns that can be analyzed and interpreted. 

A recent report from a workshop on Ecological Resource Monitoring (Olsen et al. 1997) 

distinguishes three possible types of monitoring sites that represent different scales of 

investigation: 1) survey sites (such as EMAP, the Environmental Monitoring and Assessment 

Program, described below) that are designed to be statistically representative of habitats on 

regional or national scales and where the gathered information may have management or policy 

implications; 2) networks of sites that are used for monitoring large (regional) scale patterns of 

biological resources and environmental stressors; and 3) intensive (or sentinel) sites that tend to 

be few and are used to generate process-level understanding, but which cannot be treated like 

statistical samples or directly used to represent regional trends or patterns in biological 

parameters. 

For each type of monitoring site, site selection can rely on either design-based or model-based 

inference. Design-based (or probability-based) studies justify inference to unmonitored sites 

because they rely on statistically random site selection procedures. These require few 

assumptions, but allow no flexibility in making site selections. For example, the EPA’s EMAP 

uses a sampling design for terrestrial systems involving sampling every four years at points on a 

large, hexagonal grid covering the landscape of the U. S., with points (at the landscape 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

37

characterization scale) spaced 27 km apart. SEMAP’s primary goal is to “estimate the current 

status, trends, and changes in selected indicators of condition of the nation’s ecological resources 

on a regional basis”. However, there is concern that this sampling program, while statistically 

valid, is operational “at too coarse of a scale in space and time to detect meaningful changes in 

the condition of ecological resources” (NRC 1995; p. 3). This is an issue of matching sampling 

design to program goals and figuring out how to allocate personnel and funds to maximize the 

information gained. The NRC recommended increasing sampling frequency and intensity at a 

subset of the current sites, and using stratified random sampling within regions to achieve 

particular data-quality objectives. 

Model-based procedures, in contrast, use a statistical design to draw conclusions about observed 

study sites, and any inference to unobserved sites then depends on the statistical correctness of 

the study design or model. For instance, understanding of causal ecological mechanisms can be 

gained from data collected at observed sites and then be used to extrapolate the application of 

these same mechanisms to unobserved sites. The potential problems here are the (unquantifiable) 

biases introduced with site selection, and with assumptions about the broad validity of the model. 

The need to develop regional networks or sets of monitoring sites for shorelines, although not at 

EMAP-scales, seems to be increasingly appreciated. Programs that have established regional 

networks or sets of monitoring sites often have a very broad or comprehensive goal, e.g. seeking 

trends of any kind or changes caused by any processes at some indeterminate time in the future. 

Such monitoring may have “retrospective” goals —i.e., the causes of change or stress are not 

known beforehand — or “prospective” goals where stressors are known and thus monitoring can 

be designed to be more targeted and more efficient. If likely stressors are known, it may be 

possible to stratify site selection on the basis of the site’s responsiveness to a stressor of concern 

(for example, rocky intertidal sites with habitats that are particularly sensitive to spilled oil). In 

this way, a “responsive” site might represent a class of sites that should respond in a predictable 

and similar way to that stressor. However, rarely do we have data that enable generalizations 

about such site responsiveness. 

For retrospective sampling, monitoring is likely to be done at selected sites with the hope that 

trends and changes can be extrapolated over a larger geographic area. However, having a broad 

scale of inference requires choosing sites in a statistically and ecologically valid fashion. If sites 

are not randomly chosen, then inference from data collected at a few sites is limited statistically 

only to those sites, and cannot be used to generalize (see Page et al. 1995, Beck 1997 for 

discussions about sampling designs and generalization) or to extrapolate findings to other sites in 

the region. 

An ongoing program at scales smaller than EMAP, but using similar rationales, is the Southern 

California Bight Pilot Project carried out by the Southern California Coastal Water Research 
Final Study Report – Murray et al. 

38

Project (SCCWRP) (see http://www.sccwrp.org for information). This project has the goal of 

defining and monitoring the extent and distribution of environmental degradation over the 

southern California continental shelf. Site-selection here follows a probability-based sampling 

design. The region was first divided into areas or subpopulations of interest (e.g., geographic 

zones, areas around sewage treatment plants), and then sites were chosen randomly within these 

areas. This design ensures unbiased estimates of the Bight condition and enables determination 

of the actual span of shelf where ecological conditions differ from reference areas. The scale of 

inference is thus the whole Bight, although statistical inferences also can be made about each 

area (e.g., the conditions around river and storm drain outfalls). 

The selection of intertidal sites based solely on statistical criteria is likely to result in serious 

problems if selection is made from inadequate base maps. For example, following the Exxon 

Valdez oil spill, researchers representing the state of Alaska randomly selected study sites based 

on coarse-scale maps of shorelines showing substratum types. However, when the sampling 

crews initiated their field work, they found that they were trying to compare sites varying widely 

in salinity and even, in some cases, in substratum type, thereby significantly reducing the power 

of their comparative sampling program (McDonald et al. 1995). 

Other filters to apply to a population of potential sites before randomly choosing actual sites for 

study include: 1) accessibility and other logistical concerns; 2) the size —that is, the length of the 

segment of relatively homogenous shoreline; this is because short beach segments will suffer 

from edge-effects such as sand scour at the edge of a rocky bench; 3) proximity to known 

stressors (e.g., sites near and far from an outfall site, or sites located on and away from modeled 

oil spill trajectories); and 4) desired geographic spread or range of the targeted study area. If 

comparable sites have been selected, then those spread over a broad geographic range are more 

likely to let us distinguish local events from those of a climatic or hydrographic nature: “the 

geographic scale of any biological pattern or trend is the first and most reliable clue to its cause” 

(Lewis 1982). If a common pattern is seen over a large area, then any departure from this pattern 

is strong evidence for a local impact — from a pollutant, for example (e.g., Bowman 1978, 

Christie 1985).

A rather different sampling scheme from the network approach involves using “sentinel” or 

“reference” sites. These are intensively sampled areas, ideally used to provide a linkage between 

a broad-scale survey (extensive but low-resolution) and localized, process-oriented basic 

research that enables understanding of cause and effect. Jassby (1998) argues that if sentinel sites 

can elucidate key mechanisms of interannual variability, then they may be useful for generalizing 

to other sites sharing their main features. For example, individual lakes have certain 

characteristics (e.g., annual ice cover, morphometry of the watershed) that predispose them to be 

responsive to a certain set of external forces (e.g., acid rain). If we can understand these 

predisposing features for particular stressors on rocky shores, then we may be able to extrapolate 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

39

from sentinel sites containing these features to other sites that share them. This could be regarded 

as a special case of a “model-based” design. 

Disadvantages of relying on a monitoring strategy that incorporates sentinel sites are: 1) 

considerable knowledge of the “natural history of interannual variability” is required (Jassby 

1998); 2) background variability (among populations, sites, or years) can disguise a system’s 

responsiveness to a certain stressor; and 3) sentinel sites chosen because they are sensitive to 

change may exaggerate the amount of change occurring in a region. However, intensively 

monitored sentinel sites, especially if they can be chosen in a random (or stratified random) 

fashion from a population of potential sites, may provide the best way to understand the 

mechanisms responsible for long term biotic change in a region. 

Impact Studies 

In contrast to resource monitoring programs, the purpose of some studies performed on rocky 

shores is to detect or quantify the impacts of a stressor on intertidal populations or communities. 

These studies generally focus on identifying the biological changes that have taken place 

following site exposure to the impacting agent and the location or geographic extent of the 

impact. For example, such studies may be designed to determine the effects of improving public 

access to a rocky shoreline near a populated area, or of a new outfall pipe on the coast, or of a 

small oil spill on a small section of coastline. 

There has been extensive discussion in the literature (Schmitt and Osenberg 1996, Kingsford 

1998) of experimental designs to answer these types of questions (see Chapter 1). One broad 

class of analytical methods is the Before-After-Control-Impact (BACI) design, or non-BACI 

post-impact design (e.g., Underwood 1994, Wiens and Parker 1995, Osenberg et al. 1996, 

Stewart-Oaten et al. 1992, Schmitt and Osenberg 1996). These designs rely on finding suitable 

impacted and nonimpacted (control) sites and, optimally, on being able to gather data at all sites 

both before and after the impact. Statistically powerful data are those that show temporal 

coherence among sites; that is, in the absence of an impact, all sites show similar trends. This 

outcome in turn relies on the sites being initially similar both in their biota and in their temporal 

dynamics. In practice, such designs often are asymmetrical, and include one impacted site and 

several randomly selected control sites, with the latter serving to assess natural patterns of 

temporal and spatial variability (Underwood 1994). Thus selecting appropriate control sites to 

compare with impacted sites is a critical decision, as is surveying enough sites to be able to 

factor out natural site-to-site variation. 

An alternative to Control-Impact designs is to establish sites along a gradient of disturbance or 

potential impact. Such designs can be particularly powerful where a disturbance attenuates with 
Final Study Report – Murray et al. 

40

distance from a point source, such as around oil drilling operations, sewage outfalls, or along a 

gradient of spilled oil. Using regression analyses, Ellis and Schneider (1997) compared the 

power to detect change of a Control-Impact design with a Gradient Impact Design around a wellstudied oil field in the North Sea. With equal numbers of observations for each analysis, they 

found that the Gradient Impact Design was more powerful at detecting changes in abundances of 

benthic organisms than the Control-Impact design. Additional advantages of gradient designs are 

that: 1) there is no need for potentially arbitrary selection of control sites (how far away from a 

disturbance should a control site be located?); 2) gradient analyses do not rely on data that must 

meet the requirements and assumptions for use of ANOVA or similar statistical tests; and 3) they 

provide information on the spatial scale of the impact, which is useful both for ecological 

analyses and for management and policy purposes. Ellis and Schneider (1997) caution, however, 

that similar to Control-Impact designs, investigators must be certain that all the sites are 

“comparable with respect to physical processes”, so that a gradient in a factor such as depth or 

sediment grain size is not mistaken for an impact of the pollutant. Thus, physically matching 

sites for gradient analyses is as critical as it is for other impact-detection protocols. 

Ideally, for either type of impact-detection study, we might want to have biotic surveys of many 

sites and then choose the ones that are most similar overall in “before” community composition. 

However, such surveys cost time and money and useful prior data are almost never available. 

Thus, site selection may have to depend on easier-to-quantify characteristics than biotic 

similarity (and biotic similarity alone may be misleading because of the possibility of different 

dynamics among sites). Geographic proximity is likely to be a very important parameter in 

choosing sites for impact detection, because (all else being equal) closer sites are more likely to 

have more similar biological characteristics and dynamics than broadly separated sites. Other 

parameters to be “matched” in site selection procedures have been described above. 

Numbers of Sampling Sites 

Inevitably, choices have to be made between sampling that is extensive (many sites spread over a 

broad geographic area) and intensive (few sites, but sampled with greater replication in space or 

time). How many sites should be monitored? Urquhart et al. (1998; p. 255) note that “where 

among-site variation across the region of interest is even moderate, a single site produces little 

data of relevance for inferences across the set of sites”. They add that multiple sites help little if 

there was bias in selecting them. Lewis (1980) notes that sampling only a few sites “runs the 

high risk of the data being atypical and, therefore, of little value for reaching broader 

conclusions”. In addition, sampling over several sites encompassing a greater spatial scale is 

more likely to capture community stability (i.e., natural increases and decreases in populations 

across several sites may balance each other out, Connell 1986), and managers are less likely to 

initiate actions based on changes seen at one or a few sites. Spreading sites over a large region 

also makes it more likely that one will be near a site where, for example, oil strands following a 

spill, because spilled oil is notoriously patchy. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

41

A useful approach to determining the number of sites that are required for an effective 

monitoring program may be to combine many of the advantages of a “few” with those of a 

“many” site protocol. In this type of program, a broad network of sites is established and 

investigated with moderate sampling intensity together with a few sites that are intensively 

sampled, with the smaller set of sites being chosen in such a way as to allow inference of 

process—level information to the broader region. If trends in measured biological parameters at 

these sites are coherent both through time and across sites, then the identified biological patterns 

can serve as particularly powerful templates against which changes due to an environmental 

stressor or natural shifts in physical conditions can be detected. 

In contrast, sampling for impact determination is almost always intensive and focused on a few 

impacted sites and nearby control sites, or on a series of sites along an impact gradient. For either 

extensive or intensive sampling designs, obtaining statistically and ecologically valid data on 

impacts will depend on: 1) finding sites that are geophysically matched as closely as possible, 

and 2) replicating sufficiently for each class of sites. Underwood and Chapman (1998 a, b) 

emphasize the very high variation in biological parameters among sites (“shores”) that they 

considered to be physically similar (e.g., all wave-exposed), highlighting the need for replication 

at the site-level to obtain sufficient power to detect patterns. While their sites may not have been 

geophysically matched (or stratified) as closely as recommended here, the point is well taken that 

data on natural among-site variation must be available before “among-treatment” variation can 

be ascribed to anthropogenic causes. Thus, site-level replication is a crucial component of any 

robust study design. 

Summary 

As stated by Ellis and Schneider (1997) numerous investigators have noted that “more than any 

other factor, our inability to explain natural variability places a limit on our ability to detect 

anthropogenic change”. Because differences in physical variables among sites increase this 

natural variability, careful site selection is a critical component for study programs designed to 

gain understanding of regional trends or to assess impacts on rocky intertidal populations and 

communities. If sites are not randomly selected, valid (statistical) inferences about other sites of 

interest cannot be made. If attention is not paid to matching site characteristics, then we run 

substantial risk of confounding impact-detection with natural among-site variation in biotic 

features caused by subtle geophysical differences. Quantifying impact or discussing trends in 

biota through space and time require that site selection (or at least primary site selection) is 

statistically random (e.g., potential sites are drawn from detailed maps of shorelines), and that 

geophysical characters important to community structure are matched or at least recorded. 
Final Study Report – Murray et al. 

42

Site selection protocols should thus involve: 1) identifying a set of sites that are similar in 

geophysical features and types of habitats to each other or to a disturbed or impacted location of 

interest, and then 2) randomly choosing a subset for study from this site pool (Glasby and 

Underwood 1998). In addition, sampling should be concentrated on habitats of high value (to 

humans or to the ecosystem) or of high sensitivity to suspected stressors, and, if it is useful to 

consider trends over a large region, on habitats that are broadly present. Microhabitats such as 

tidepools and crevices that are individually unique are less likely to be useful for sampling 

programs that seek to understand a larger area of shoreline. In designing monitoring programs, a 

balance must be struck between intensive sampling of a few sites and extensive sampling of 

many sites so that a better picture of biological trends and dynamics can be attained over a 

broader region. This approach argues for establishing a broad network of sites that are sampled 

with lower intensity (perhaps only in one zone, or only for a few key species, see Chapter 3), 

combined with a few sentinel sites that receive intensive sampling. Besides providing processlevel information that may apply throughout the broader region, such sentinel sites can also 

provide valuable data about the components of variability (e.g., within sites, among sites, and 

among years), which in turn can help interpret patterns seen over larger spatial and temporal 

scales. 

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Final Study Report – Murray et al. 

48

Chapter 3. 

Biological Units 

By 

Megan N. Dethier

 Tatoosh Island, Washington 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

49

Introduction 

The biological units targeted by a sampling program can vary from individual-based parameters 

such as the size of a particular limpet species’ gonads, to population-level parameters such as 

counts of all macroscopic organisms, to higher taxonomic units such as the numbers of phyla 

(Fig. 3-1). The biological units to be selected will vary (as always) with the goals of the sampling 

program and with available knowledge about the ecology of the populations and communities 

being studied. The investigator will want to choose the most informative biological units ― i. e., 

those that best address the goals of the study and that have the potential to provide statistically 

powerful answers to the specific research questions. Ideally, the chosen biological units also will 

have known causal links with any stressors being studied. Unfortunately, rarely are clear causal 

relationships between stressors and responses of rocky shore organisms known, even when only 

a single identifiable stressor is under consideration. 

Species-Level Sampling 

Sampling the abundances of one or more species populations at target sites is a common 

component of most rocky shore sampling programs. There are several advantages to specieslevel sampling. 1) The species, or local population, is the basic unit of the majority of ecological 

research; ecologists are comfortable thinking in terms of species populations, and there are 

established sampling designs and procedures for determining the abundances of species varying 

in size and distribution. 2) Researchers usually explore the ecological processes affecting 

communities at the species level. Thus, background information on trophic position, life history, 

recruitment patterns, and other ecologically important topics is often available for the most 

common coastal species. 3) The abundances of populations, whether measured as density, 

percent cover, or biomass (see Chapters 6, 7), presumably integrate and reflect local 

environmental conditions operating at the study site. Individual-based parameters such as 

gonadal production may be more sensitive to unusually good or bad environmental conditions 

(e.g., exposure to pollutants, nutrient availability, or changes in predation pressure), but changes 

in environmental factors should ultimately be manifest directly or indirectly in the size of a 

population. Moreover, abundance responses in populations can usually be measured over short 

time scales when abrupt changes in abiotic or biotic conditions significantly increase mortality 

rates. However, resistant and long-lived species might not show immediate abundance shifts, but 

instead may show effects over longer time scales due to reduced larval production or 

recruitment. 4) Even when sampling is not targeted towards determining the effect of a particular 

stressor, if abundance data are collected on a diversity of species types (e. g., long and shortlived species, producers and consumers, or species with different dispersal shadows) then we 

should be able to detect changes in one of these populations that correspond with the onset of a 

stressor. 5) Alternatively, by focusing on a limited number of ecologically important species, 
Final Study Report – Murray et al. 

50

investigators need only recognize the species of interest and data collection will not require 

identification of all of the taxa found in a community or assemblage. 

 

Fig 3-1. Choices of biological units in rocky intertidal sampling programs. Obtaining data on 

species abundances is often the focus of intertidal sampling programs. Data can be collected for 

all species in the habitat or for selected “key” or “indicator” species. Species data can be 

assigned to higher taxonomic categories or to functional groups but collecting data only at 

supra-species categories limits options because data for individual species cannot be 

reconstituted. Down-a-level sampling programs focus on individual-based parameters that may 

be more sensitive to environmental change than the abundances of species or functional groups. 

Several disadvantages of species-level sampling programs exist. These include designing 

sampling strategies that account for natural variability at the population level in both space and 

time, and the inherent difficulties in identifying a priori the appropriate species to sample. 

Numerous studies have demonstrated high levels of variation in the abundances of rocky 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

51

intertidal plant and animal populations due to spatial patchiness and temporal dynamics. This 

variation can be driven by natural abiotic parameters such as changing water temperatures, 

exposure to large storm waves, or fluxes in sand movement, and biotic processes including 

spatially variable patterns of predation and recruitment. Such high noise to signal ratios can 

make it particularly difficult to statistically detect changes at the population level given the limits 

of most sampling programs. Even carefully designed Before-After-Control-Impact (BACI) 

sampling programs (see Chapter 1) can become uninformative when species abundances vary 

greatly among sites or over time. Likewise, if the compared sites track different temporal 

courses, there will be a significant site x time interaction resulting from factors unrelated to the 

stressor of interest. For example, Osenberg et al. (1994) found a large effect size (i.e., a large 

impact) on population-level abundance data in response to a pollutant; however, this effect was 

very difficult to detect statistically because of high within and among site natural variability (i.e., 

high noise to signal ratio) in the abundance data. 

The problem of high natural noise levels has led to concerns that a truly informative, rocky 

intertidal monitoring program relying on species abundance data cannot be developed. However, 

the degree of among-site variation in biological parameters can be reduced through careful 

selection of the sites and populations to be studied (Chapter 2;), and the employment of 

appropriate and well crafted sampling designs (Chapters 4, 5;). Lewis (1982; p. 260) notes: 

“While our objective is the detection of either a unidirectional trend or a persistent departure 

from normal, the cycles and fluctuations that constitute the normal make the task difficult. But at 

least they can be recognized for what they are — by an experienced field naturalist — and many 

can be discounted...”. For all of these reasons, selection of the biological units to be sampled is a 

critical component of any rocky intertidal research program. This decision affects the ability to 

detect differences between treatments and controls or over spatial and temporal scales, and 

ultimately to gain understanding of causal links between environmental and population 

parameters. 

Unfortunately, opinions about “what species to sample” are almost as diverse as rocky intertidal 

researchers. Generally, the tendency is to identify key species, or as stated by Clarke (1997) 

“those whose presence or absence in certain environments has major repercussions in the 

community”. If a study is designed to detect present or future effects of a particular stressor (e.g., 

oil spills, sewage effluents) or management action (e.g., establishing reserve protection), then socalled “indicator species” might be appropriate to sample. These should be taxa known to be 

particularly resistant (e.g., the polychaete Capitella capitata which is abundant around sewage 

discharge sites) or sensitive (e.g., the bivalve Brachidontes rodriguezi whose numbers decline in 

areas highly affected by sewage effluents; López Gappa et al. 1990, 1993) to the stressor or 

action. However, few species that are good “biomonitors” or “indicators” of particular stressors 

have been unequivocally identified for rocky intertidal systems. Requirements for a good species 

for biomonitoring are reviewed in Underwood and Peterson (1988), Keough and Quinn (1991), 
Final Study Report – Murray et al. 

52

and Loeb and Spacie (1994); these include: 1) wide distributions to allow for comparisons 

among geographic areas, 2) a well-known autecology to reduce the chances of reaching false 

conclusions if changes are detected by the sampling program, 3) sensitivity to the stressor of 

concern but not to variations in other environmental conditions that likely occur over the study 

area, 4) the ability to be to sampled with precision and accuracy, and 5) the capacity to serve as a 

representative of a wider range of species or ecological processes. 

In addition, political and public concerns may enter into the choice of target species and 

influence the design of monitoring or impact studies. For example, there may be pressure to 

monitor certain “charismatic” species or species of high conservation interest such as sea or 

shore birds or marine mammals such as sea otters, or species of economical value. Identifying a 

species that fulfills these requirements, while also meeting the criteria for a good biomonitor or 

indicator, may not be possible especially when species selection is of secondary importance to 

site selection in a region. In these cases, if sites are selected randomly, not all chosen sites may 

contain suitable populations of a targeted indicator species. Underwood and Peterson (1988) also 

caution against choosing a “millstone” species (i.e., a species selected because of its historical 

use), instead of a keystone species (sensu Paine 1966) known to play an important role in 

community organization. Selection of politically-expedient charismatic or “millstone” species to 

serve as the basis for a research or monitoring program may jeopardize the scientific value of the 

program at the outset unless the program goal is simply to monitor the abundance of that special 

species. 

Often researchers are asked to design sampling programs for monitoring spatial and temporal 

changes in biota in anticipation of a future unidentified perturbation. However, the a priori 

selection of appropriate biomonitors for such programs may not be possible because the 

conditions or stressors of concern are likely unknown and multiple. Therefore, a species selected 

as a good indicator for detecting sewage pollution may not be good for assessing the effects of 

human foot traffic or overexploitation. As a consequence, when a single comprehensive study is 

desired, investigators may hedge their bets by selecting one or more species thought to play key 

ecological roles in the ecosystem or by sampling all macroscopic organisms in the community. 

Lewis (1982) has argued vigorously for focusing sampling on populations of the dominant 

structure-forming species (e.g., mussels, surfgrass) and key grazers and predators in the 

community because most other rocky shore organisms will depend on these “key” species. Thus, 

other unstudied species populations should show patterns of change that correlate with changes 

in the key species. Many dominant or ecologically important species in rocky intertidal 

communities are large, long-lived, and easy to identify, offering the additional advantage of 

being simpler to sample with accuracy and precision. Houghton et al. (1997), for example, found 

that sampling four dominant taxa (Fucus, Lottiid limpets, Littorina, and Nucella) provided most 

of the information needed to detect functional changes in rocky intertidal communities on 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

53

sheltered shores in Prince William Sound, Alaska, following the Exxon Valdez oil spill. 

Similarly, Ambrose et al. (1994; see also Engle et al. 1994) selected 10 ecologically important 

and well-understood species or species groups (e.g., mytilid mussels, acorn and gooseneck 

barnacles, Anthopleura spp., Silvetia ( = Pelvetia)) as the basis for a monitoring program 

designed to enable detection of the effects of a major disturbance, such as a large oil spill, on 

California shores. Long-lived or ecologically dominant species, however, might not respond to 

changing environmental conditions or stress as rapidly as short-lived annuals or less common 

species. In addition, some ecologically important species, such as sea stars, may be too mobile 

and patchy in their distributions for designing efficient sampling programs that can statistically 

track changes in their densities over time. 

The uncertainties associated with knowing which species to sample have led other researchers to 

focus their sampling efforts on all or most species in an intertidal community. The arguments for 

this community-level approach are that: 

1) a single “canary-in-the-mine” indicator species for rocky shore ecosystems 

has yet to be identified, 

2) with few exceptions, how changes in the abundances of key species affect 

other species is unknown in rocky intertidal communities, 

3) rare species may be more sensitive to changing environmental conditions or 

the presence of pollutants than more common, ell-studied ones, 

4) sampling more than one species presents the opportunity to examine 

coherence in trends among multiple components of the community, which in 

turn strengthens conclusions about the effects of changing conditions or 

impacts (e.g., Schroeter et al. 1993), and 

5) gathering data on only a few species compromises the ability to examine 

changes in community parameters and to perform useful assemblage-level 

multivariate analyses. 

Rare species seem to be particularly numerous on rocky shores and present significant problems 

because by definition they will show up in only a few sampling units and will be difficult to 

sample with accuracy and precision. In addition, their scarcity presents difficulties during data 

analysis because they usually exhibit high variation in abundance among replicate samples and 

the numerical data describing their distributions and abundances through space and time are 

zero-rich, violating assumptions of most univariate and multivariate statistical tests. Ignoring rare 

species, however, also presents the risk of excluding taxa that might be highly responsive to 

changing environmental conditions, the presence of stressors, or to experimental treatments. The 
Final Study Report – Murray et al. 

54

debates on the value of rare species in sampling programs designed to detect ecologically 

meaningful changes in aquatic communities are on-going (Cao et al. 1998, Marchant 1999, Cao 

and Williams 1999). Clearly, more research is needed to improve understanding of the ecological 

roles of many of these rare species in intertidal and other aquatic ecosystems, including their 

resistance and sensitivity to disturbances and changing environmental conditions. One analytical 

solution (L. Tear, pers. comm.) is to treat rare species differently from species for which it is 

possible to collect quantitative data. Criteria for determining rare vs. common species can be set 

and the species composition of these two groups can be compared separately between times and 

locations. It may be more useful to note which species are “rare” or “common” and how those 

lists change at a site over time or between sites than to try to find a metric and a method of 

analysis appropriate for a combined dataset that includes both species types. 

Although comprehensive in scope, sampling programs that track all species in a rocky intertidal 

community have major disadvantages. Principal among these are: 1) the observers performing 

the field work must have the taxonomic expertise to discriminate all encountered taxa; 2) much 

more time and cost will be required to carry out field sampling and data reduction and analysis 

tasks compared with studies that focus on only a few select species, and; 3) no single sampling 

design or method can adequately assess all species in an intertidal community. Different 

approaches are required to optimize sampling of mobile and sessile species, abundant and scarce 

species, and large and small species, resulting in the need for complex, mixed sampling designs 

when carrying out comprehensive sampling programs. If only a few key populations are targeted, 

then it might be feasible to employ separate sampling strategies for each population of interest to 

best capture information on their abundances (e.g., for common vs. rare species). 

Under circumstances where prior data are available, either over several sites or over several 

years, an informative approach is to focus data gathering on species that show the lowest spatial 

or temporal variation (e.g., lower error to mean ratios). This strategy can reduce among-sample 

variation or noise and increase statistical power when attempts are made to detect differences or 

changes between sets of samples. Ideally, the populations chosen for focused sampling will 

include a diversity of species types (e.g., based on their population abundances, trophic positions 

in the community, and life histories). For example, on the Olympic coast of Washington, 

candidate species for such a focused sampling program include barnacles that occupy the very 

high intertidal zone, certain limpets, abundant seaweeds in wave-protected habitats such as 

Fucus gardneri and Endocladia muricata, the anemone Anthopleura elegantissima, and crustose 

coralline algae (Dethier, unpub. data). However, these species may not show this same low 

variability among sampling units in other geographic regions. Data obtained from such a 

sampling program can be augmented by less frequent, intense sampling that includes all species 

populations in the community, perhaps even as simple checklists. These data could allow 

community-level comparisons of parameters such as richness and diversity and facilitate the use 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

55

of multivariate techniques that may help establish relationships between changes in species 

populations and variations in treatments or environmental conditions. 

Additional data that may be informative to gather at the species level include measurements of 

the distributions of species populations, either over short horizontal spatial scales or across the 

entire intertidal zone. Because almost all intertidal plants and animals are restricted in their 

distributions to particular tidal zones, changes in their vertical distributions may provide 

ecologically important information. For example, a gradual rise in the elevation of a barnacle 

band on the shore might suggest a rise in sea level or a reduction in exposure to desiccating 

conditions. Abrupt loss of the top of an intertidal algal band corresponding with an oil spill might 

provide a useful measure of impact, even if the individuals found in the central part of the 

species distribution remain healthy. Loss of high-shore mussels on north— but not south—facing 

shores on the coast of Washington, for example, helped to differentiate losses from a nearsimultaneous oil spill and a major freeze event (Dethier 1991). Often such distributional 

information can be obtained simply and accurately, and at the needed scale, by taking a series of 

photographs during each site visit using a consistent reference point. Shifts in distributions over 

short horizontal scales within the same vertical tidal range also may be important to document. 

This will be particularly true for long-term monitoring programs that employ fixed plots because 

species abundances can decrease or increase inside plots but show the opposite effects in 

adjacent, unsampled areas. Such situations can lead to misleading conclusions if comparisons 

among sites or over time are based exclusively on data taken from the fixed plots, and leave 

undetected real changes in patch size, shape, and distribution. Some of the advantages and 

disadvantages of fixed plot sampling are discussed in Chapter 4. 

Down-a-Level: Individual-Based Sampling 

Several authors, including Jack Lewis, an experienced marine ecologist who has monitored 

rocky shore populations for decades (e.g., Lewis 1976, Lewis et al. 1982), argue that 

measurements of the individual performances of one or more key species at a site are more 

sensitive indicators of environmental change than abundance data. Indices of performance 

include growth rate, gonadal output, certain physiological parameters of individual animals, and 

the recruitment strength of the population. Thus, Lewis and coworkers (e.g., Heip et al. 1987) 

have concentrated their monitoring efforts on measuring parameters that provide information 

about the status of a population, such as size and age structure, reproductive condition, and 

recruitment strength. Reproductive cycles of various molluscs in the U. K., for example, are 

highly sensitive to climatic and hydrographic change (studies in Heip et al. 1987). Often, 

pollutants impact gonadal development and certain biochemical processes, and when these 

connections are known, measures of such individual species’ performances can be used as 

powerful biomonitors. Zeh et al. (1981) also have stressed the value of measuring size structures 

of populations through time, because these data provide information on a population’s 

development and serve as a sensitive means for detecting change in population status. Osenberg 
Final Study Report – Murray et al. 

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et al. (1994) argue for following body size and other individual-based parameters because they 

found that these were generally more consistent through time at control sites and more variable 

at impacted sites. They concluded that the statistical power to detect change in these parameters 

exceeded the power available using population-based parameters such as density, where data 

were more variable among sites and times. 

A possible disadvantage of relying on individual-based parameters is that the chosen measures 

may vary greatly among sites, to the extent that among-site differences may not be 

distinguishable from differences resulting from large-scale disturbances. Gathering performance 

data also is time-consuming and may require destructive sampling (e.g., to measure gonadal 

sizes) and careful timing (e.g., to obtain gravid specimens when reproduction is highly seasonal). 

For instance, growth rates in at least some intertidal invertebrates are so responsive to local 

environmental conditions (e.g., population density, competition, availability of food resources) 

that they cannot be used as an index of broader regional patterns. Likewise, other performance 

parameters (such as recruitment, maximum body size, or population age structure) may vary 

greatly over local spatial scales or due to different site histories. If parameters are consistent 

enough within a site to establish a baseline (as in the case described by Osenberg et al. 1994), 

however, then changes through time may be important indicators of changing environmental 

conditions or of site disturbance. Before such individual-based performance data become the 

focus of any study, more information is needed to determine which species are good and 

sensitive integrators of environmental conditions and to establish baseline performance 

expectations under natural (stressor-free) conditions. Selected approaches to individual-based 

studies of intertidal seaweeds and macroinvertebrates are discussed in Chapter 8. 

Up-a-Level: Supra-Species Sampling 

Because identifying all species in a community requires considerable expertise and time and 

because some species of ecological importance can be difficult to consistently discriminate and 

sample, other ways to meaningfully categorize biological units have been sought. Approaches to 

this categorization have varied depending on the investigator and the habitat being studied. For 

example, some investigators who work in soft-bottom benthic communities favor grouping 

sampled biological units into higher taxonomic categories. Alternative approaches used in rocky 

intertidal and subtidal habitats include categorization of species into guilds or functional groups. 

Arguments concerning the value of this supra-species level sampling vary but generally hinge on 

trade-offs between the unwanted loss of information and increased potential for obtaining 

misleading results versus greater sampling efficiency and a savings in study costs. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

57

Higher Taxonomic Categories. Several studies, mostly performed in habitats other than the 

rocky intertidal zone, have demonstrated that data gathered at higher taxonomic levels (e.g., 

genus, family, or even division or phylum) can substitute for more time-consuming species-level 

sampling (Keough and Quinn 1991, Underwood 1996). For example, Kratz et al. (1994) found in 

alpine lakes that quantifying rotifers at the species level resulted in variable and difficult-tointerpret data. However, when data were grouped by genus they were less variable because of 

compensatory processes within the aggregation, and showed strong effects of lake acidity on 

rotifer abundances. In sedimentary marine habitats, workers have found that quantifying the 

abundances of polychaetous annelids by family instead of by species effectively describes trends 

as well as sensitivity to stresses from pollution (e.g., Ferraro and Cole 1992, James et al. 1995, 

Olsgard et al. 1997). For example, using this approach Warwick (1988a,b) found no substantial 

loss of sensitivity in detecting patterns at the family versus the species level. He reported that 

“taxonomic sufficiency is required only to the level that indicates the community response”, and 

that huge savings in time and money can result from gathering data at higher taxonomic levels. A 

possible functional explanation for this outcome is that variation in natural environmental 

conditions, such as sediment grain size or water depth, may influence the fauna through species 

replacement (Warwick 1988a). In contrast, exposure to anthropogenic stressors modifies the 

community at a higher taxonomic level because species belonging to the same family (or even 

phylum) are similar in their abilities to respond to the altered conditions. Underwood (1996) 

notes, however, that the rules for reducing taxonomic effort must be known, and that this 

requires understanding of how supra-species levels respond to impacts. Unfortunately, 

mechanistic understanding of why supra-species analyses work to detect changes in spatial 

pattern due to disturbance has yet to be developed. Often, data are gathered at the supra-species 

level not because of a tested functional similarity in responses among lower-level taxa, but 

because of limited time or taxonomic expertise (e.g., Morrisey et al. 1992). This illustrates both 

the advantages and disadvantages of relying on higher taxonomic categories in sampling 

programs. Sampling species by lumping them into higher taxonomic groupings is easier, 

simplifies data analysis, and is, therefore, less costly; however, this approach is often taken 

without ecological justification and, therefore, the results and conclusions of such studies may 

lack validity and be misleading.

A cogent example of how sampling higher-level groups can lead to loss of information when 

studying rocky intertidal populations can be found in recent research on two barnacle species. 

Suchanek (pers. comm.) found that two congeners of barnacles had very different sensitivities to 

Exxon Valdez oil in the field. Collecting barnacle abundance data at the genus level would be 

simpler and more efficient in this situation but would fail to accurately characterize the impact of 

oil on these species and lead to errors in interpretation. However, it could be argued that changes 

in the distribution and abundance of a single species are not always ecologically important, 
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whereas changes occurring in all co-occurring congeners or throughout a family are indicative of 

serious and significant community modifications. 

Another disadvantage of gathering data at the supra-species level is that this approach precludes 

analyses of biodiversity based on species richness. Lumping information to analyze patterns at 

higher taxonomic levels can always be done after collecting data at the species level, but 

discrimination to the species level of resolution can only occur at the time of the initial data 

gathering. Any study that requires inventories of all species in a community, however, requires 

that the investigators have extensive taxonomic expertise and results in significant increases in 

field and laboratory sampling time. Oliver and Beattie (1996) illustrated a potentially useful 

compromise for sampling arthropod biodiversity and determining species turnover in different 

forest types. They found that collections sorted by non-specialists into “morphospecies” (taxa 

that differ from each other clearly, based on external features) showed similar diversity patterns 

and trends to those generated by taxonomic specialists working at lower taxonomic levels. They 

also found that some of these morphospecies could serve as “surrogate taxa” that show strong 

relationships with other taxa. However, they cautioned against extending this approach to other 

organisms and habitat types without careful empirical testing. Clearly, research is needed to 

determine the ecological utility of using lumped species, morphospecies, or surrogate taxa when 

performing rocky intertidal studies. 

Functional Groups. An alternative approach to using systematic criteria for lumping organisms 

into biological units is to group species with similar functional characteristics such as body form, 

trophic position (“guild”), or life history pattern (Figs. 3—2). The rationale for this approach is 

that the various species within a functional group (e.g., mobile deposit—feeding worms, fine 

filamentous algae, microalgae—consuming limpets) may be unpredictably present through space 

and time, while the abundance of the group as a whole remains relatively stable. For example, 

different species belonging to a functional group may colonize a rocky intertidal surface at 

different places and times, but generally their responses to major ecological processes will be 

similar. Functional groups can be those that respond to the environment in a similar way 

(response groups) or those that have similar effects on the rest of their communities (effect 

groups).

Species that use similar resources in a similar manner should be indicative of the processes that 

control those resources (Underwood and Petraitis 1993). These relationships have been 

demonstrated repeatedly for soft-sediment infauna (e.g., Wilson 1991, Posey et al. 1995, but see 

Weinberg 1984 for an exception), epibionts growing on mangrove roots (Farnsworth and Ellison 

1996), and for algae occurring on rocky substrata (reviewed in Steneck and Dethier 1994, also 

Hixon and Brostoff 1996). In addition, macroalgal primary productivities and other ecological 

attributes have been found to be associated with functional-form groups (Littler and Littler 1980, 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

59

Littler and Arnold 1982). Upright, canopy-forming algae, for example, are more susceptible to 

damage from human foot traffic than low-lying turfs or crusts and thus, as a functional group, 

constitute a strong indicator of trampling disturbance (Povey and Keough 1991, Brosnan and 

Crumrine 1994, but see Fletcher and Frid 1996). In addition, ephemeral green algae often replace 

larger, brown seaweeds and become more abundant in polluted habitats (Keough and Quinn 

1991). Functional group approaches also have been used successfully (Littler and Littler 1984, 

Murray and Littler 1984; Steneck and Dethier 1994) to analyze macrophyte patterns on rocky 

shores. If the study goals are to determine the stability of an ecological community, or the effects 

of large-scale ecological forces, data analysis at the level of functional groups may be useful and 

informative (Hay 1994). For example, these kinds of data would clearly and simply describe a 

change in community composition from larger, longer-lived kelps to smaller, opportunistic algal 

species. Sampling at this level of taxonomic discrimination is clearly faster, requires less 

expertise, and is less costly compared with sampling at the species level. However, analyses 

based on a functional group approach also can be less able to detect biological effects of changes 

in environmental conditions (Phillips et al. 1997). 

Besides sometimes being less informative, another potential disadvantage of using a functional 

group approach in an intertidal sampling program is that, as always, the proper interpretation of 

patterns or trends depends on knowledge of the natural histories of the sampled organisms. 

Species within a guild may use one resource (e.g., space) in a similar way but be very different 

from one another in other ways (Menge et al. 1983, Underwood and Petraitis 1993). For 

example, a change in dominance from Mytilus californianus, a long-lived, competitive species, 

to its congener, M. trossulus, a shorter-lived, smaller, and faster growing mussel, would not be 

detected if sampling was restricted to supra-species or functional-group biological units. It may 

be common to have such variation in life history characteristics, or even pollution tolerance, 

among species assigned to a particular functional group since groups usually are based on 

morphology or trophic position. Better empirical knowledge of the functional equivalence of 

species is needed before investigators rely too heavily on a functional-group approach when 

designing intertidal sampling programs. In addition, functional groupings have been based on a 

wide range of criteria that may differ from study to study so that consistent associations between 

a particular functional group and its ecological attributes are not always apparent (Wilson 1999). 

The functional group approach also is clearly coarse-grained; it may detect large-scale changes 

but may not have the sensitivity to detect early changes in conditions that might be detectable 

through more fine-grained, species-level sampling programs. 
Final Study Report – Murray et al. 

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Fig. 3-2. Diagrammatic representation of a scheme for classifying seaweeds into seven 

functional groups (modified from Steneck and Dethier 1994). The functional groups (specific 

morphological form in parentheses), range of thallus sizes, and morphologies of representative 

genera are presented for each group. 

Community-Level Metrics. Analyses performed on population-based parameters may not always 

allow detection of ecologically meaningful changes among sites or over time. Moreover, when
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

61

changes are detected in population or individual attributes for only one or a few species, the 

representative nature of these changes may be uncertain. In these cases, or to integrate the trends 

exhibited in community structure by all or most sampled species, community-level analyses are 

in order. Clarke (1997) argues that approaches involving the whole assemblage of species in a 

habitat are more realistic than the study of the fate of only selected species. The search for 

bioindicator species often has been paralleled by a search for a parameter that describes 

responses of the entire community in a compact and meaningful way. Karr (1994) notes: 

“Biological monitoring must seek ecological attributes for which natural variation is low but that 

are influenced to some significant extent by human actions”. The most commonly used 

community-level metric of this type is diversity, which can be expressed either as species 

richness (i.e., the number of species or taxa present per unit area) or as an index integrating 

richness with species abundances in the community. Usually, richness or a diversity index is 

calculated for each sample and the resultant means are analyzed using univariate statistics to 

determine temporal or spatial differences among the sampled communities. The popularity of 

diversity indices probably stems from their being thought of as indicators of ecosystem 

wellbeing (Magurran 1988). 

Habitat-specific alternatives to diversity exist such as the nematode to copepod ratio, or the 

annelid pollution index for soft sediments (Keough and Quinn 1991). Karr (1991) used an “Index 

of Biological Integrity” (IBI) to evaluate the status of fish communities in stream ecosystems 

affected by human activities. This index integrated parameters addressing attributes of 

individuals, populations, communities, and ecosystems and included metrics describing species 

richness and composition, trophic composition, and fish abundances and condition. Others have 

worked to apply the IBI concept to marine systems, especially estuaries (Weisberg et al. 1997). 

For example, a variety of parameters, including diversity, abundance of individuals, biomass, 

and percent of pollution-indicative taxa were used by Weisberg et al. (1997) to create an 

integrated descriptive metric for evaluating the status of estuarine habitats. To our knowledge, no 

such attempts have been made to develop a similar integrated metric for describing the condition 

of rocky shore communities or ecosystems. 

The use of species richness and diversity indices to describe community status stems from the 

theoretical relationship between stability and diversity, and from simulations suggesting that 

diversity indices should have greater statistical power to detect differences among communities 

than analyses based on single species. Too frequently, univariate analyses performed on 

population-level data fail to detect ecologically meaningful differences because of inadequate 

statistical power resulting from high variance among sample units, a problem that can be 

overcome but at the expense of taking an extreme number of replicates or very large sampling 

units. A community-level approach based on species richness or diversity, however, may 

improve the statistical power of univariate tests. Hypothetically, unnatural stresses should cause 

some species to become locally extinct, thereby lowering species richness or decreasing 
Final Study Report – Murray et al. 

62

evenness in the abundances of remaining taxa (if they are not replaced by stress-resistant 

organisms). Although numerous studies (e.g., Littler and Murray 1975, Weisberg et al. 1997) 

have shown relationships between species richness or diversity and anthropogenic impacts on 

aquatic communities, consistent relationships do not always occur. For example, trampling, a 

type of stressor on rocky shores, doesn’t always affect species richness, even though the 

abundances of individual taxa may be strongly impacted (Keough and Quinn 1991, but see 

Fletcher and Frid 1996). Moreover, intermediate levels of disturbance may result in higher 

species diversity in affected communities compared with those that experience either lower or 

higher levels of perturbation (e.g., Sousa 1979a,b). As discussed for supra-species parameters, 

species diversity should be more stable through time than individual species abundances because 

of compensatory responses within the community. However, only a few studies (Zeh et al. 1981, 

Karr 1994, Dethier unpubl.) have been performed to support this assumption. Another 

disadvantage of relying on diversity metrics is that diversity is not a “unique” measure, i.e., two 

sites with very different species richness and relative abundances among species can have the 

same diversity value. Clearly, before diversity is accepted as a key parameter for describing 

changes in rocky shore communities due to perturbations, its use must be tested across a gradient 

of habitat types and impact intensities. 

Estimates of species richness depend very strongly on the size and number of sample units, the 

level of taxonomic expertise of the observers, working conditions, observer fatigue, and external 

variables such as season or even time of day. Therefore, any study that relies on richness data 

must be carefully designed to account for these variables. Additionally, there are a myriad of 

indices that attempt to quantitatively integrate richness and evenness components of diversity, 

each with their own set of attributes (Pielou 1975, Magurran 1988), making it difficult to arrive 

at a universal index of choice. Other potential disadvantages of relying on species richness or 

diversity measures to demonstrate impacts of disturbances on intertidal communities include: 

1) the lack of clear and unambiguous causal links between the index and 

stressors as discussed previously, 

2) the fact that richness/stressor relationships may be nonlinear so that a change 

in the measured index may not be detected until changes in the biota have 

become severe, 

3) the potential for being misled by richness patterns in a selected subset of the 

resident taxa, because not all taxa may show the same trends or patterns 

(especially in soft-sediment communities), 

4) uncertainty in determining what constitutes a significant ecological change in 

terms of diversity measures, and
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

63

5) the lack of acceptance by some resource managers and lawyers of richness as 

a metric describing community status, because they are accustomed to 

discussing damages to communities in terms of measured losses in the 

numbers of particular species. 

In ecological terms, it is often the change of the entire community that matters, not simply the 

change in one or a few species. Changes in species composition and relative abundances of a set 

of species in an assemblage may provide a strong signal about an environmental factor of interest 

(e.g., pollution discharges or a change in sea level) because the types and abundances of species 

that form a community effectively integrate and “record” such events (Philippi et al. 1998). 

Multivariate analyses provide the tools to look at this bigger picture (Underwood 1996), retain 

information on all sampled species within a community, and may be able to reduce the noise 

caused by the responses of individual species. In this sense, different species may act as 

replicates of each other’s responses, or their noise contributions may cancel each other out, 

improving the ability to detect patterns in overall community response (Faith et al. 1991). 

There is a bewildering variety of multivariate techniques of potential use in monitoring or impact 

detection programs, or for describing and analyzing spatial and temporal changes in intertidal 

communities (e.g., see for example Volume 172 of the Journal of Experimental Marine Biology 

and Ecology “Changes in Marine Communities” dedicated to this topic). Legendre and 

Legendre (1983) review these types of analyses and their appropriate uses. Although other 

multivariate approaches can provide valuable analysis of community-level data in marine 

systems (e.g., discriminant analysis; Murray and Horn 1989, Keough and Quinn 1991), three 

types of analysis are probably most often used in studies of benthic marine communities. These 

are cluster analysis, non-metric multidimensional scaling (MDS), and principal component 

analysis (PCA). All of these procedures use species-abundance data to calculate similarities 

between pairs of samples. Cluster analysis uses an algorithm to build a dendrogram displaying 

similarities between samples and groups of samples. MDS is an ordination technique that uses 

rank distances to represent similarities between samples in two or more dimensions of unit-less 

space. MDS has proven to be a particularly valuable tool for marine ecological studies because it 

does not require the usual assumptions of multivariate normality and, therefore, readily works on 

zero-rich abundance data sets. MDS also can be used effectively on parameters such as variance 

to mean ratio (Warwick and Clarke 1993) or even simple presence/absence data (Prentice 1977, 

Field et al. 1982, Minchin 1987, Clarke 1993). Hence, if observers have the necessary taxonomic 

expertise, MDS of presence/absence or ranks data obtained from rapid surveys may prove to be 

quite powerful for detecting changes in whole communities. PCA, another ordination procedure, 

also produces plots of samples in two or more dimensions with the axes serving more or less as 

lines of best fit so as to sequentially represent as much of the variation as possible in the data set. 
Final Study Report – Murray et al. 

64

Fig. 3-3. Distributions of species clusters in relation to quadrat position and locations of outfall 

and control transects at Wilson Cove, San Clemente Island, California, showing effects of 

sewage on rocky intertidal community structure. (Redrawn from Littler and Murray 1975 with 

updated nomenclature). 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

65

Problems are encountered with zero rich species data, but PCA is particularly useful when 

applied to environmental data expressed in different measurement units. Also, PCA axes have 

units and it is possible to calculate statistical correlations between axes and original variables and 

to correlate PCA scores for sample groups, such as sites, to species abundance or other data. For 

example, cluster analysis was used by Littler and Murray (1975) to identify intertidal zones and 

communities impacted by sewage discharge (Fig. 3-3). Warwick and Clarke (1991) and Gray et 

al. (1990) have used MDS to discriminate between polluted and unpolluted soft sediment sites 

and Schoch (1999) found that MDS ordination can discriminate effectively between 

communities found on rocky shores of different slope angles (Fig. 3-4). Among other uses, PCA 

was selected to identify seasonal signals in environmental conditions in a study of coldtemperate zone rocky intertidal macrophytes (Murray and Horn 1989). 

PRIMER (Clarke and Gorley 2001) is a user-friendly Windows program that readily incorporates 

data from Microsoft Excel and other formats. PRIMER performs cluster, MDS, PCA, and 

several other informative analyses, including two other valuable procedures ANOSIM (or 

analysis of similarities, Clarke and Green 1988) and SIMPER (similarity percentages). 

ANOSIM, a procedure introduced to detect environmental impacts, is becoming widely used 

(e.g., Gray et al. 1988, Warwick 1988b, Chapman et al. 1995) for testing hypotheses about 

spatial and temporal changes in marine communities (e.g., assessing perturbed vs. not perturbed 

study sites). SIMPER provides the breakdown of the contribution of each species to similarity 

values calculated within and among sites or sample groups. Further discussion of these 

procedures can be found in Clarke (1993). 

A disadvantage of many multivariate analyses is that they are better at identifying patterns than 

explaining them. This is because most are not designed for hypothesis testing; in addition, unlike 

factorial ANOVAs, they cannot test for interactions that may provide critically important 

information (Underwood 1996). For example, BACI analyses specifically seek interactions 

between locations (perturbed vs. un-perturbed) and time (before vs. after) (Underwood 1994). 

However, multivariate procedures such as Cluster analysis, MDS, or PCA can be used to identify 

patterns and then studies can be designed to test specific hypotheses on target species (e.g., those 

highlighted as important by the SIMPER procedure). Differences among MDS clusters also can 

be tested statistically using Multiple Response Permutation Procedures (Zimmerman et al. 1985). 

Philippi et al. (1998) note that while differences in species composition among areas may be 

striking, it is more difficult to define (or statistically analyze) trends through time in composition. 

In addition, changes in species composition may be caused by factors (e.g., succession) other 

than the environmental factor of concern. Overall, however, multivariate procedures are 

becoming increasingly useful tools for examining patterns involving most or all community taxa, 

and hold promise for detecting subtle and ecologically-important changes in community features. 
Final Study Report – Murray et al. 

66

Fig. 3-4. MDS comparisons of rocky shore community structure among three lower zone 

segment groups on San Juan Island, Washington. MDS plot shows that beach segments are 

tightly grouped according to their respective slope groups and that slope groups are clearly 

separated in MDS space. MDS ordinations based on community data collected from beach 

segments with high (> 60°), moderate (20-35°), and low (< 10°) slope angles (Stress = 0.11). 

One-way ANOSIM with 280 permutations, global R = 0.87; significance level = 0.004; (pairwise 

tests with 10 permutations each: High vs Moderate, High vs Low, and Moderate vs Low yielded 

significance levels of 0.1 for all comparisons). (Modified from Schoch 1999). 

Summary 

Of the biological units targeted in intertidal monitoring, impact-detection, and other research 

programs, the species-level (population) is the most commonly sampled unit. A major problem 

with species-level sampling is the high variability in abundances that occur through space and 

time; in addition, there is no a priori way to choose the “best” species to sample. Biomonitors or 

indicator species have yet to be defined for the range of stressors and changing environmental 

conditions that affect rocky intertidal communities. Species commonly followed during 

monitoring and other study programs are large, abundant, space-occupying taxa. If one or only a 

few species are to be studied, keystone species known to play an important role in organizing the 

community should be targeted. Politically expedient species, such as those of high charismatic 

value, or “millstone” species, ones that have been studied historically but without consideration 

of alternatives, should not be selected without ecological justification. 

Down-a-level individual-based parameters such as gonadal production, growth rate, or size may 

be more sensitive than population parameters to unusually good or bad environmental 

conditions. The statistical power to detect change in these parameters also may exceed the power 

available using population-based abundance data such as density, because the latter are usually 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

67

more variable among sample replicates. However, data for individual-based parameters are time 

consuming to gather, and background data are needed to determine which species and parameters 

should be sampled. 

Biological units consisting of lumped categories, either taxonomic (e.g., families) or functional 

(e.g., functional groups or guilds) can be sampled with greater efficiency and in some cases yield 

the sensitivity needed to detect community responses to changing environmental conditions and 

the presence of stressors. However, their use must be tested in each system or community before 

such groupings become the foundation of any intertidal sampling program. Community-level 

metrics such as species diversity provide information that integrates the whole suite of species in 

the community. Unfortunately, the sensitivity of various diversity measures to stressors or other 

environmental conditions has seldom been tested on rocky shores. This is a critical area in need 

of more research. One compromise approach for determining the biological units in an intertidal 

sampling program is to perform both population or individual-based sampling on dominant taxa, 

together with qualitative sampling (e.g., presence/absence data) of all taxa in the community. In 

this way, multivariate tools can be used effectively to detect and analyze differences in 

community patterns. Multivariate tools such as MDS and ANOSIM are increasingly being used 

to successfully detect changing community patterns in marine communities and to relate these 

patterns to changes in environmental conditions. 

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Chapter 4. 

Sampling Design 

By 

Richard F. Ambrose 

 Shaw’s Cove, Laguna Beach, California 
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Introduction 

In rare cases, it is possible to determine the abundance of an organism by counting all of the 

individuals in an area, making it simple to look for changes in a population or differences 

between populations. This is usually impossible, though, and so sampling is performed to 

provide an estimate of abundances or other parameters of interest. Regardless of the details of 

sampling methodology, the overarching goal is to obtain an accurate, unbiased estimate of a 

parameter. In addition the efficiency of a selected sampling approach is of concern, because the 

time or money available to carry out the study is always limiting. 

This chapter focuses on decisions about the overall design of the sampling program, especially 

how many samples need to be taken and how the sampling units should be arranged at a site 

(Fig. 4-1). Later chapters consider the types of sampling units (Chapter 5) or the particular 

methodology that can be used to assess individual parameters (Chapter 8) or the abundances of 

populations (Chapters 6 and 7). 

The decision about what sampling design to use in a study is a fundamental decision that will 

determine what inferences can be made from data collected, and even whether the data will be 

valid for use in the study. The issues are primarily statistical, so this chapter begins with a brief 

discussion of statistical considerations. The next section covers the topic of how sampling units 

are positioned in a study area. Random, systematic, and targeted placement, and the various 

methods for stratifying sampling units in the field are then discussed. The final section of this 

chapter briefly discusses how to determine the appropriate number of samples to take. 

Statistical Considerations 

Assumptions 

To ensure that estimates are unbiased, and to satisfy the assumptions of most parametric 

statistical tests, the collected data must have independent and normal error distributions, 

homogeneity of error variation among groups, and additivity of effects (Green 1979). 

Independence of errors is perhaps the most critical assumption (Glass et al. 1972). As Green 

(1979) points out, it is the only assumption in most statistical methods for which “violation is 

both serious and impossible to cure after the data have been collected”. The sampling design 

chosen will determine whether or not this assumption is met. 

Random sampling is generally considered necessary to ensure independence of errors. Individual 

samples need to be random to be considered replicate samples. A related problem concerning the 

lack of independence among replicate samples is the problem of “pseudoreplication.” 

Pseudoreplication, which can take many forms, has been a problem in many ecological studies 

(Hurlbert 1984). A common cause of pseudoreplication in field studies is the incomplete 

randomization of sampling or experimental units. For example, in Figure 4-2 the sampling 

schemes with quadrats clumped together are pseudoreplicates because these quadrats are not 

likely to be independent of each other and, hence, they are not true replicates. If the dark 
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rectangles are control plots and the light rectangles are, for example, predator removal plots, then 

differences between treatments in the unacceptable designs might simply be due to natural 

differences on different parts of a rocky reef for the aggregated design, or on different rocky 

reefs for the isolative segregation design. 

Fig. 4-1. Decision tree for developing a sampling design.

Violations of the other assumptions are common in ecological data. For example, abundances of 

organisms tend to be skewed, with a few abundant species and many rare species, and 

heterogeneity of variances often occurs when the variance depends on the mean. In data that 

initially fail these assumptions, various transformations can sometimes be used to bring the data 

into conformity with the assumptions. Also, moderate failure of some assumptions, such as 

normality, has little effect on the outcome of statistical tests (Stewart-Oaten 1995). Glass et al. 

(1972) also discuss the practical consequences of violations of assumptions. 
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Fig. 4-2. Examples of acceptable and unacceptable sampling designs. The rectangles represent 

sampling units, with shading representing different treatments. Here, unacceptable designs 

provide pseudoreplication. More examples and details are given in Hurlbert (1984). 

Statistical Power 

In most cases, collected data will be used to determine whether there is a significant difference 

between different samples. There is often too much emphasis on making a Type I error when 

conducting statistical tests, that is, rejecting the null hypothesis when in fact it is true (Table 4-1). 

In many uses of statistical tests, such as assessing the efficacy of a new drug, it is clear why a 

Type I error (i.e., deciding that the new drug is effective when in reality it is not) should be 

avoided. However, it is also important to consider the probability of making a Type II error, that 

is, failing to reject the null hypothesis when in fact it is false. Several researchers have pointed 

out that a Type II error may be especially serious when evaluating possible environmental 

impacts (Schroeter et al. 1993, Osenberg et al. 1994, Wiens and Parker 1995). In these cases, a 

researcher might mistakenly conclude that there is no environmental impact (i.e., fail to reject the 

null hypothesis) when in reality there is an impact. For this reason, an increasing number of 

researchers have emphasized the importance of considering the statistical power of an analysis 

(Andrew and Mapstone 1987, Peterman 1990, Fairweather 1991, Mapstone 1995). 

Statistical power is defined as the probability that a test will lead to the correct rejection of the 

null hypothesis. Power is the complement of Type II error (β), and so is expressed as 1- β. Five 

parameters are relevant for analyses of power: power, significance level (α), variance, sample 

size, and effect size. Knowing (or specifying) any four of these allows the calculation of the fifth 

for a particular statistical procedure. Power increases with increasing effect size and higher α

level, and decreases with increasing sample variance. Because the variance of a sample decreases 

with increasing sample size, a change in sample size influences power. For this reason, power 

analysis is often used to determine the sample size needed in a study. 
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As discussed above, there is an implicit trade-off between Type I and Type II error. The 

relationship between power and Type I error (α) is not a simple one. Some of the relationships of 

most interest for monitoring programs include: if sample size is held constant, as is often the case 

for monitoring programs because of time or money constraints, α and power will be directly 

related; for example, relaxing α from 0.05 to 0.10 will result in increased power to detect an 

effect size or difference. If effect size and α are held constant, then power will increase as sample 

size increases. 

Table 4-1. Alternatives in hypothesis testing and the relationships with 

Type I and Type II errors. 

A discussion of the actual steps required for the calculation of power is beyond the scope of this 

chapter. Traditionally, few ecologists have calculated the power of their statistical tests, perhaps 

because it wasn’t easy or convenient to do so. It is still possible to calculate power using tables 

or charts provided by many sources (e.g., Cohen 1988). However, there now exist a wide variety 

of computer programs for calculating power, some of which are very user-friendly. Thomas and 

Krebs (1997) reviewed many of these programs. 

Power cuts across many levels of sampling design. A common cause of low power in ecological 

studies is the high degree of spatial and temporal variability that is characteristic of most 

communities (Osenberg et al. 1994), and in particular rocky intertidal communities. Thus, many 

of the issues concerning selection of sampling units and the layout and disposition of sampling 

units revolve around means of reducing unnecessary variation (“noise”) and obtaining sufficient 

numbers of samples to achieve the level of statistical power required to detect the effect size or 

“signal” of interest. 

Finally, the proper interpretation of statistical tests requires the researcher to distinguish between 

statistical significance and ecological significance. Statistics tell us how likely it is, for example, 

that a difference in the abundance of a species from one time period to the next is due to chance 

alone. Statistics do not tell us whether such a difference is important from an ecological 

perspective. In some cases, efficient sampling designs or large sample sizes can give high power 

to detect very small differences, differences that may not matter in the context of the ecological 

processes occurring in the system. The use of statistics is important for determining whether a 

difference is real, but it is up to the researcher to state whether the detected difference is of 

ecological importance. There are no simple guidelines for determining what effect size matters. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

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However, given the wide fluctuations in abundances experienced by many marine algae, 

invertebrates, and fish, the goal of detecting a 50% change in abundance with 80% power has 

frequently been adopted for environmental assessments. 

Location of Sampling Units 

One of the critical decisions in designing a sampling program is how to place the sampling units 

in the study area. This decision determines the nature of the information collected, and thus the 

accuracy and the inferences that can be drawn from these data. Many books and papers discuss 

this topic. For example, Cochran (1977) provides a general discussion, Green (1979) directs his 

overview at environmental biologists, while Greig-Smith (1983) focuses on vegetation sampling 

(which, because of the sedentary nature of the target organisms and a frequent focus on cover, 

addresses many of the same issues encountered in intertidal sampling). Andrew and Mapstone 

(1987) and Kingsford and Battershill (1998) discuss sampling design issues related to general 

marine ecology, while Gonor and Kemp (1978) focus specifically on intertidal sampling. 

Distribution of Sampling Effort 

The general goal of sampling in a particular area is to obtain representative samples of the 

population(s) of interest. Several different approaches can be taken, as discussed in the following 

sections. However, even before the approach for locating sampling units is determined, a basic 

question about the sampling program must be answered: what will and will not be studied? The 

answer to this question influences both how the samples should be located in the study area and 

what sorts of inferences can be made from the data; for this reason, the decision should be made 

before the study begins. For example, in rocky intertidal monitoring or impact studies one often 

must decide whether or not tidepools should be sampled. If tidepools are to be excluded, then 

sampling units that would ordinarily be placed in tidepools are not sampled, and instead are relocated elsewhere. Operationally, some rules about excluding some sampling locations need to 

be decided beforehand. For example, tidepools need to be defined (e.g., persistent water > 5 cm 

deep), and rules for rejecting a particular location (e.g., reject if > 40% of the quadrat is covered 

by a tidepool) and for re-locating the sampling unit (e.g., re-assign random coordinates, or flip 

quadrat upcoast until a valid location is encountered) need to be decided. Finally, the decision to 

exclude tidepools influences the inferences that can be drawn from the data collected, since the 

data would then relate to non-tidepool rocky intertidal habitats only. 

Establishing Sample Locations 

Random. As discussed earlier, independence of errors is one of the most critical assumptions for 

statistical analyses of data, and random sampling is the best way to assure that this assumption is 

met. There are several different approaches to positioning randomly located sampling units, 

whether for a one-time survey or for repeated sampling when the quadrats are located randomly 

for each sampling period (Fig. 4-3). The most straightforward approach is to lay two transect 

lines down at right angles to each other as axes for a coordinate system. The transects can be 
Final Study Report – Murray et al. 

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located along the periphery of the study site (as an “L”) or through the center of the site (as a 

“+”). A pair of random numbers is chosen for each quadrat, and the corresponding position along 

the axes located. The most precise means of locating a particular position would be to use one or 

two transect lines to determine distances, but a rough measure, such as pacing, is sufficient and 

much faster and more convenient (and can be employed by one person). 

Fig. 4-3. Schematic drawing illustrating A. random, B. systematic and C. targeted approaches to 

locating sampling units. Random quadrat locations were determined using a random number 

generator; targeted quadrat locations were determined “by eye.” In this example, the true 

density is 8.3 individuals/m2, random = 9.3, systematic = 11.1 and targeted = 33.3 

individuals/m2. 

A second approach to randomly locating sampling units is to use the “random walk.” From an 

arbitrary starting point, a pair of random numbers is used to determine the distance and direction 

to the next sampling location. From that location, a new pair of random numbers is used to 

determine the distance and direction to the next sampling location, and so on. A variation on this 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores 

81

approach is to use a number of fixed positions placed throughout the study area, and to use pairs 

of random numbers to determine distance and direction for sampling locations, each determined 

from the fixed position. After sampling one to several locations at one position, the process is 

repeated for each of the other fixed positions, so there is in effect a “circle” of sampling units, at 

varying distances and directions, around each fixed position. Although a GPS (Global 

Positioning System) could be used to locate quadrats randomly without having to resort to the 

above methods, portable units that supply sufficient accuracy are not yet economically available 

to meet the needs of most rocky intertidal sampling applications. 

Note that haphazard sampling is not random sampling. Greig-Smith (1983) states that haphazard 

sampling of a plot, such as by walking over an area and throwing the quadrat over a shoulder, 

will almost always result in a non-random distribution of sample units. Sampling units are likely 

to be more spaced out than would occur with truly random placement, and the edges of the study 

area are likely to be underrepresented. Greig-Smith asserts that the extra trouble of employing a 

more objective method of randomizing, such as laying down two lines at right angles as axes and 

using a pair of random numbers as co-ordinates to position each sample unit, is worth the effort. 

In spite of the advantages of randomization, many ecologists nonetheless locate their quadrats in 

a haphazard way. The approach suggested by Greig-Smith can be quite time-consuming to 

implement, especially over a large rocky intertidal area, and logistically difficult because of the 

presence of large tidepools, crevices, and other topographical features that characterize rocky 

intertidal habitats. In theory, haphazard sampling avoids the biases that might arise when an 

investigator places sampling units in “appropriate” locations. Of course, the possibility of 

conscious or subconscious bias still remains. Haphazard sampling trades off statistical rigor for 

convenience; whether this trade-off is worthwhile depends on the circumstances. For example, 

this trade-off may be acceptable for a quick informal survey of a site for an individual 

investigator, but not for samples taken for an impact assessment, which may later be subject to 

extreme scrutiny in a legal setting. 

Systematic. One alternative to truly random location of sampling units is to place the sampling 

units systematically through the study area. A common approach to systematic sampling is to 

place sampling units uniformly across a study site, as in a grid. Greig-Smith (1983) discusses the 

advantages and consequences of systematic sampling. The main advantages are: (1) the estimate 

of the mean may be more accurate than with random samples. This is because the sampling units 

are spread throughout the study area, whereas in random sampling some areas may be sampled 

more intensely than others just by chance alone; (2) it may be easier to carry out systematic 

sampling than random sampling. Of course, the main disadvantage is that the samples are not 

randomly taken, and hence the basic statistical assumption of independence of errors might not 

be met. Greig-Smith (1983) states that there is no indication of the precision of the mean with 

systematic sampling, and hence no possibility of assessing the significance of its difference to a 

mean obtained using similar procedures in another area.
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One objection raised about systematic sampling is that it can produce misleading results if the 

spacing of sampling units corresponds to some underlying spatial pattern in the community. For 

example, sandy beaches often have cusps whose pattern is determined by the prevailing wave 

pattern, and the biota on the cusps may differ from the biota between cusps. If sampling units are 

uniformly placed on the same scale as the cusps, sampling may always occur on the cusps rather 

than between them, and the results will not reflect the actual beach community. Therefore, 

whenever systematic sampling is used, the investigator should carefully consider whether there 

might be some underlying pattern of natural variation that could bias the results. 

Targeted. A third possible approach to locating sampling units is for the investigator to decide 

where to place each unit. For estimating parameters such as average density in a habitat, this 

approach is unacceptable (Greig-Smith 1983). Investigator bias in the choice of location is very 

likely with this approach, and hence the assumption of independence of errors may be severely 

violated. For most applications, a method of removing investigator choice in the location of 

sampling units (i.e., random, haphazard or systematic locations) is essential in order to be able to 

analyze the data statistically. 

Although investigator bias in locating sampling units is to be avoided, there are of course many 

legitimate choices investigators make about where sampling units should be located. For 

example, particular habitat types or species assemblages may be targeted for study. When a 

subset of a study area is chosen for investigation, sampling outside the chosen area is 

unnecessary and inefficient. For example, if an investigator is interested in the species occurring 

in surfgrass beds, there is no point in sampling outside surfgrass beds. Restricting sampling to 

the area of interest is common sense. Within the targeted area, however, it is best if sampling 

units are located randomly without investigator bias. 

Stratification. Since organisms are not distributed evenly throughout the intertidal zone, the 

variability associated with their cover can be markedly different over a small area. A varying 

spatial pattern within a study area can result in an overall reduction in sampling precision 

(Andrew and Mapstone 1987). When a study area is not homogeneous, stratification, the 

subdivision of an area into more homogeneous areas with samples allocated among these 

subdivided areas, can be used to reduce the influence of spatial variability. If the chosen 

stratification is meaningful, the overall precision of the sampling effort will increase as a result 

of increased sampling precision within subdivisions. A good overview of stratification can be 

found in Andrew and Mapstone (1987), with Cochran (1977) providing a more detailed, 

quantitative presentation of the topic. 

Once stratification is imposed, a decision must still be made about how to allocate sampling units 

among the strata. Several methods can be used. In the simplest case (“Stratified Simple Random 

Sampling” in Andrew and Mapstone 1987), no information about the nature of the strata is used, 

and an equal number of samples are allocated to each stratum (Fig. 4-4A). In a slightly more 

sophisticated approach, sampling units are allocated in proportion to area (“Proportional 

Stratified Sampling” in Andrew and Mapstone 1987). For example, if 100 sampling units were to 
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be allocated to 3 strata covering 20%, 50%, and 30% of the site, then 20, 50, and 30 quadrats 

would be allocated, respectively. In both of these methods, no information about differences in 

spatial distributions among the strata is used (Fig. 4-4B). 

Fig. 4-4. Location of sampling units using different methods of stratification. Shaded symbols 

represent the occurrence of individuals to be sampled. A. Stratified Simple Random Sampling. 

Equal numbers of sampling units are allocated to each stratum. B. Proportional Stratified 

Sampling. Sampling units are allocated in proportion to the area of each stratum. In the 

example, the lower stratum has twice the area of the upper stratum, and so has six quadrats 

compared to three quadrats in the upper stratum. C. Stratified Sampling with Optimal 

Allocation. Sampling units are allocated on the basis of within-quadrat spatial variance within 

each stratum. In the example, the upper stratum has twice the within-quadrat variance, and so 

has six quadrats compared to three quadrats in the lower stratum. 
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The most sophisticated method allocates sampling units on the basis of per-quadrat spatial 

variance of each species within each stratum, with more samples allocated to areas with higher 

variances, in a so-called “optimum” allocation scheme (Fig. 4-4C, Cochran 1977; “Stratified 

Sampling with Optimal Allocation” in Andrew and Mapstone 1987). By adjusting the number of 

samples to the variability within each stratum, the precision of the estimates for each stratum can 

be maximized. That is, few samples need to be taken in a stratum with very uniform distribution 

of a species in order to obtain a precise estimate of its mean abundance, whereas a stratum with 

high variability will require many samples in order to obtain an estimate of the mean with similar 

precision1

. 

For an optimum allocation scheme, an estimate of variation is needed for each stratum before 

sampling can begin. Pilot studies can be used to obtain these estimates (Andrew and Mapstone 

1987). On the other hand, simple visual estimates of species cover within each of the strata, 

which can be made without any actual sampling, provide an acceptable method of obtaining 

estimates of variation without having the additional time and expense of pilot studies (W. 

Cumberland, personal communication). Spatial variance estimates can be calculated as vij = sqrt 

[(coverij) * (1 - coverij)] where vij denotes the spatial variance of the ith species in the jth stratum 

(Miller and Ambrose 2000). The variance is calculated for each stratum, then normalized by 

dividing by the sum of variances for all strata. For example, if there are four strata, the 

normalized variance for species 1 in stratum 1 is V1,1 = v1,1 / (v1,1 + v1,2 + v1,3+ v1,4). The sample 

size for species 1 in stratum 1 can be calculated by multiplying the total number of sample 

quadrats to be allocated across the entire site by V1,1. 

Regardless of the approach used, quadrats are positioned within each stratum just as they would 

be if the entire study area was treated as a single unit (e.g., randomly distributed). An overall 

estimate of a parameter such as species abundance is made by combining the estimates from 

individual strata, weighted appropriately. 

Simple stratification schemes are fairly common in intertidal research. The most obvious 

stratification is along elevational zones, such as in the low, mid and high intertidal zone. We are 

not aware of any intertidal studies employing an optimum allocation scheme. As noted below, 

Miller and Ambrose (2000) found that stratified random quadrats had better accuracy than purely 

random quadrats for five of six species examined, and that the optimum quadrat allocation 

method was usually more accurate than allocation in proportion to stratum area. 

In practice, quadrats are commonly stratified along vertical transects (i.e., along elevational 

gradients) (Ambrose et al. 1995) rather than in the proportional or optimum allocation 

procedures. This is a logistically simpler way to approach stratified random sampling; rather than 

having to place quadrats a random distance along two dimensions, distance along only one 

dimension (along the transect) is varied randomly within each stratum. The cost of the simplified 

logistics is a greater potential for spatial autocorrelation, because the quadrats are constrained to 

 

1

 Cochran (1977) discusses several other criteria (in addition to minimizing the variance of the mean) for allocating 

quadrats according to the optimum allocation scheme. 
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be closer to one another than would be the case for truly random stratified sampling. It seems 

likely that the problem of greater spatial autocorrelation will be small, but in any case stratified 

random quadrats along transect lines will not be more accurate than purely stratified random 

quadrats, and so they will generally be less accurate than transects (Miller and Ambrose 2000). 

Comparison of Approaches 

In spite of the clear importance of the method used for laying out sampling units, few studies 

have actually studied the implications of different approaches. Miller and Ambrose (2000) used 

computer simulated subsampling of actual rocky intertidal data to compare different approaches 

for distributing the sampling effort across a study area. They compared the accuracy of random 

points, transects, randomly placed quadrats, proportional stratified quadrats and optimal stratified 

quadrats (Miller and Ambrose 2000). Randomly placed, single point-contacts provided the most 

accurate estimates of cover. With quadrats, some form of stratified random sampling usually 

gave better accuracy than simple random placement. In nearly all stratified cases, optimum 

allocation of sample units, where quadrats are allocated among strata according to the amount of 

variability within each stratum, yielded higher accuracy than did allocation in proportion to the 

area of the strata. With one exception, line transects placed perpendicular to the elevational 

contours (“vertical transects”) approached or exceeded the accuracy of the best-stratified quadrat 

efforts. The greater accuracy of line transects may be related to the maximum linear dimension 

of the sampling unit and the spatial patterns of the species studied. All six species investigated by 

Miller and Ambrose had aggregated distributions. In this situation, especially, sample points that 

are close to each other are more likely to yield similar values than points that are far apart 

(Palmer and White 1994, Palmer and van der Maarel 1995, Hurlbert 1984). Randomly placed 

quadrats may have been more likely to fall entirely within or entirely between patches than did 

the line transects. The lower accuracy of random quadrats is due to the fact that they constitute 

groupings of points, so they capture too much spatial autocorrelation. Transects spread the points 

over a larger area and thus are less influenced by spatial autocorrelation than quadrats, but even 

the points along transects are not independent. With quadrats and transects, some level of 

pseudoreplication, and consequently inaccurate estimate of cover, is inevitable. Increasing the 

sampling effort improved the accuracy of the cover estimates, but for a given effort transects 

provided a better estimate of cover than randomly placed quadrats. 

The “low” sampling effort used in Miller and Ambrose (2000), equivalent to sampling a transect 

every 3 m, yielded an accuracy of roughly 50%. As an illustration of what this sort of accuracy 

means, consider the case of Balanus. The cover of Balanus at one of the study sites, White’s 

Point, was 10.6%. If one were to sample using vertical transects every 3 m, the first sample could 

easily yield an estimate of 15% (the upper quartile of the simulated sampling) and a second 

sample an estimate of 5% (the lower quartile). If these samples were taken on different dates, one 

might conclude that Balanus cover had declined sharply, even though the actual cover had not 

changed. This modeled effort was a reasonable one for most field sampling. For example, recent 

baseline studies along the southern California coast used line transects spaced every 3 m along a 

60 m baseline (Engle et al. 1995), the same spacing used for the low effort simulations here. 

Even at higher sampling efforts, accuracy was such that one-quarter of the time, cover 
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86

estimates for most common intertidal species can be expected to be more than 10-15% above or 

below the true cover value due simply to within-site sampling error. 

The accuracy of estimates for rare species was consistently poor since sampling units often 

missed such species altogether. Species richness was substantially underestimated by all 

sampling approaches tested. It appears that the traditional approaches to sampling intertidal 

organisms are insufficient for assessing the number of species at a site. Accurate estimates of 

species richness may require supplemental sampling specifically for that purpose. 

These results illustrate the great influence that choice of sampling unit and location has on the 

accuracy of cover estimates in rocky intertidal communities. The importance of choosing an 

appropriate sampling method and placement is magnified when species have patchy 

distributions. If species were randomly or evenly dispersed, the different sampling approaches 

would make little difference. But the real distribution of rocky intertidal organisms is usually not 

random or uniform, so decisions about sampling units and placement can substantially influence 

the accuracy of survey results. Ecologists must be aware of these effects and design studies, 

experiments, and monitoring programs accordingly. 

Even the best sampling design is likely to have limited accuracy in habitats that have as much 

spatial variability as the rocky intertidal zone. One-quarter of the time, a reasonable sampling 

effort using the most accurate sampling unit and placement would likely yield estimates of the 

mean that are more than 25% higher or lower than the true mean. Tripling the sampling effort 

may improve the accuracy in estimating cover from ± 25% to ± 10-15% for common species, but 

this probably represents a practical limit for accuracy. Even at this higher intensity, the common 

sampling approaches cannot accurately estimate the cover of rare species or the species richness 

of a site. For general surveys, a rough estimate of the cover of different common species may be 

sufficient for an overview of a rocky intertidal community. However, for many purposes, such as 

environmental monitoring, impact assessment, and biodiversity surveys, this level of accuracy is 

likely to be insufficient, and alternative approaches (e.g., fixed plots, visual scans) will be 

required. 

One-Time (“One-Off’) Versus Repeated Assessments 

Two different types of sampling can be planned for a site. A one-time or “one-off’ assessment 

provides a snapshot of species abundances or distributions at a site, usually as a part of a larger 

program examining a number of different sites or for collecting data to examine a particular 

ecological question. In this type of assessment, an accurate estimate of abundance over the study 

area is likely to be a high priority. Any of the methods discussed above for locating sampling 

units could be used for such one-time assessments. Another approach is to conduct repeated 

assessments at a particular site at a number of different times. Although this latter type of 

sampling may be part of a larger program examining a number of different sites, the temporal 

component means that an accurate estimate of temporal change at each individual site will likely 

be an important study goal. 
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Two approaches to the layout of sampling units in repeated assessments are commonly used. The 

simplest approach is to locate sampling units exactly as if performing a one-time assessment. For 

example, if a stratified random quadrat approach is to be used, the same strata would be used for 

each sampling period, and new random locations within each stratum would be sampled each 

time. An alternative approach is to sample the exact same locations during each sampling period. 

Methods for laying out random locations have been discussed above; in the following section, 

issues that are unique to fixed plot sampling designs are discussed. 

Fixed Plots 

A fixed plot provides specific information about changes that occur in the area circumscribed by 

that plot over time. Because each sample is taken from the same location, differences between 

sampling periods can be confidently assigned to actual changes occurring in plot contents. In 

contrast, if new sampling locations are established during each sampling period, changes 

detected between sampling periods might alternatively be due to differences among locations in 

addition to differences over time. Fixed plots are used to provide better “signal” resolution by 

reducing “noise” resulting from samples being taken in different locations during different 

sampling periods. 

The initial step for establishing fixed plots is no different from the approaches discussed above; 

that is, a random or stratified random design can be used, or particular areas or assemblages can 

be targeted. However, the decision on how to locate the sampling units has important 

consequences for data interpretation, and the rationale for positioning fixed plots might differ 

from the rationale used in a one-time assessment. Some sort of randomized location of sampling 

units will provide the best estimate of the abundances of species at the site, as well as the 

strongest statistical foundation. However, randomizing plot locations, even in the context of a 

stratified random sampling design, will still result in substantial variation among sampling units, 

and unless an extremely large sample size is used, it is possible that the high level of variation 

among samples will make it difficult to detect temporal differences in mean abundances (Dethier 

and Tear, personal communication). Recently, several monitoring programs have adopted a 

“target assemblage” approach, wherein sampling units are located in particular assemblages of 

intertidal species, rather than randomly located throughout the study site (Richards and Davis 

1988, Ambrose et al. 1995). Consistent with the decision to use fixed plots to reduce variability 

in the data, targeting sampling locations on particular species assemblages further reduces 

variability. Long-term monitoring data from fixed plots located in target assemblages has high 

power to detect changes in the abundances of common intertidal species (Spitzer, Ambrose and 

Raimondi, unpublished observations). 

In theory, even sampling units in targeted assemblages, such as barnacle and mussel 

communities, could be located in a random manner. However, the occurrence of target species in 

small, discontinuous patches and the need for sample location to match the dimensions of sample 

plots means that randomization is often logistically difficult. Recent monitoring programs 

(Richards and Davis 1988, Ambrose et al. 1995) have used investigator choice to locate fixed 

plots. Plots were established at five locations using as criteria: 1) the best cover or abundance of 
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88

the species making up the targeted assemblage, and 2) topographical features as relatively flat 

horizontal rock surfaces of sufficient shape and size to facilitate photographic analysis. Because 

these plots are not random samples of the targeted assemblages, some statistical comparisons are 

not possible. Imagine that one location had an extensive area of high-density mussel beds, while 

another location had only a small area of high-density mussels plus scattered mussels elsewhere. 

If all five quadrats could fit into the high-density mussel assemblage at both sites, the mean 

cover would be similar even though overall mussel abundance is clearly higher at the first site. 

Therefore, it is not legitimate to compare the cover of mussels at one site to the cover at another 

site. However, the main purpose of many monitoring programs is to look for changes in 

abundances over time, and the temporal dynamics of abundance data obtained from fixed plots 

can be analyzed statistically. 

When fixed (permanent) plots are used, it is important to mark them so that they can be relocated 

for subsequent re-sampling. Simple approaches such as hammering in nails or placing small 

discs of marine epoxy at quadrat corners may suffice for short-term studies in well-known 

locations, but such marks will not persist or be easy enough to find when many sites are followed 

over an extended period of time. More permanent marking can be achieved by drilling holes into 

the substratum, inserting plastic screw anchors, and then screwing in stainless steel or brass 

screws. These markers last well for a number of years, but after decades can be overgrown by 

biota and become hard to locate (in part because of their small size). For very long-term 

monitoring, marine epoxy (e.g., Z-Spar) can be used to cement large stainless steel bolts (1/4 to 

3/8 inch diameter) into holes drilled with battery- or gas-powered drills. These large bolts can be 

easily re-located (if human use in an area is low, 5 - 8 cm of bolt can be exposed), which can 

save an amazing amount of time during subsequent sampling, and will persist for decades. If the 

bolts are big enough, a sensitive metal detector can be used to relocate hidden bolts when the 

general area of the marker is known but the specific marker cannot be found. This is especially 

useful in mussel beds, where a thick cover of mussels can grow over bolts, making it impossible 

to locate them visually without severely disrupting the bed. 

Regardless of the type of marker used, it is important to carefully map each quadrat in case 

markers are lost or covered (like in mussel beds) and difficult to locate. Reference bolts, large 

bolts placed strategically throughout the study area, are useful for mapping. Measurements 

(distance and bearing) to each quadrat from a minimum of two reference bolts should be taken, 

so that quadrats with missing markers can be relocated by triangulation. If an accurate GPS is 

available, readings can be made at each quadrat. This will greatly facilitate the construction of 

accurate site maps if the coordinates are input into a Geographic Information System (GIS). 

However, economical GPS systems currently are unable to take the place of accurate distance 

and bearing readings for relocating lost markers in the field. 

It is also very useful to take photographs of the overall site and the area around each quadrat 

from known reference points. A number of photographs should be taken from different angles 

with all nearby quadrat markers in place. If it is especially likely that the markers will be hidden 

(as in a mussel bed but we also have found that it can be surprisingly difficult to locate bolts 

even in low Endocladia muricata algal turfs), a large number of photos will prove to be useful. 
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Photos can be placed in an album or sealed in plastic laminate and brought into the field, along 

with site maps and measurements, to facilitate plot relocation. 

Comparison of Fixed Versus Non-fixed Plots 

Although many of the advantages and disadvantages of using fixed versus non-fixed plots have 

been mentioned above, these issues are summarized here. Random plots give an unbiased 

estimate of what is at the site, which is what one wants for comparing species abundances at 

different sites. Because of the extreme spatial heterogeneity that characterizes most rocky 

intertidal sites, however, a large number of samples must be taken at each site to obtain 

reasonably accurate estimates of abundance and to obtain sufficient statistical power to detect 

ecologically meaningful abundance differences between or among sites. Also, if sampling 

locations are newly randomized during each sampling period, comparison of abundances from 

one time to the next can be compromised by the confounding of spatial and temporal changes; 

that is, changes from one sampling period to the next could be due to the fact that sampling 

locations were different between sampling periods. These problems can be minimized by taking 

enough samples, but sufficiently large sample sizes rarely can be taken in intertidal studies 

because of limitations on field time and the funds available for field sampling. 

Fixed plots give up the ability to estimate overall abundances at a site in return for achieving 

lower variability in the measured abundance parameter (e.g., density or cover) among sampling 

units and greater statistical ability to detect changes over time. If sampling locations are 

originally determined at random, then the initial samples can be considered representative of the 

study area. However, subsequent samples may not represent the entire area. Moreover, the 

numbers of sampling units that might be satisfactory for other less heterogeneous habitat types 

are likely to yield very high variability in the rocky intertidal zone because of the patchiness of 

species distributions (Dethier and Tear, personal communication). Regardless of how the plot 

locations are determined, population data from fixed plots must be analyzed using repeatedmeasures ANOVA models because the same organisms will be sampled repeatedly. 

Targeted plot locations, as used by Richards and Davis (1988) and Ambrose et al. (1995), reduce 

the variability among plots and therefore provide better statistical power for detecting changes in 

abundances over time (Spitzer, Ambrose and Raimondi, unpublished observations). However, 

these plots are not random samples of a population, and so cannot be considered representative 

of the abundances of species at a site. Therefore, it is meaningless to compare abundances at one 

site to abundances at another when the sampling design incorporates fixed plots. Thus, 

inferences about abundances per se are limited in fixed plot sampling designs to within-site 

changes over time. However, it is possible to compare the dynamics of species abundances at 

different sites. For example, it is possible to determine whether abundances generally increased 

or decreased at the same time at a number of different sites. 
Final Study Report – Murray et al. 

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Number of Samples: How Many is Enough? 

Gonor and Kemp (1978) and Mace (1964) discuss some of the issues related to determining the 

number of samples that should be taken. Andrew and Mapstone (1987) also discuss this topic, 

and argue for the value of pilot data for making this and other important decisions when 

designing a sampling program. 

The appropriate number of samples needed for a particular study depends on a variety of factors, 

including the density and spatial distribution of the species, the level of precision desired, and the 

goal of the study. Andrew and Mapstone (1987) cite a number of papers reviewing studies 

concerning sample sizes, mainly for benthic organisms. One generalization emerging from these 

studies is that the number of samples needed to achieve a particular precision is closely related to 

population density (and the size of sampling units used): as the density of a population increases, 

the number of samples needed for a particular precision declines. Although these previous 

studies may provide a general starting point for determining the number of samples needed in a 

particular study, it is at best a rough starting point. Andrew and Mapstone (1987) argue that pilot 

studies are the best means of making these sorts of decisions. 

Kingsford and Battershill (1998) present three different approaches for determining the number 

of samples needed for a study. First, they propose plotting the number of replicates versus SE / 

mean (where SE = standard error = SD / √n), with data taken from pilot sampling. This will yield 

a negative decay curve, and the appropriate number of samples is determined by inspection 

(where the curve levels off, and there is little improvement in SE / mean with more replicates). 

Second, they present a formula from Andrew and Mapstone (1987) where a desired level of 

precision is required. 

 

where p = desired precision (e.g., 0.15) as a proportion of the mean, x = mean of the samples, 

and SD = standard deviation of the samples. Finally, they present a formula from Snedecor and 

Cochran (1980, p. 441) for number of samples required to obtain an abundance estimate with an 

allowable error, in terms of confidence limits. 

 

where L = predetermined allowable error (size of 95% confidence limits) on sample mean and s

2

= sample variance. 

These three approaches are illustrated with hypothetical data given in Table 4-2. The plot of 

sample size versus SE as proportion of the mean shows a declining function, where initially the 

addition of more quadrats causes a rapid decline in standard error, but the curve levels off at a 
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fairly small sample size (Fig. 4-5A). The initial steep decline levels off at four quadrats, with a 

proportional standard error of about 0.10. The gradual decline afterwards reaches a proportional 

standard error of about 0.07 at nine or ten quadrats, with little improvement in precision 

afterwards. Using the values from Table 4-2 and p = 0.15, Equation 4.1 gives [6.28 / (0.15 * 

23.3)]2 = 3.2 quadrats. Note that a lower desired precision, say 5% of the mean, would require a 

much larger sample size of 29 quadrats (Fig. 4-5B). This drops to seven quadrats for 10% of the 

mean. Using the values from Table 4-2 and an allowable error of 5 (that is, with the mean of 

23.3, the 95% confidence limits are ± 5), Equation 4.2 gives 4 * (6.28)2

 / 52 = 6.3 quadrats. 

Again, the width of the confidence limits has a large effect on the sample size required (Fig. 

4-5C). If the 95% confidence limits are to be ± 2, then 39 quadrats will be required. This drops 

rapidly to nine quadrats with ± 4. 

Although the three approaches use different means of estimating the appropriate sample size, in 

this example the answers are reasonably consistent. The graphical approach indicates that four to 

ten quadrats would be appropriate, with only a modest improvement in precision by going to ten 

quadrats. Equation 4.1 indicates three to seven quadrats would suffice, using a moderate range of 

the desired precision. Equation 4.2 indicates four to nine quadrats will satisfy the criteria being 

employed, again using a moderate range for the 95% confidence interval. 

The number of samples needed in a study also can be determined using the relationships of 

statistical power. Recall that there are four interrelated parameters associated with statistical 

power: power (1-β, the probability that a test will lead to the correct rejection of the null 

hypothesis), significance level (α), effect size, and variance, and that variance is a function of the 

variability of a sample and sample size. We can take advantage of the interrelationships of these 

parameters to calculate the sample size needed for a particular study. For example, if we decide 

we want to detect a 50% change in abundance at α = 0.05 and 80% power, preliminary data on 

sample variance can be used to determine the sample size needed. If variability within the 

sampled population is low, than fewer samples will be needed to achieve these parameter values 

than if variability is high. There are now many readily available computer programs that can 

calculate power (see Thomas and Krebs 1997 for review). 

Using the power formulas with the hypothetical data given in Table 4-2, we must first decide on 

the statistical test that will be used. For the sake of example, say we want to use a t-test to see if 

there is a significant difference in the mean abundance of a species at two sites. Assume that the 

variances of the two populations are equal (both 6.28) and set α = 0.05. To calculate the 

appropriate sample size, we must decide on the effect size (i.e., the size of the difference) we 

wish to detect and the power of the test. Figure 4-5D shows how power varies with different 

sample sizes for two different effect sizes. For example, a sample size of six is needed to detect a 

difference of 11.6, or half of the mean of the population shown in Table 4-2, with a power of 

82%. A sample size of four would have only 59% power, while a sample size of nine would have 

96% power. A difference of 11.6 is a rather large difference, and we might instead want to detect 

a difference of 5.8, or 25% of the mean — to detect a difference of this size, a sample size of 

four would have only 20% power. Achieving 80% power would require a sample size of 19. This 

is somewhat larger than the sample size estimated using the other methods. 
Final Study Report – Murray et al. 

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A completely different approach to determining sample size is often taken when the parameter of 

concern is species richness rather than abundance. A species accumulation curve is plotted, 

where the cumulative number of species included in the samples is plotted on the y-axis and the 

number of samples taken is plotted on the x-axis. Species typically continue to accumulate, but at 

a decreasing rate; the appropriate number of samples is chosen somewhat subjectively as either 

the point at which the species accumulation curve more or less levels out, or as the point at 

which a large fraction of the species (e.g., 90%) are included. 

Table 4-2. Hypothetical data showing abundance of Species x in 20 quadrats. 

“SE / mean” gives the SE as a proportion of the mean for the previous quadrats. 

For example, SE / mean for quadrat 5 is calculated based on values in quadrats 

1 through 5.

Although the previous discussion has focused on the sample size needed to get appropriate 

estimates of species abundance and species richness, a similar approach can be used to determine 

how many samples are needed to characterize communities (Streever and Bloom 1993). Because 

a community can consist of many species, each with different abundances, any method for 

determining sample size must keep track of many variables simultaneously. One approach is to 

use a measure of similarity, such as Morisita’s index of similarity, which incorporates 

information about species identities, species abundances, and species richness. A sampling effort 
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curve can be constructed by plotting the similarity of two sample sets from the same community 

against progressively larger sampling efforts. Progressively greater sampling efforts yield more 

accurate representations of the community, so similarity increases. When the sampling effort is 

sufficient to represent the community, the curve levels off (typically at a value of one). 

Fig. 4-5. Comparison of four methods for determining appropriate sample size. Examples use 

hypothetical data given in Table 4-2. A. Graphical display of standard error versus sample 

number. B. Number of quadrats as a function of desired precision, calculated using Equation 

4.1. C. Number of quadrats as a function of the size of 95% Confidence Limits (CI), calculated 

using Equation 4.2. D. Statistical power as a function of sample size. Power curves were 

calculated with σ = 6.28 and α = 0.05. Power analyses conducted using the two-sample t-test 

from Russ Lenth’s Power and Sample-size Page, at: 

http://www.stat.uiowa.edu/~.rlenth/Power/index.html. 

Impact Assessment 

A common and important purpose of environmental sampling is to assess whether a particular 

event or disturbance has had a significant environmental impact. There is a large literature 

devoted to this topic. Many of the issues discussed in this chapter need to be considered when 

assessing impacts. There is also the issue about the location of sampling efforts, such as which 

locations along a coast to sample. This question of sample locations concerns a larger scale (see 

Chapter 2) than the issues discussed in this chapter, of where to place sampling units within one 
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location. A strong design for detecting ecological impacts is the Before-After-Control-Impact 

(BACI) design and its variations. For example, one such design attempts to avoid the 

confounding influence of natural spatial and temporal variability by sampling a pair of impact 

and control sites a number of times before an impact occurs, and a number of times after the 

impact occurs (Stewart-Oaten et al. 1986). In the absence of an impact, the difference between 

the control and impact sites (called “delta”) would be expected to be the same; a significant 

change in delta indicates an impact. 

Among the many difficulties associated with the assessment of real impacts, one of the most 

problematic is the fact that “before” data generally are not available or cannot be collected. Some 

impacts started before anyone thought to study the impacted habitats. Accidental impacts such as 

oil spills occur at unpredictable times and places. Although regional long-term monitoring 

programs may be able to provide the data necessary for a BACI analysis, appropriate data often 

will not exist and other approaches must be used. Wiens and Parker (1995) discuss a variety of 

approaches that may be possible for accidental spills, including control-impact and gradient 

designs (see also brief descriptions in Chapter 1). Detailed discussion of these issues, which are 

beyond the scope of this chapter, are given in Green (1979), Stewart-Oaten et al. (1986), 

Underwood (1991, 1992, 1993, 1994), Schmitt and Osenberg (1996), and Kingsford and 

Battershill (1998). 

Summary 

There is no single optimal sampling design for all studies. Instead, the design must be matched to 

the goals and constraints of each individual study. Modern ecological research in rocky intertidal 

communities often involves controlled experiments (Underwood 1997). Nonetheless, sampling 

to detect patterns of abundance or distribution, either on its own or in conjunction with 

experiments, remains an important part of ecological research. Sometimes, sampling is targeted 

on a specific component of the intertidal community, perhaps even a single species. In these 

cases, knowledge about the biology and distribution of that component can be used to design a 

specific study that usually will be strongly focused on the targeted component. Although most of 

the issues discussed in this chapter (such as determining the location of sampling units and the 

number of samples needed) still apply, the focus of such targeted studies will be narrower and 

the results obtained are likely to be more clear-cut compared with the outcome of a more 

generalized monitoring study. 

On the other hand, when the study goal is to understand spatial or temporal patterns in the whole 

community, the decisions may not be so clear-cut. Some monitoring studies, for example, are 

designed to gain efficiency by identifying only target or indicator species for sampling. However, 

by necessity most general ecological monitoring studies must take a very broad view of their 

systems. This is because there generally is no way of knowing beforehand which components of 

the system may change or where the change might occur. The decisions to be made in designing an 

effective monitoring program that tracks targeted species become more difficult, too, because more 

trade-offs are likely to be involved. For example, many problems arise because each species has its 

own unique characteristics (including abundance and spatial patterns). 
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Thus, the optimal scheme for locating sampling units is likely to differ (Miller and Ambrose 

2000). And, even if one scheme such as the stratified random approach can be decided upon, the 

most appropriate way of stratifying the habitat is likely to be different for different species. 

Further, although a careful analysis of the appropriate sample size can be done for a species, that 

number will certainly differ from the number needed for another species. 

Although species- and site-specific differences make it impossible to prescribe a universal 

sampling design, the general guidelines given in this chapter will help ensure that a sampling 

design is statistically rigorous and efficient. Perhaps the most important guideline is that 

sampling units are located in a way that ensures independence; this usually means randomizing 

locations. A second important guideline is to avoid placing sampling units too close together to 

avoid pseudoreplication. Although the most egregious pseudoreplication errors, such as placing 

all replicates of one treatment on one rocky intertidal bench and all replicates of another 

treatment on a different bench, may be obvious, care must also be taken to avoid high spatial 

autocorrelation from placing sampling units too close together. With the typical clumped 

distribution of rocky intertidal species, sampling units distributed closely in space are likely to 

fall in the same habitat patch. For this reason, transects, which spread sampling points along a 

line, generally give a more accurate estimate of species abundances at a site, particularly when 

they cross environmental gradients (such as tidal elevation). Finally, a conscious effort should be 

made at the sampling design stage to minimize variance. This often means using some kind of 

stratification scheme in placing sampling units in the field. In the rocky intertidal, common 

appropriate strata include different tidal elevations (and co-occurring species assemblages) and 

different habitat types (e.g., horizontal benches, crevices, and tidepools). 

Literature Cited 

Ambrose, R. F., J. M. Engle, P. T. Raimondi, J. Altstatt, and M. Wilson. 1995. Rocky intertidal 

and subtidal resources: Santa Barbara County mainland. Report to the Minerals 

Management Service, Pacific OCS Region. OCS Study MIMS 95-0067. 

Andrew, N. L. and B. C. Mapstone. 1987. Sampling and the description of spatial pattern in 

marine ecology. Oceanogr. Mar. Biol., Ann. Rev. 25: 39-90. 

Cochran, W. G. 1977. Sampling techniques. John Wiley & Sons, New York, USA. 

Cohen, J. 1988. Statistical power analysis for the behavioral sciences, second edition. Lawrence 

Erlbaum Associates, Hillsdale, New Jersey, USA. 

Engle, J. M., K. D. Lafferty, J. E. Dugan, D. L. Martin, N. Mode, R. F. Ambrose, and P. T. 

Raimondi. 1995. Second year study plan for inventory of coastal ecological resources of 

the northern Channel Islands and Ventura/Los Angeles Counties. Report to the California 

Coastal Commission, 45 Fremont Street, Suite 2000, San Francisco, CA 94105-2219. 
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Fairweather, P. G. 1991. Statistical power and design requirements for environmental 

monitoring. Aust. J. Mar. Freshwater Res. 42: 555-67.

Glass, G. V., P. D. Peckham, and J. R. Sanders. 1972. Consequences of failure to meet 

assumptions underlying the fixed effects analyses of variance and covariance. Rev. Educ. 

Res. 42: 237-88. 

Gonor, J. J. and P. F. Kemp. 1978. Procedures for quantitative ecological assessments in 

intertidal environments. U.S. Environmental Protection Agency Report EPA-600/3-78-

087. 

Green, R. H. 1979. Sampling design and statistical methods for environmental biologists. John 

Wiley & Sons, New York, New York, USA. 

Greig-Smith, P. 1983. Quantitative plant ecology. Third edition. University of California Press, 

Berkeley, California, USA. 

Hurlbert, S. T. 1984. Pseudoreplication and the design of ecological field experiments. Ecol. 

Monogr. 54: 187-211. 

Kingsford, M. and C. Battershill. 1998. Studying temperate marine environments: a handbook 

for ecologists. Canterbury University Press, Christchurch, New Zealand. 

Mace, A. E. 1964. Sample-size determination. Reinhold Publishing Co., New York, New York, 

USA. 

Mapstone, B. D. 1995. Scalable decision rules for environmental impact studies: effect size, 

Type I, and Type II errors. Ecol. Appl. 5: 401-10. 

Miller, A. W. and R. F. Ambrose. 2000. Optimum sampling of patchy distributions: comparison 

of different sampling designs in rocky intertidal habitats. Mar. Ecol. Progr. Ser. 196: 1-

14. 

Morista, M. 1959. Measuring of interspecific association and similarity between communities. 

Memoirs of the Faculty of Science, Kyushu University, Series E, Biology 3: 65-80. 

Osenberg, C. W., R. J. Schmitt, S. J. Holbrook, K. E. Abu-Saba, and R. Flegal. 1994. Detection 

of environmental impacts: natural variability, effect size, and power analysis. Ecol. Appl. 

4: 16-30. 

Palmer, M. W. and P. S. White. 1994. Scale dependence and the species-area relationship. Amer. 

Nat. 144: 717-740. 

Palmer, M. W. and E. van der Maarel. 1995. Variance in species richness, species association, 

and niche limitation. Oikos 73: 203-2 13. 
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Peterman, R. M. 1990. The importance of reporting statistical power: the forest decline and 

acidic deposition example. Ecology 71: 2024-2027. 

Richards, D. V. and G. E. Davis. 1988. Rocky intertidal communities monitoring handbook. 

Channel Islands National Park, U.S. Dept. of the Interior. Channel Islands National Park, 

1901 Spinnaker Dr., Ventura, CA 93001. 

Schmitt, R. J. and C. W. Osenberg. 1996. Detecting ecological impacts: concepts and application 

in coastal habitats. Academic Press, London, UK. 

Schroeter, S. C., J. D. Dixon, J. Kastendiek, R. O. Smith, and J. R. Bence. 1993. Detecting the 

ecological effects of environmental impacts: a case study of kelp forest invertebrates. 

Ecol. Appl. 3: 331—50. 

Stewart-Oaten, Allan. 1995. Rules and judgments in statistics: three examples. Ecology 76: 

2001-2009. 

Stewart-Oaten, A., W. M. Murdoch, and K. R. Parker. 1986. Environmental impact assessment: 

‘pseudoreplication’ in time? Ecology 67: 929-940. 

Streever, W. J. and S. A. Bloom. 1993. The self-similarity curve: a new method of determining 

the sampling effort required to characterize communities. J. Freshwater Biol. 8: 401-3. 

Thomas, L., and C. 3. Krebs. 1997. A review of statistical analysis software. Bull. Ecol. Soc. 

Amer. 78: 126-39. 

Underwood, A. J. 1991. Beyond BACI: experimental designs for detecting human environmental 

impacts on temporal variations in natural populations. Aust. J. Mar. Freshwater Res. 42: 

569-587. 

Underwood, A. J. 1992. Beyond BACI: the detection of environmental impacts on populations in 

the real, but variable world. J. Exp. Mar. Biol. Ecol. 161: 145-178. 

Underwood, A. J. 1993. The mechanics of spatially replicated sampling programmes to detect 

environmental impacts in a variable world. Aust. J. Ecology 18: 99-116. 

Underwood, A. J. 1994. On beyond BACI: Sampling designs that might reliably detect 

environmental disturbances. Ecol. Appl. 4: 3-15. 

Underwood, A. J. 1997. Experiments in ecology: their logical design and interpretation using 

analysis of variance. Cambridge University Press, Cambridge, UK. 

Wiens, J. A. and K. R. Parker. 1995. Analyzing the effects of accidental environmental impacts: 

approaches and assumptions. Ecol. Appl. 5: 1069-1083. 
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Chapter 5. 

Transects, Quadrats, and Other Sampling Units 

By 

Richard F. Ambrose 

 BLM study site near Fisherman’s Cove, Santa Catalina Island, California 
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Introduction 

One of the most fundamental decisions that must be made concerning a sampling program is the 

choice of sampling units, which is the topic of this chapter. A wide variety of sampling units can 

be used for intertidal sampling. The most common units include line transects and plots or 

quadrats (Fig. 5-1). In addition, plotless designs are sometimes used. 

The choice of sampling unit depends on the goals of the sampling program, and especially the 

species to be sampled. Chapter 2 addressed how to decide where to sample on the scale of study 

sites. Chapter 4 considered issues of sampling design, including how the sampling units should 

be placed at a site. This chapter discusses how to choose the type of sampling units in order to 

get accurate estimates of species abundances at a study site. 

Sampling can be conducted using either quadrat or plot methods or plotless methods. Plots, 

which are the most commonly used sampling units, are discussed first. Plotless designs, which 

utilize some scheme to determine which elements in the environment are sampled, are discussed 

next. Plotless methods have rarely been used in intertidal habitats, but they might actually be the 

best choice for some problematic species, such as those with large individuals occurring at low 

densities. Finally, we consider sampling strategies for two intertidal habitats that provide special 

challenges, tidepools and boulderfields. 

Quadrat or Plot-Based Methods 

Quadrats and line transects are widely used sampling units. Quadrats are suitable for sampling 

populations with a variety of spatial patterns and densities, assuming an appropriate quadrat size 

(Engeman et al. 1994). As noted below, sampling plots can be labor intensive when observations 

are sparse, unevenly distributed, or otherwise difficult to obtain (Engeman et al. 1994), and in 

these instances a plotless method might be more appropriate. Otherwise, plot methods will be the 

preferred choice for sampling intertidal organisms. 

Two plot-based methods are considered here, line transects and quadrats. Line transects, which 

are essentially one-dimensional plots (although some transect types are considered to be plotless 

methods by Engeman et al. 1994), are described first, followed by two-dimensional plots that 

cover an area of the substratum. Finally, the effectiveness of these two methods and the 

dimensions of sampling units are briefly compared. 
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Fig. 5-1. Decision tree for choosing type and size of sampling units. 

Line Transects 

Line transects are used primarily to estimate the cover of attached or sedentary organisms and 

have a long history of use in vegetation sampling (e.g., Greig-Smith 1983). There are two main 

approaches to line transect sampling: line intercept and point contacts. Transect lines also are 

often used to define bands, but these are two-dimensional sampling units, and are considered 

below when sampling with plots and quadrats is discussed. 
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In the line-intercept method, the distance along the transect line that overlies each sampled 

biological unit or category is recorded. For example, a 5-m line intercept transect in a surfgrass 

community might record sections of surfgrass interspersed with sections of rock or sand (Table 

5-1). Cover is determined by adding all of the segments intercepted by each category and 

dividing by the total line length (500 cm). In the example listed in Table 5-1, surfgrass cover is 

92%, rock 3%, and sand 5% along the 5 m transect line. 

Table 5-1. Example of data collected in a surfgrass community 

 using a line intercept transect method. In this example, the 

transect is 5 m long. 

Line-intercept transects are relatively quick to sample (at least in some situations) and can be 

somewhat less subject to sampler bias (e.g., judgments about whether a species that is very close to a 

contact point is actually contacted) than point-contact methods. However, intercept sampling 

assumes a species has either 100% or 0% cover over the minimum defined intercept unit. Thus, the 

use of intercepts is not well suited to situations where species boundaries are not well defined or 

where species are mixed together. In the case of interspersed species, accurately recording large 

numbers of very small intercepts for each species may be impossible. Thus, a less-accurate shortcut 

must be taken such as deciding that the minimum unit for recording an intercept is 1 cm. Similarly, 

small gaps in canopy cover, which might occur when sampling sparsely distributed leaves of 

surfgrass (Phyllospadix spp.), are typically ignored, resulting in an overestimate of canopy cover. 

The point-contact transect is a linear version of the point-contact methods applied to twodimensional plots that are described in more detail in Chapter 6. Point-contact transects are used 

more commonly in marine than in terrestrial habitats. In the standard point-contact transect, a 
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predetermined distance along the transect serves as contacted item can be determined by 

dropping a pin or rod, or by visually judging what lies directly under the contact position along 

the transect (Fig. 5-2). The latter method is much faster, but requires careful decisions about the 

actual position of the contact point to avoid bias such as recording a contact for a species that is 

close to, but not touched by, the contact point. The distance between contact points depends on 

the resolution needed and the length of the transect; common distances in intertidal sampling are 

every 10 cm and every 1 m. Random numbers also can be used to determine contact point 

locations. Choice of sampling interval depends in part on the length of the transect, with long 

transects (100 m or more) having larger distances between contact points. Cover is determined 

by dividing the number of contacts for a particular species or sampled category by the total 

number of contact points recorded along the transect. Following the surfgrass example given in 

Table 5-1, a point-contact transect sampled every 10 cm might record surfgrass under 46 points, 

rock under 2 points, and sand under 2 points, for an estimated percent cover of 92% for 

surfgrass, 4% for rock and 4% for sand (Table 5-2). 

Table 5-2. Example of data collected in a surfgrass community 

using a point-contact transect method. In this example, contacts 

were recorded every 10 cm along a 5 m transect. 

One advantage of transects is that they spread sampling across a large area, which can help 

minimize problems with spatial autocorrelation (see Chapter 4 and below; Miller and Ambrose 

2000). However, the traditional transect only spreads sampling along one dimension and samples 

a very narrow area (a line) along the second dimension. A modification of the traditional pointcontact transect can be used to remedy this deficiency by spreading sampling points away from 

the transect line in the second dimension. In this procedure, each contact point is located by a 

random distance along a transect line and a random distance away from the transect line (e.g., at 

right angles to the transect, with points alternating on one side or the other of the transect line). 

Because this approach has elements of a point-contact transect and a point-contact quadrat, this 

can be referred to as a point-contact hybrid; it is analogous to a band transect sampled with point 

contacts. Dethier has been using this hybrid approach in rocky intertidal monitoring programs, 

using one transect positioned at each of four vertical elevations at each study site. 
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 Fig. 5-2. Point-contact line transect. In these surfgrass transects, contacts are determined by 

 visually recording the species directly under the contact point. 

Line-intercept and point-contact transects provide very similar information about rocky intertidal 

habitats. Both yield estimates of percent cover of sessile (or sedentary) organisms, and both 

obtain data that can be used to calculate species diversity indices. If the order of collected data is 

maintained, both approaches can provide information describing the spatial structure of the 

habitat, such as whether rock coverage of 20% occurs in one large block or is dispersed in small 

areas or whether a species occurs at one end of the transect. In practice, spatial information is 

more often obtained when performing line intercept sampling because of the logistics of data 

recording — maintaining the species identity and order of 50-100 point contacts is very difficult 

on field data sheets. However, bar code readers (battery-powered, hand-held field units similar to 

those used in markets) can be programmed to maintain the order of point-contact data, and have 

the additional advantage of loading data directly into a computer database instead of manually 

(Ambrose and Miller, personal observations). Some handheld computers or Personal Data 

Assistants (i.e., PDAs such as Handspring Visor and some Palm Pilots) now accept a bar code 

reader in their expansion slots, allowing data to be scanned directly into databases that are 

downloaded directly to personal computers. 
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Plots or Quadrats

Unlike line transects, plots, and quadrats have two dimensions and cover an area of substratum. 

Plots and quadrats are used to estimate cover, density, or biomass of both attached and mobile 

organisms (see Chapter 6). The difference between quadrats and plots is somewhat semantic. 

Quadrats are regularly shaped and relatively small, usually of a size that can be contained within 

a portable quadrat frame. Plots generally are irregular in shape, although some are not, and are 

generally larger than quadrats. 

 Fig. 5-3. Quadrat used as photoplot for sampling cover of algae and sessile animals. 

Quadrats can be rectangular, square or circular, and can be a wide range of sizes (see below). 

Relatively small (≤ 1 m2

) quadrats are widely used in intertidal sampling programs, probably 

because they provide a good combination of convenience and the appropriate scale for the 

organisms being studied. Smaller quadrats are easily carried from sampling location to location, 

and can be easily searched or photographed for complete and thorough sampling (Fig. 5-3). 

Quadrats and plots can be positioned randomly in an area, or targeted for particular conditions; 

the advantages and disadvantages of these approaches are discussed in Chapter 4. Regardless of 

how they are located, quadrats and plots can be permanently fixed at a particular place, so the 

same location is sampled repeatedly through time, or they can be placed in a different location 

during each sampling period; these approaches also are discussed in Chapter 4. Quadrats are 

used to delimit the area to be sampled, but the particular method of sampling can vary from nondestructive counts or point contacts (Chapter 6) to destructive harvesting (Chapter 7). 
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Band transects are considered a special type of quadrat, rectangular in shape but much longer in 

one dimension than the other. Band transects are particularly useful for sampling large but 

relatively uncommon species that are distributed over large areas, such as sea stars and kelps. 

Band transects can be established independent of other sampling units (Fig. 5-4), or they can be 

sampled in conjunction with transects laid out for line-intercept or point contact sampling, or 

even along transects laid out to locate other sampling units in the area. A wand (e.g., a 0.5-m or 

1-m length of PVC pipe) can be used in conjunction with a transect line to determine the limits 

of the band. With one end of the wand held against a transect tape, the other end sets the outer 

limit of the band while the sampler moves along the tape. Moreover, it will be easy to decide 

whether most of the target organisms are clearly in or out of the band, so the wand need only be 

placed for organisms close to the outer band limits. The wand can be used on only one side or on 

both sides of the tape, but if frequent “checks” are needed it is best to use the wand on one side 

only. 

Fig. 5-4. Band transect used for sampling kelp densities. The transect is searched at a prescribed 

width (e.g., 0.5 m) along each side of the line using a 1.0 m wand. 
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Another approach for estimating the densities of relatively uncommon species is to use plots. 

When the sampling area reaches several square meters, it is usually referred to as a plot instead 

of a quadrat. Plots tend to be fixed at a particular location and sampled repeatedly through time. 

However, there are many variations. For example, a plot might be fixed, but subsamples inside 

the plot are chosen at random during each sampling period (Kinnetics Laboratories, Inc. 1992). 

Plots can be shaped to follow natural landforms and boundaries (Fig. 5-5). For example, a plot 

for censusing sea stars can contour around a headland and encompass both flat and steep slopes 

within the appropriate tidal heights. Plots also are useful for sampling species that occur in 

particular microhabitats, such as abalone that often occupy deep cracks and crevices. In many 

situations, it is difficult to achieve such a close match between appropriate habitat and the 

sampling unit when using quadrats or band transects. A disadvantage of irregularly shaped plots 

is that their irregular boundaries make it difficult to determine plot areas, a requirement if 

multiple plots are used to obtain density data and comparisons are to be attempted among sites. 

Also, it may be difficult to reconstruct plot boundaries during each sampling period, especially if 

plots are large and irregular in shape, and boundary markers are obscured by algae or sand. In 

these cases, good site maps, with distances and bearings from a variety of marked reference 

points, are essential, but even still it can take substantial time and effort to determine plot 

boundaries. It is possible to combine both approaches in a sampling program, choosing regular 

plots or band transects when these fit the local conditions and using irregular plots when they are 

more appropriate for the site topography (Ambrose et al. 1995). 

 Fig. 5-5. Irregular plot used for long-term monitoring of abalone densities. 
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Little work has been done to assess the effect of different shapes of sampling units. Some 

“quadrats” are circular, which eliminates the extra edge effect in the corners of rectangular 

quadrats. In addition, a circular sampling area can sometimes be quicker and more convenient to 

sample compared with rectangular quadrats. For example, Ambrose et al. (1995) sampled owl 

limpets with a circular sampling unit whose boundaries were set by sweeping a 1 m-long line 

around a single fixed stainless steel bolt. For these sampling units, only one bolt is needed to 

mark each quadrat and a simple line (rather than a quadrat frame) can determine the area to be 

sampled. Most commonly, however, quadrats are square or rectangular. Littler and Littler (1985) 

report that rectangular quadrats have an advantage over square or circular plots of equal area 

because they may incorporate a greater diversity of populations. This advantage will be greatest 

when the long axis of the quadrat is oriented parallel to the environmental gradient. In rocky 

intertidal habitats, this gradient often corresponds with vertical tidal height so rectangular 

quadrats are oriented with their long axes parallel to the shoreline. Often, the choice of shape 

may be due more to sampling logistics than sampling theory. For example, many researchers use 

rectangular photoquadrats with dimensions matching the framing of a 35-mm slide (e.g., 50 cm x 

75 cm or 30 cm x 50 cm). 

Comparing Transects and Quadrats 

Quadrats are usually more appropriate for mobile species, but line transects and quadrats are 

both commonly used to sample seaweeds and sessile invertebrates in rocky intertidal sampling 

programs. The choice of sampling unit depends on the questions being asked, species to be 

studied, temporal dimensions of the study, and so forth. For sampling to determine species 

abundances, both line transects and plots or quadrats can provide accurate estimates if employed 

using well designed and appropriate sampling strategies. 

As mentioned in Chapter 4, Miller and Ambrose (2000) used computer simulated sampling of 

actual rocky intertidal data to compare point-contact transects and point-contact quadrats using 

different sampling designs. With one exception, transects placed perpendicular to the elevational 

contours and the shoreline (“vertical transects”) provided more accurate estimates of overall 

abundance than the best quadrat efforts. This was due to the aggregated (clumped), spatial 

patterns displayed by species in the intertidal zone and the fact that there is an environmental 

gradient due to tidal ebb and flow and air exposure. In this situation, sampled points that are 

close to each other are more likely to yield similar values than points that are farther away. Pointcontact quadrats are groupings of points, and so will capture more spatial autocorrelation than 

point-contact transects, which spread the same number of points over a larger area. 

For a relatively quick survey of the abundances of macrophytes and sessile invertebrates at a site, 

vertical transects running from the upper to the lower intertidal zone are probably the most 

efficient kinds of sampling units. Vertical transects are relatively easy to set up, especially 
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compared with establishing strata and randomizing quadrat locations, and quick to sample. If the 

order of contact points is maintained, a rough map of species distributions can be produced when 

performing vertical transect surveys. 

Size of Sampling Units 

Decisions about the size of a sampling unit revolve around the issue of scale. The appropriate 

size for a sampling unit is the size that matches the scale of the phenomenon of interest. If it is 

important to count the number of new barnacle recruits in the barnacle zone, where recruit 

density is extremely high, a 1 m2 quadrat would be much too large. Not only would counting the 

high number of barnacles in this quadrat take too long, but the count would likely be inaccurate. 

Similarly, in most places a 1 m2

 quadrat would be too small to sample sea star or other large, 

low-density organisms. The appropriate quadrat size also depends on the sampling method being 

used. For example, barnacles may be sampled with a 0.05 m2 quadrat when they are individually 

counted for density estimates, but a 0.375 m2 quadrat when they are sampled with a point-contact 

method for cover estimates. 

Unfortunately, sample unit sizes for rocky intertidal work have not been standardized. Gonor and 

Kemp (1978) compiled information on quadrat size from more than 20 rocky intertidal studies; a 

subset of these results, along with other more recent studies, are shown in Table 5-3. Target 

species included coralline algae, barnacles, limpets, mussels, and snails, as well as 

“miscellaneous” species that encompassed the entire intertidal assemblage. Quadrat sizes mostly 

varied from 0.1 m2 to 1 m2,although there were a number of variations, including large quadrats 

(e.g., 25 m2) that were subsampled (e.g., Boalch et al. 1974, Menge 1974, Kinnetics 

Laboratories, Inc. 1992). 

There is no simple rule for determining the appropriate size of sampling unit for different 

organisms. This is not surprising given the extreme variability in the sizes and abundances of 

rocky intertidal organisms, especially since the same species can have widely different 

distributions and abundances at different sites. However, there are some general guidelines, 

summarized by Gonor and Kemp (1978) and described briefly here. 

The two main approaches to determining sample unit size are: 1) to maximize the number of 

species included in the sample, and 2) to minimize the variance of the mean for abundance data. 

As the size of the sample unit increases, the sample encompasses a larger fraction of the entire 

area (all other things being equal), and so more and more species are likely to be included. Thus, 

the number of species included in a sample is expected to increase as the sample unit size 

increases, rather rapidly at first and then more slowly. (The same effect occurs as the number of 

samples taken increases.) The optimal sample unit size approximates the size where the addition 

of new species levels off with increases in the area sampled. This approach is appropriate when 

the study focus includes species richness or community-level metrics. 
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The second approach aims to minimize the variance of the mean associated with sampling for 

abundance. Minimizing variance is important because sampling programs often are concerned 

with detecting differences in mean abundances between sites or times, and lower variance will 

provide greater statistical power to detect such differences. (Other strategies for reducing 

variance based on the location of sampling units are discussed in Chapter 4.) Sample unit size 

affects the variance of the mean because most, if not all, intertidal organisms are patchily 

distributed. For patchily distributed organisms, variance will be highest when the sample unit 

size matches the scale on which the patchiness occurs (Greig-Smith 1983). At sample unit sizes 

larger than this, variance decreases until it is approximately equal to the mean (a characteristic of 

random distributions). At this size, the sampling unit is so much larger than the scale of 

patchiness that the sample appears to have adopted a random distribution. (A similar effect 

occurs if the sampling unit is much smaller than the scale of patchiness; see Green 1979.) By 

eliminating the extra variance caused by patchiness, the estimate of variance will be minimized. 

The issues of sample unit size and number of sampling units used in a study are closely related 

since both involve sampling effort. Increasing either the size or number of sampling units can 

result in more species being included in a sample and lower variances. Note that sample unit size 

and the number of replicates that can be taken during a sampling period are frequently inversely 

related, since, all other things being equal, a larger sample unit size takes more time to sample so 

that fewer sample units can be included. In some cases, more accurate estimates of abundance at 

a site may be achieved by having more, smaller sampling units distributed throughout the area. 

Finally, it is worth noting that sample unit sizes often are strongly influenced by other 

considerations. Smaller quadrats will be more susceptible to edge effects (see Chapter 6), such as 

occur when observers consistently include individuals that should be excluded and vice versa 

(Greig-Smith 1983). There are also important logistical and economic considerations. In most 

cases, larger sample units will be more expensive to sample than smaller units. Cochran (1977) 

discusses methods for optimizing sample unit size based on both the cost of each unit and the 

variance when a unit of that size is used. Logistically, some large quadrats also may be too 

unwieldy in the field. Furthermore, many intertidal sampling programs include a wide variety of 

species, and each of these could have a different “optimal” sample unit size. Although some 

diversity of sampling approaches is to be expected (e.g., different sampling unit sizes for 

attached biota and sea stars), the logistics, not to mention the extra time, of setting out and 

sampling different sized sampling units for each species sampled would make such 

“optimization” infeasible. Consequently, rocky intertidal sampling programs often employ a 

single quadrat size to sample the abundances of most species. 
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Table 5-3. Typical sample unit sizes for common intertidal species. From Gonor and Kemp 

(1978) and other sources. 

Plotless Designs 

Although quadrats and plots are commonly used for estimating species densities, sampling these 

can be labor intensive when observations are sparse, unevenly distributed, or otherwise difficult 

to obtain (Engeman et al. 1994). Plotless sampling has been introduced as an easier approach for 

obtaining density estimates (Cottam 1947, Persson 1971). Plotless designs have been extensively 

developed for vegetation sampling, particularly for forest vegetation (Greig-Smith 1983), but 

rarely are used for sampling intertidal populations. 
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Distance Sampling Methods

Many different plotless approaches have been developed, most of which involve making 

measurements to individuals in the population being sampled. In a thorough evaluation of 

plotless approaches, Engeman et al. (1994) compared the performance of 25 different methods 

using simulations of different spatial patterns, sample sizes, and population densities. The 

following discussion adopts the terminology given in Engeman et al. (1994), which also provides 

formulae for the different methods. Some of the most common and best-performing plotless 

methods are briefly discussed below. 

In the simplest basic distance method, measurements are made from randomly placed sample 

points to the closest individual in the population (Cottam et al. 1953); variations include making 

measurements from individuals (usually the closest individual) to their nearest neighbors, 

including second nearest neighbors, and different combinations. The Kendall-Moran estimation 

methods (Kendall and Moran 1963) incorporate the total area searched for the closest individual 

and its nearest neighbor. The ordered distance method (Morisita 1957, Pollard 1971) involves 

measuring the distance from a random sampling point to the g

th closest individual (hence the 

ordering). At least for a random spatial pattern, the variance of the estimate decreases as g 

increases, but using g > 3 may be impractical in the field (Pollard 1971). Angled-order methods 

include the point-centered-quarter method, one of the oldest plotless methods. In this method, the 

area around a random point is divided into four quarters and the distance to the closest individual 

in each quarter is measured (Cottam et al. 1953). In a more general sense, the area around the 

random sample point is divided into k equiangular sectors and the distance to the g

th closest 

individual in each sector is measured (Morisita 1957). Thus, for the point-centered-quarter 

method, k = 4 and g = 1. Morisita (1957) considered k = 4 and g = 3 to be a practical limit. The 

variable area transect method is a combination of distance and quadrat methods. A fixed-width 

(strip or band) transect is searched from a random point until the g

th individual is encountered in 

the strip (Parker 1979). 

Engeman et al. (1994) concluded that the best performing estimators were angled-order with g = 

3 (AO3Q), followed by angled-order with g = 2 (AO2Q) (both with k = 4). These were followed 

by a Kendall-Moran estimator that pools across all sample points the search areas for the closest 

individual, its nearest neighbor, and the second nearest neighbor (KM2P), an ordered-distance 

estimator with g = 3 (OD3C), and the variable area transect (VAT). All of these methods 

performed well with nonrandom spatial patterns, especially aggregated patterns, which are 

common in intertidal habitats. The formulae for these density estimators are given in Table 5-4. 

Although the best two plotless methods were angled-ordered methods, Engeman et al. (1994) 

agreed with Pollard (1971) that their advantages are out-weighed by the practical difficulties of 

dividing the plane around the sampling points into quadrants and then deciding into which 

quadrant an individual belongs as part of the process for determining and measuring the g

th
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112

closest individuals in the quadrant. The angled-order methods also require locating more 

individuals at each sample point than the other methods. Engeman et al. (1994) believe that it is 

usually more useful to sample more spatial points with less effort per point. For these reasons, 

Engeman et al. (1994) consider KM2P, OD3C and VAT to be the three most practical Plotless 

Density Estimators (PDEs) (Table 5-4). Each of these methods involves locating three 

population individuals per random sample point. Engeman et al. (1994) note that the availability 

of reliable software could influence the choice of method. In particular, the algorithm for 

calculating KM2P is complicated, whereas it is simple to calculate OD3C and VAT. 

Table 5-4. Formulae for the best performing plotless density estimators evaluated by Engeman et 

al. (1994). Symbols are: N = the sample size (number of random sample points used to gather 

distance measurements); R(g)ij = the distance from the ith sample point to the gth closest individual 

in the jth sector; pi, ni, and mi = the number of closest individuals, nearest neighbors and second 

nearest neighbors, respectively; Ci = the total search area at the ith sample point for the closest 

individual, its nearest neighbor and the second nearest neighbor combined; R(3)i = the distance 

from the ith sample point to the third closest individual; w = the width of the strip transect; li = 

the length searched from the random point to the gth individual. 

Some plotless designs are most appropriate for conspicuous organisms that occur at low 

densities, such as trees. “Line-of-sight” methods, which require a clear line of sight to the objects 

of interest (see Buckland et al. 1993), could only be applied for conspicuous species not hidden 

in cracks. Even with large individuals occurring at low densities, such as sea stars, plotless 

designs may require a considerable amount of time searching for the appropriate “nearest” 

organism to measure, since all surrounding cracks and crevices would need to be examined 

before a decision could be made about which individual was nearest. Nonetheless, Engeman et 

al. (1994) consider the evaluated designs to be suitable for conditions when an area must be 
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113

thoroughly searched. Plotless designs are not suitable for species with spreading cover (colonial 

invertebrates, most algae), since individuals cannot be easily identified, and plotless designs 

would be inefficient for taxa with many small individuals, such as limpets and snails. 

Timed Search 

The timed search is a different approach to plotless sampling that is sometimes used in intertidal 

sampling programs. Timed searches can be used to generate a species list for a site, or to provide 

a quantitative or semi-quantitative indication of species abundances; this approach is most 

applicable where target organisms are quite rare, so a very large area must be searched to 

encounter individuals. Timed searches are especially useful when targeted organisms occur over 

a large area, but suitable habitat is patchily distributed; in this way, unsuitable habitat or easily 

censused areas can be covered very quickly, and most search effort concentrated on the most 

promising habitats. Two approaches are used. In the first, a general area is identified for the 

search. Then, this entire area is searched for a set period of time, say 30 minutes, and the number 

of individuals of the target species observed during that time is recorded. The searcher needs to 

be systematic, but depending on the size of the general search area, the searcher may not cover 

the entire area. If the site is sampled repeatedly over time, the same general area is searched each 

time. The second approach is similar to the first, but the area searched is measured so that 

density can be estimated. A systematic, thorough search of the entire area is essential in this case, 

so searching often starts along one boundary of the search area and proceeds systematically 

back-and-forth towards the other side of the area. This approach results in a plot whose shape 

and area will vary from sampling period to period, and from place to place, depending on search 

efficiency, environmental conditions, the number of individuals encountered, and other factors. 

Unlike a timed search without regard to the area sampled, this approach has the advantage of 

allowing abundance comparisons among sites because search data can be reported as numbers of 

individuals per unit area (i. e., density). 

The outcome of a timed search depends heavily on the skill and patience of the searcher. For 

rocky intertidal biodiversity surveys, the searcher must have expert knowledge of algae and 

invertebrates. Depth and breadth of knowledge will differ, even among experienced intertidal 

biologists, so comparing species lists generated by different individuals will be problematic. 

Between-individual differences can be minimized by using standardized checklists of common 

species. For estimating the abundances of targeted species, searchers with a good search image 

or knowledge of the habits of the species also may be much more effective at finding individuals. 

Thus, a fairly large discrepancy among searchers would be expected for cryptic or hidden species 

such as octopus and perhaps abalone, but less discrepancy would be expected for conspicuous 

species such as most sea stars. In addition, there is a trade-off between thorough searching of 

difficult habitat and spreading the search over a broad area; individual searchers who concentrate 
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114

on one or the other extreme may encounter very different numbers of targeted organisms. The 

limitations of timed searches can be minimized by having the same individual carry out all of the 

sampling. Obviously, this will not be possible with large or long-lasting monitoring programs, so 

comparisons among sites or sampling periods must be done very cautiously. Even where a single 

individual can perform all of the searches, there will be a variety of factors affecting the 

efficiency of searching that vary from time to time and from place to place 

Timed searches are most useful for estimating abundance when the number of target organisms 

expected at a site is small. In fact, the greatest utility of a timed search may be when no 

individuals are found, because it provides concrete evidence that the species was, at best, very 

uncommon at a site at a particular time. If the species later occurs commonly at the site, there 

will be good evidence for an increase in abundance. Without specific data on the abundance of a 

species at the site, it could be argued that it was present but simply not noted earlier. Considering 

that many monitoring programs could continue over decades under different personnel, or that 

later sampling programs might rely on data collected at a site earlier, the evidence about a 

particular species of interest from a timed search can be valuable in spite of the difficulties of 

interpreting abundance in a quantitative sense. 

Timed searches also can be a relatively simple method of obtaining a more complete species list 

for a site than, for example, quadrat sampling alone. Typical transect and quadrat-sampling 

efforts under sample species richness by a substantial amount (Miller and Ambrose 2000); 

although in theory transects and quadrats would eventually include nearly all species, the effort 

required to achieve this ideal would be impractical. As long as some of the caveats mentioned 

above are considered, species lists generated by timed searches can provide a means for 

comparing data among different sites. 

Special Habitats 

Most of the discussion in this and other chapters focuses on rocky intertidal habitats consisting of 

relatively planar solid benches. Obviously, there are many other types of habitat features, even 

on otherwise planar benches, including cracks, deep crevices, holes, hummocks, tidepools and so 

forth. These features are typically excluded from studies and ignored by not placing sampling 

units in them (e.g., not placing quadrats in deep crevices) or easily incorporated into a standard 

sampling design (e.g., counting sea stars in cracks within a large fixed plot). In this section, two 

of the most common types of habitats in the rocky intertidal zone that require special 

considerations for sampling are discussed. 
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Tidepools

Because of their uniqueness, tidepools are not recommended as a habitat for monitoring or 

impact assessment studies except where very local impacts are of interest (see Chapter 2). In 

most rocky intertidal sampling programs, sampling units that fall largely within tidepools are reallocated to other, more appropriate locations. “Tidepools” must be operationally defined, such 

as an area of persistent water greater than 5 cm deep, to ensure unbiased application of this rule. 

If tidepools are to be sampled, the normal sampling approaches must be modified. Sampling the 

biota of tidepools presents some special challenges because of the three-dimensional nature and 

highly variable size of pools. Two basic approaches are possible: 1) each pool can be treated as 

one irregularly-shaped plot and the biota in it sampled accordingly, or 2) sampling can be nested 

within each pool in an analogous way to sampling a stretch of planar bedrock. 

In the first approach, the pool/plot can be surveyed using visual scans or random points to 

quantify algae and sessile animals, and counts of mobile organisms can be made in the whole 

pool or in random subsamples (Dethier 1984). Special attention must be paid to parallax 

problems in these three-dimensional habitats; for example, it must be determined if the pool is to 

be treated as a two-dimensional plot (such as if data were being gathered from a photograph 

taken from above the pool) or if the sides of the pool are to be sampled to encompass their true 

area. Either approach is appropriate as long as it is consistently applied. Inventories tend to focus 

on the amount of resource per unit area of shoreline, so a two-dimensional sampling approach for 

tidepools might be best for these purposes. For ecological processes, however, sampling the 

actual pool surface area probably will result in more useful information. The approach taken in 

boulderfields for resolving this dilemma is discussed below. Treating each pool as a whole plot 

may be most appropriate when the community of each entire pool is of concern, such as when 

looking at impacts of souvenir collectors or major storms. 

In the second approach, each pool is treated as a stratum and then subsampled, either by running 

transect lines with random points through the pool or, more commonly, by placing randomly 

located quadrats within it (e.g., Lubchenco 1982, Benedetti-Cecchi and Cinelli 1995). This 

subsampling approach is more appropriate when pools are viewed as just one habitat stratum 

(analogous to the mid-intertidal zone, for instance) in which patterns and processes are being 

studied. 

Boulderfields 

Many rocky shores consist of unconsolidated rock with varying degrees of substratum stability. 

Boulderfields are often excluded from quantitative sampling in rocky intertidal monitoring 

efforts, perhaps because of inherent difficulties in sampling them. When boulderfields have been 
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included in some intertidal inventories, the methods used to assess the abundances of organisms 

generally have not accounted for the surface relief or the undersides of boulders and, therefore, 

only provide limited understanding of the contribution of this habitat to intertidal resources. 

Gonor and Kemp’s (1978) instructions for quantitative sampling on rocky shores simply 

recommend sampling algae and epifauna of unconsolidated beaches (consisting of gravel, cobble 

or boulders) by the quadrat methods described for solid rock benches. However, Gonor and 

Kemp also noted that “no one method is applicable” and that the increased surface area produced 

by the relief of these habitats may “appreciably affect percent cover estimates as well as 

density”. Clearly, standard methods for sampling solid rocky benches are not well suited for 

boulderfields. 

Boulderfields present some of the same types of problems as tidepools, since boulders also are 

highly three-dimensional and of variable size. Proper sampling of boulder habitats requires a 

modification of standard rocky intertidal sampling procedures, which, especially for algae and 

sessile invertebrates, focus on a vertical projection for a point contact or quadrat. This is 

appropriate for a roughly horizontal, simple surface, such as many rocky intertidal bench 

habitats. However, vertical projections are less suitable for vertical surfaces and are not possible 

for the undersides of boulders. Thus, the standard point contact techniques, whether along a 

transect or in a quadrat, are not well suited for boulderfields. Quadrats can still be used, but the 

methods for non-destructively sampling attached organisms in quadrats (see Chapter 6) must be 

modified, as discussed below. Sampling mobile organisms in boulder fields is not much different 

from sampling on rocky benches, although boulders must be turned over to find all organisms. 

A related issue is the way abundance is expressed. Common methods for determining 

abundances generally express results as abundance per square meter of shoreline habitat. 

Developed for the more or less planar solid benches of the rocky intertidal zone, these techniques 

are less suitable for boulderfields because they do not account for the three-dimensionality of the 

boulders and may also exclude organisms living in the spaces formed between or underneath 

boulders or in crevices. An appropriate sampling method for describing intertidal community 

characteristics (species richness and abundance) in boulderfield habitats should account for the 

substratum available for attachment by fauna and flora (i.e., the true substratum surface area).

Pless and Ambrose (unpublished observations) developed an approach for sampling 

boulderfields in order to compare their communities with the communities on solid rock benches. 

The edges of a horizontally leveled sampling quadrat were vertically projected onto the 

substratum and the contours marked with a lumber crayon or chalk (Fig. 5-6). To assess the 

extent of available substratum (the true substratum surface area), the total area of rock substrata 

within the lumber chalk marks was estimated using small wire quadrats of different dimensions 

(2 x 2 cm, 4 x 4 cm, 5 x 5 cm, 10 x 10 cm) as a visual reference. Solid benches are more or less 

flat, so the true substratum surface area is approximately equal to the area of the sampling 
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117

quadrat. The three-dimensional surface relief of boulderfields, however, can amount to a 

substantially larger surface area than that of a plot. The surface of boulders was measured 

separately by top, side, or bottom surfaces within the boundaries of a sampling quadrat. Solid 

benches were measured similarly, predominantly top surfaces but also sides when the surface 

was not entirely flat. Macroscopic organisms were sampled within the marked boundaries of the 

0.25 m2 quadrats. Estimates were determined separately for each substratum surface orientation 

category (top, side, bottom), which is useful for some purposes but not necessary for an 

inventory. Boulders were temporarily overturned to assess the abundances of organisms found 

on their undersides. Cover of macrophytes and sessile macroinvertebrates, such as mussels, 

sponges, tubeworms, tunicates, or bryozoans, was determined by visual estimates of the area 

covered by the individual species as a measure for biomass. 

Fig. 5-6. Projection of sampling quadrats onto habitat surfaces. On a rock bench, the surface 

area of rock under the projection is close to the nominal quadrat area, in this case 50*50 = 2500 

cm

2

. In the boulderfield, the surface area of rock under the projection is much greater than the 

nominal quadrat area because of the sides and undersides of the boulders. Moreover, cover 

based on the plan view (i.e., see from above) will underestimate the abundance of species living 

on the sides or bottoms of the 

Dethier et al. (1993) compared cover estimates based on visual and random-point sampling in 

quadrats and concluded that visual estimates gave a more accurate representation of relative 

coverage of sessile organisms, although both methods tended to overestimate uncommon species 

(see Chapter 6). Visual estimates are also logistically simpler and faster than using pins or other 

ways of identifying contact points, particularly in boulder fields when not all surfaces are 
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accessible from above. Considering time-effectiveness, a critical parameter in intertidal work, as 

well as precision and accuracy, a combination of visual estimates of cover and measurements of 

surface area was chosen for this study. Where a species covered less than 4 cm2 (the smallest 

wire quadrat), its occurrence was simply noted and later assigned a value of 1 cm2. Where algae 

occurred in several layers, each canopy was assessed separately and, thus, the total could exceed 

100%. 

The method described above was developed so it could be applied consistently in both boulder 

field and rock bench habitats. Better methods could be developed for boulderfields alone. For 

example, quadrats impose a flat surface of arbitrary constant size on a fundamentally threedimensional surface of varying sizes. The standard quadrat size is particularly problematic when 

some boulders fit entirely within the quadrat but other boulders do not. To avoid this problem, 

the sampling unit could be an individual boulder. Boulders could be selected at random, perhaps 

stratified by size in the boulder field, and organisms on and around the boulder sampled. 

Summary 

As with all other decisions concerning sampling, the appropriate sampling unit for a particular 

situation depends on the goals of the sampling program. The sampling unit determines, in part, 

the type of data collected. It is not possible to specify a simple prescription to be followed 

because each sampling program is unique. This explains at least in part the great diversity of 

sampling units that have been used in rocky intertidal studies. However, some general 

considerations are presented in this section. 

For sampling that involves counts of individuals, quadrats or plots are usually used. Most 

commonly, a rectangular or square quadrat is appropriate, with size dependent on the density of 

individuals being sampled and logistics. When density is low, a plot or band transect is needed, 

or else a very large number of smaller quadrats will be required to obtain an accurate estimate of 

abundance. Plotless methods rarely have been used in rocky intertidal studies but should be 

considered for larger, species such as sea stars and abalone. 

The placement of sampling units in a study area was considered in detail in Chapter 4, but one 

aspect is relevant to the choice of sample unit. When program goals include a description of the 

abundances of a variety of species, a long, linear sampling unit (such as a line or band transect) 

that crosses different patch types or environmental gradients will provide the most accurate and 

efficient estimate of mean abundances (Clapman 1932, Bormann 1953, Miller and Ambrose 

2000). The linear sampling unit spreads the sampling effort over a greater portion of the site, and 

thus is likely to include samples taken in different habitat patches. 

When repeated samples at a site are desired to track the performance of specific individuals or 

assemblages, permanent or fixed plots can be used to ensure that all samples include the same 
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119

spot. Fixed transects can be used for sampling the same general area, but it is difficult to 

establish transects precisely enough that the exact same spots can be repetitively sampled. Fixed 

quadrats, on the other hand, can be relocated with great precision. 

Finally, it is worth noting that the discussion of sampling units in this chapter concerns relatively 

conspicuous macroalgae and macroinvertebrates. Most general studies of rocky intertidal 

communities and impacts on these communities will have a similar focus. However, specific, 

targeted studies may require different sampling approaches. For example, cryptic species, 

especially those occurring in holes or crevices or boring in rock, may not be sampled well with 

the sampling units described here. In other cases, natural sampling units may be more 

appropriate. For example, species occurring in kelp holdfasts may be sampled using holdfasts as 

the sampling unit (Jones 1973), and organisms occurring in intertidal boulderfields might be best 

sampled using individual boulders as the sampling unit (Pless and Ambrose, unpublished 

observations). 

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intertidal and subtidal resources: Santa Barbara County mainland. Report to the Minerals 

Management Service. Pacific OCS Region. OCS Study MMS 95-0067. 

Benedetti-Cecchi, L. and F. Cinelli. 1995. Habitat heterogeneity, sea urchin grazing and the 

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Birkeland, C., A. A. Reimer, and J. R. Young. 1976. Survey of marine communities in Panama 

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Boalch, G. T., N. A. Holme, N. A. Jephson, and J. M. C. Sidwell. 1974. A re-survey of Colman’s 

intertidal traverses at Wembury, South Devon. J. Mar. Biol. Assoc., UK 54: 551-553.

Bormann, F. H. 1953. The statistical efficiency of sample plot size and shape in forest ecology. 

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Buckland, S. T., D. R. Anderson, K. P. Burnham, and J. L. Laake. 1993. Distance sampling: 

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Chow, V. 1976. The importance of size in the intertidal distribution of Littorina scutulata.

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Clapman, A. R. 1932. The form of the observational unit in quantitative ecology. J. Ecol. 20: 

192-197. 

Cochran, W. G. 1977. Sampling techniques, third edition. John Wiley & Sons, New York, New 

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Connell, J. H. 1961. The influence of interspecific competition and other factors on the 

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Cottam, G. 1947. A point method for making rapid surveys of woodlands. Bull. Ecol. Soc. Amer. 

28: 60. 

Cottam, G., J. T. Curtis, and B. W. Hale. 1953. Some sampling characteristics of a population of 

randomly dispersed individuals. Ecology 34: 741-757. 

Dethier, M. N. 1984. Disturbance and recovery in intertidal pools: maintenance of mosaic 

patterns. Ecol. Monogr. 54: 99-118. 

Dethier, M. N., E. S. Graham, S. Cohen, and L. M. Tear. 1993. Visual vs. random-point percent 

cover estimations: “objective’ is not always better. Mar Ecol Progr. Ser. 96: 93-100. 

Engeman, R. M., R. T. Sugihara, L. F. Pank, and W. E. Dusenberry. 1994. A comparison of 

plotless density estimators using Monte Carlo simulation. Ecology 75: 1769-1779. 

Frank, P. W. 1975. Latitudinal variation in the life history features of the black turban snail 

Tegula funebralis. Mar. Biol. 31: 181-192. 

Gonor, J. J. and P. F. Kemp. 1978. Procedures for quantitative ecological assessments in 

intertidal environments. U.S. Environmental Protection Agency Report EPA-600/3-78-

087. 

Green, R. H. 1979. Sampling design and statistical methods for environmental biologists. John 

Wiley & Sons, New York, New York, USA. 

Greig-Smith, P. 1983. Quantitative Plant Ecology. Third Edition. University of California Press, 

Berkeley, California, USA. 

Jones, D. L. 1973. Variation in the trophic structure and species composition of some 

invertebrate communities in polluted kelp forests in the North Sea. Mar. Biol. 20: 351-

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Kendall, M. G. and P. A. P. Moran. 1963. Geometrical probability. Griffin, London, UK. 

Kennedy, V. S. 1976. Desiccation, higher temperatures, and upper intertidal limits of three 

species of sea mussels in New Zealand. Mar. Biol. 35: 127-137. 

Kinnetics Laboratories, Inc. 1992. Study of the rocky intertidal communities of Central and 

Northern California. Final Report KLI-R-91-8 to the Minerals Management Service, 

Pacific OCS Region. OCS Study MMS 91-0089. 

Littler, M. M. 1971. Standing stock measurements of crustose coralline algae (Rhodophyta) and 

other saxicolous organisms. J. Exp. Mar. Biol. Ecol. 6: 91-99. 

Littler, M. M. and D. S. Littler. 1985. Nondestructive sampling. Pages 161-175 in M. M. Littler, 

and D. S. Littler, editors. Handbook of phycological methods. Ecological field methods: 

macroalgae. Cambridge University Press, Cambridge, UK. 

Lubchenco, J. 1982. Effects of grazers and algal competitors on fucoid colonization in tide pools. 

J. Phycol. 18: 544-550. 

Menge, B. A. 1972. Foraging strategy of a starfish in relation to actual prey availability and 

environmental predictability. Ecol. Monogr. 42: 25-50. 

Menge, J. L. 1974. Prey selection and foraging period of the intertidal predaceous snail 

Acanthina punctulata. Oecologia 17: 293-316. 

Miller, A. W. and R. F. Ambrose. 2000. Optimum sampling of patchy distributions: Comparison 

of different sampling designs in rocky intertidal habitats. Mar. Ecol. Progr. Ser. 196: 1-

14. 

Morisita, M. 1957. A new method for the estimation of density by spacing method applicable to 

nonrandomly distributed populations. Physiol. Ecol. 7: 134-144. (In Japanese, available 

as Forest Service translation number 11116, USDA Forest Service, Washington, D.C.) 

Parker, K. R. 1979. Density estimation by variable area transect. J. Wildlife Manag. 43: 484-492. 

Persson, O. 1971. The robustness of estimating density by distance measurements. Pages 175-

187 in G. P. Patil, E.C. Pielou and W.E. Waters, eds. Statistical Ecology, Vol. 2. 

Pennsylvania State University Press, University Park, Pennsylvania. 

Pollard, J. H. 1971. On distance estimators of density in randomly distributed forests. Biometrics 

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Richards, D. V. and G. E. Davis. 1988. Rocky intertidal communities monitoring handbook. 

Channel Islands National Park, U.S. Dept. of the Interior. Channel Islands National Park, 

1901 Spinnaker Dr., Ventura, California. 

Riemer, A. A. 1976. Description of a Tetraclita stalactifera panamensis community on a rocky 

shore of Panama. Mar. Biol. 35: 225-238. 

Russell, G. 1973. The litus line: a reassessment. Oikos 24: 158-161. 

Sutherland, J. P. 1970. Dynamics of high and low populations of the limpet Acmaea scabra 

(Gould). Ecol. Monogr. 40: 169-188. 

Underwood, A. J. 1976. Analysis of patterns of dispersion of intertidal prosobranch gastropods 

in relation to macroalgae and rockpools. Oecologia 25: 145-154. 
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Chapter 6. 

Quantifying Abundance: Density and Cover 

By 

Steven N. Murray

 Shaw’s Cove, Laguna Beach, California 
Final Study Report – Murray et al. 

124

Introduction 

Most rocky intertidal studies require quantification of abundance, either of individual species or 

other taxonomic units of the investigator’s choice. Data indicating species abundances can be 

collected quickly using subjective scales or by determining the presence of species in defined 

sampling units. Robust studies of species abundance, however, require more objective 

approaches that extend beyond subjective estimates or simple presence or absence 

determinations. Three kinds of quantitative data are used to express the abundances of rocky 

intertidal organisms in these more powerful studies: numerical counts or density, percent cover, 

and biomass. The particular method of quantifying abundance will vary with the nature of the 

sampled taxa and the specific goals of the study. Counts are used most often for expressing the 

abundances of mobile animals and larger seaweeds (e.g., kelps) where individual genets can 

readily be distinguished. Percent cover is commonly used for quantifying the abundances of most 

seaweeds, colonial organisms, such as sponges and bryozoans, and many species of sessile 

invertebrates including barnacles, mussels, and tube-dwelling worms and molluscs. 

Alternatively, the abundances of macroalgal and macroinvertebrate populations can be quantified 

in terms of biomass. Biomass data might be favored or required if investigators are interested in 

the energetic contributions of populations to an intertidal community. 

This chapter reviews various methods of quantifying the density and cover of rocky intertidal 

populations using non-destructive sampling procedures. Methods for determining biomass, 

which usually require that organisms be extracted and returned to the laboratory, are considered 

in Chapter 7. Procedures used to collect abundance data during rapid surveys and while using 

plotless and line transect sampling methods are briefly discussed. Emphasis in this chapter, 

however, has been placed on plot or quadrat-based methods for determining density and cover of 

intertidal macroalgae and macroinvertebrates. As discussed in Chapter 5, differences between 

plots and quadrats are somewhat semantic and the terms will be used as functional synonyms in 

this Chapter. Additional discussions of plotless and line transect sampling approaches can be 

found in Chapter 5. 

Rapid Surveys 

The goals of some studies might not require quantitative estimates of numerical abundance, 

cover, or biomass and can be met by less rigorous and less labor-intensive sampling procedures 

(Fig. 6-1). Subjective or semi-quantitative approaches are most useful for broad scale surveys 

(e.g., Crisp and Southward 1958; Dawson 1959, 1965; Boudouresque 1969, 1971, Baker and 

Crothers 1987) where they offer the advantage of providing rapid, integrated estimates of species 

abundances in often-patchy environments. Subjective data can be collected in such rapid surveys 

by making scaled abundance estimates for species integrated over large sections of habitat, or by 

applying scalar approaches to discreet sampling units such as quadrats distributed along transect 

lines. 
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Fig. 6-1. A summary of approaches for obtaining data when performing rapid surveys of rocky 

intertidal populations. 

For example, in his surveys of 44 rocky intertidal sites Dawson (1959, 1965) subjectively 

assigned species to one of three categories (rare to scant, occasional to frequent, and common to 

abundant) based on field observations performed over undefined areas extending out from a 

fixed transect line. More defined qualitative observations also can be used to assign species to 

arbitrary abundance categories or scales (e.g., ACFOR: abundant, common, frequent, occasional, 

or rare) using quadrats. One such approach was developed by Braun-Blanquet (1927) who 

proposed two scales for categorizing subjective observations of vegetation abundance, one for 

combining the number and cover of a species and the other providing a measure of sociability or 

growth pattern (Table 6-1). Another approach described by Hawkins and Jones (1992), relies on 

seven subjective abundance categories and defines the criteria for each category for each type of 

intertidal organism (Table 6-2). This scheme is an extension of a five-category system developed 

by Crisp and Southward (1958) in their broad-scale study of the biogeography of rocky shore 

species in the English Channel. 

Quick surveys also can be performed by determining only the presence or absence of a taxon in 

defined samples such as quadrats or intervals distributed along transect lines. These data can then 

be used to calculate frequency (i.e., the proportion of the total number of sample units within 

which a given species has been recorded), a representation of how common the taxon is in the 

study area. Frequency data are automatically derived from any quantitative sampling program 

where sampling units are identified and density, cover, or biomass data are taken. Lastly, 
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quantitative cover data can be obtained efficiently in rapid surveys, particularly for conspicuous 

sessile invertebrates and seaweeds that are easy to identify, by recording point contacts along 

transect lines (see Chapter 5 for discussion of sampling point-contact sampling procedures). 

Transect lines also can be used to perform rapid video surveys with data being extracted in the 

laboratory by standard line sampling procedures. However, as discussed later in this chapter, 

resolution and problems resulting from three-dimensional algal canopies and invertebrate 

assemblages will limit the ability to collect data. Nevertheless, video transects can be used 

effectively in rapid surveys to quantify the cover of easy to identify, habitat-structuring intertidal 

populations. 

Table 6-1. The Braun-Blanquet system for providing semi-quantitative or subjective 

assessments of vegetation abundance (after Kershaw 1973). The first six rows provide 

information on abundance whereas the second five rows describe sociability or growth form. 

The use of semi-quantitative abundance data will be limited and its collection is recommended 

only when coarse-scale descriptions of species distributions and abundances are required (Creese 

and Kingsford 1998). This is because subjective abundance estimates can vary considerably from 

investigator to investigator and, depending on the sampling design, uncertainties can exist about 

the specific habitats assessed. Semi-quantitative abundance data also create problems in 

statistical analysis and make it difficult to detect changes in populations over long periods of 

time (Raffaelli and Hawkins 1996). 
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Table 6-2. Abundance scale categories for different groups of rocky shore organisms from the 

North Atlantic (after Hawkins and Jones 1992). Organism categories listed are for the UK and 

need to be modified for other regions. Scales: E = Extremely Abundant; S = Superabundant; A = 

Abundant; C = Common; F = Frequent; 0 = Occasional; R = Rare; N = Not found (all cases). R 

assignments based on 30 min search. 
Final Study Report – Murray et al. 

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Plotless and Line Transect Methods 

Various plotless and line transect methods also can be used to obtain density or cover data in 

intertidal sampling programs (Fig. 6-2). These include distance-based techniques and markrecapture methods for density, and the use of multiple points scattered randomly or 

systematically throughout the study area and points or intercept lengths along transect lines for 

cover. Terrestrial plant ecologists have largely developed and used plotless methods for 

determining species densities. A discussion of these approaches is presented in Chapter 5. 

Although plotless techniques seldom have been employed in intertidal studies, Loya (1978) has 

described their use for sampling coral reef populations. Mark-recapture methods most often are 

used to obtain density data on highly mobile animals, such as vertebrates, where direct counting 

is impractical. However, mark-recapture techniques generally are not applicable for studying 

intertidal invertebrates, most of which are small and slow moving, except for large, highly 

mobile crustaceans such as crabs and lobsters. Unfortunately, even for these organisms, markrecapture methods are difficult to perform because of tagging (see Chapter 8) and observational 

difficulties. 

Fig. 6-2. A summary of non-destructive, plotless approaches for obtaining abundance data on 

rocky intertidal populations. 

Cover of intertidal organisms is usually measured using plots or quadrats, although cover also 

can be estimated without using plot-based sampling units. For example, points can be positioned 
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randomly throughout the study area using transect tapes or other methods, or regularly spaced 

along randomly located transect lines. As discussed in Chapter 5, point sampling along transect 

lines can be an efficient and repeatable procedure for obtaining cover estimates of rocky 

intertidal organisms during quick, broad-scale surveys. In most robust, quantitative studies, 

however, point sampling is used with discreet plots or quadrats to provide the statistical 

advantages of multiple sampling units. Although a lengthy record exists for employing line 

intercept methods to determine the cover of terrestrial vegetation (Greig-Smith 1983), this form 

of sampling has been much less used in intertidal work, particularly during recent years. 

Additional discussions of distance-based techniques, line intercept procedures, and point 

sampling can be found in the previous discussion of transects, quadrats, and other sampling units 

(Chapter 5). A discussion of the use of mark-recapture methods for estimating population 

densities is available in Krebs (1989). 

Fig. 6-3. A summary of non-destructive, plot-based approaches for obtaining abundance data on 

rocky intertidal populations. 
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Plot or Quadrat-Based Methods 

Plot or quadrat-based methods for determining abundance will be emphasized in the discussions 

presented here and in Chapter 7. These methods are employed commonly to quantify the cover 

or density of macroorganisms in rocky intertidal monitoring, impact, baseline, and experimental 

studies, particularly those that require repeated assessments (Fig. 6-3). Gonor and Kemp (1978), 

Littler and Littler (1985), and Creese and Kingsford (1998) provide good previous accounts of 

non-destructive sampling methods for quantifying the abundances of intertidal populations. 

Other discussions of sampling topics treated in this chapter can be found in Kershaw (1973), 

Mueller-Dombois and Ellenberg (1974), Greig-Smith (1983), Andrew and Mapstone (1987), 

Krebs (1989), Hayek and Buzas (1997), Hawkins and Jones (1992), Brower, Zar, and von Ende 

(1998), and Kingsford and Battershill (1998). 

Density 

Direct counts of the number of individuals is perhaps the most intuitive means of expressing 

abundance and is clearly the most commonly used, non-destructive method for sampling the 

abundances of mobile intertidal invertebrates such as limpets, turban snails, crabs, littorines, and 

chitons. To facilitate comparisons with other studies where quadrat sizes or the area being 

sampled differ, counts of organisms should be converted to density or the number of individuals 

per unit area of intertidal surface (preferably per square meter). Most investigators use regularlyshaped quadrats for sampling intertidal seaweeds and macroinvertebrates although large, 

irregularly-shaped areas might be necessary for sampling certain, patchily distributed organisms 

such as sea stars and abalone (see Chapter 5 and Ambrose et al. 1992). Numerical counts not 

only provide a useful parameter for expressing abundance but, together with size-frequency data, 

can form the basis for describing demographic attributes of populations. Numerical counts also 

are useful for calculating various indices that describe community structure and composition 

(e.g., diversity indices; Magurran 1988) or that compare communities (e.g., similarity indices; 

Pielou 1984) based on species abundances. 

Obtaining accurate counts requires the ability to discern individuals, a task that is difficult, if not 

impossible, for most seaweeds and many encrusting animals (e.g., sponges and colonial 

ascidians). Similar problems have long been recognized by terrestrial ecologists interested in 

sampling rhizomatous or stoloniferous herbs and mosses (Kershaw 1973, Mueller-Dombois and 

Ellenberg 1974, Greig-Smith 1983). Despite the conceptual simplicity of counting organisms in 

plots or quadrats, this task can be time consuming and difficult to employ, particularly when 

organisms are small and numerous, such as acorn barnacles or smaller species of littorine snails. 

Accurate counts also can be difficult to obtain for abundant organisms with scattered spatial 

distributions because of difficulties in remembering which individuals have been tallied during 
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the counting process. To keep track of counted individuals, organisms can be marked as they are 

encountered using a wax pencil, lumber crayon, or chalk. Use of a hand-held mechanical counter 

can speed up the counting process when organisms are abundant (> 50). Smaller quadrats can be 

processed more efficiently and accurately than larger ones when counting small, very abundant 

organisms. Alternatively, smaller quadrat sections can be subsampled when using quadrats with 

dimensions better designed for sampling larger, less numerous species. The use of more than one 

quadrat size should be considered in the design of population-based studies where there are 

substantial differences in the sizes and densities of the organisms being sampled (Kingsford and 

Battershill 1998). 

All plots or quadrats have boundaries and difficulties arise in determining when to include or 

exclude organisms positioned across plot borders. This problem is exacerbated by observer 

parallax because the angle at which the plot is viewed in the field actually sets its boundaries. 

Hence, observers should attempt to reduce parallax error by viewing plot or quadrat boundaries 

at an angle perpendicular to the substratum. Using plots or quadrats with a smaller perimeter to 

area ratio (Krebs 1989) also can reduce these edge effects. Boundary problems can bias the 

counting process and result in overestimates of numerical abundance, even by experienced 

investigators who can be tempted to include all organisms located along plot borders. To 

eliminate bias, consistent procedures should be established for counting organisms found on plot 

boundaries. These procedures or sampling rules must not include all organisms located along 

plot borders because to do so would be equivalent to uniformly expanding the plot area. 

Sampling rules for plot borders should be developed a-priori to avoid bias when performing 

counts (Fig. 6-4). For example, the proportion of an organism located inside plot or quadrat 

boundaries can be used to decide whether or not the organism should be counted. This rule is 

most easily applied for large, regularly shaped organisms where an individual is counted if it 

resides at least 50% within the plot (Gonor and Kemp 1978). For sessile animals and plants, 

inclusion should be based only on the attachment area or holdfast; organisms attached outside 

plot boundaries but with body parts or fronds that lie within plot borders should not be included 

in plot counts. For organisms where size and shape make it difficult to determine the proportion 

included within the plot, individuals can be omitted from counts if they are positioned across two 

of a plot’s four sides (Gonor and Kemp 1978). For rectangular plots, the two borders should 

include one large and one small side so that the sides selected bias neither inclusion nor 

exclusion. The specific sides of the plot to be excluded should be identified prior to counting and 

held consistent throughout the study to simplify sampling and avoid the temptation of making 

adjustments that result in the unwarranted inclusion of rare species in plot counts. 
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Fig. 6-4. Examples of procedures for counting large seaweeds and macroinvertebrates in field 

plots. For seaweeds and sessile animals, only individuals attached to surfaces within plot 

boundaries are counted when taking density data. For mobile animals, a-priori sampling rules 

should be used to determine whether an individual is to be counted. For example, for large, 

regularly shaped animals it may be decided a-priori that an individual will be counted if50% or 

more of its body lies inside plot boundaries. For small, sessile or mobile animals and small 

seaweeds, organisms often are included in counts if they touch two of the four plot borders but 

are not included if they touch the other two. Based on the former counting strategy, sea stars a 

and f are not included in counts because more than 50% of their bodies lie outside plot 

boundaries. If the latter counting strategy is to be employed, urchins 1 and 2 and seaweeds i and 

iv are not included in counts because they lie across the upper and left plot borders which have 

been designated for exclusion. 

Cover 

Although density data usually can be collected for mobile invertebrates, kelps, and other large 

algae, it is usually impossible to discern and count individuals of most seaweeds and colonial 

invertebrates such as sponges and bryozoans. Discriminating individual seaweeds or genets is 

often impossible because holdfasts of neighboring individuals can grow tightly together and even 

fuse, and because cryptic heterotrichous basal systems can give rise to multiple, upright fronds 
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(Fig. 6-5). Interestingly some red algal germlings also can coalesce during early development, 

resulting in the production of multiple chimeric fronds from a single basal system (Maggs and 

Cheney 1990, Murray and Dixon 1992). For colonial invertebrates, quantifying the numbers of 

colony members or colonies might be less important than measuring the area of the occupied 

substratum. Sessile barnacles, mussels, and tube-dwelling worms and molluscs usually can be 

discriminated in the field, but these organisms often are so numerous that counts can be 

extremely time-consuming and of less ecological importance than the quantification of occupied 

space (Fig. 6-6). Hence, investigators generally use percent cover to express the abundances of 

most seaweeds and colonial invertebrates. Similarly, the abundances of many sessile 

invertebrates often are reported as percent cover unless the study goals require density data. 

Fig. 6-5. Coralline algal turf consisting of Lithothrix aspergillum and Corallina pinnatifolia with 

multiple upright axes arising from an uncertain number of individual crustose bases. For many 

seaweeds, it is impossible to determine the actual number of discreet individuals that make up a 

patch or clump. 

Percent cover is the percentage (or proportion) of the surface area of the sample unit (e.g., plot) 

covered by invertebrate bodies or seaweed thalli. In intertidal studies, percent cover also is 

commonly used to quantify the amount of sand, tar, unoccupied rocky substratum, or substratum 

type. Unlike the previously described procedures for counting organisms, percent cover 

estimates usually are made on all material overlying the perpendicular projection of the 

substratum area contained within plot borders. Thus, when using plots, cover estimates should be 
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134

made from a viewing angle perpendicular to the substratum to standardize the plot area to that 

approximating its planar surface. This procedure will make the cover of a plot occurring on a 

horizontal substratum equivalent to the cover of the same-sized plot placed against a vertical wall 

when viewed normal to the wall’s surface, irrespective of the substratum topography. 

Nevertheless, whether plots are positioned horizontally or vertically, the actual surface areas of 

the substrata being sampled will almost surely vary among plots because of differences in 

topographical relief. Unless the goals of the study require more precise treatment of 

topographical heterogeneity (e.g., see Trudgill 1988, Underwood and Chapman 1989, Kingsford 

and Battershill 1998), however, investigators usually consider all plots of the same dimensions to 

sample equivalent areas. Since the planar area of a plot can be calculated from its dimensions, 

this area can be used to convert percent cover to metric data when this is required. 

Fig. 6-6. Dense aggregation of barnacles occupying a flat, rocky surface in the upper intertidal 

zone. It is often difficult to obtain accurate counts of small, densely aggregated barnacles and 

other invertebrates that occur in densities of several thousand per m2

. 

A common difficulty in estimating the cover of intertidal organisms is layering or multiple 

occupancy of the space directly above the primary substratum (Fig. 6-7). Layering can be due to 

overlapping parts of the same individual or the shared occupancy of the vertical extension of the 

primary substratum by more than one organism. For example, erect fronds of most seaweeds 

collapse during low tide leaving the entire alga lying horizontally across the rock surface. 

Although the fronds of many temperate intertidal seaweeds usually are less than 10-20 cm in 

length, kelps and other large algae can have fronds that reach lengths greater than 1 m. Thus, the 
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fronds of larger seaweeds form canopies that cover other organisms during low tide. Layering 

also occurs at smaller scales when smaller algae or invertebrates occur as epibionts on seaweeds 

or on the shells of organisms. Thus, cover is stratified vertically on most shores but generally at 

scales of only tens of centimeters, except where larger algal canopies are present. 

Although layering is common in seaweed-dominated communities, sessile invertebrates also can 

contribute to the three-dimensional structure of intertidal communities. For example, barnacles 

provide substratum for other organisms and mussels can form thick, layered beds that offer 

attachment surfaces and living space for numerous invertebrates and seaweeds. Most researchers 

attempting to include all of these organisms when making cover estimates handle layering by 

making separate determinations of overstory and understory layers (Littler and Littler 1985, 

Raffaelli and Hawkins 1996). Because of layering, it is very common for individual plots to 

support more than 100% cover, particularly in seaweed-dominated intertidal communities and 

mussel beds. 

Fig. 6-7. Layering is common in intertidal habitats occupied by large, canopy-forming 

seaweeds such as Eisenia arborea in southern California. 

There are three basic methods for obtaining estimates of the percent cover of rocky intertidal 

populations: 1) scanning plots visually, 2) determining the number of point intercepts or contacts 

along a line or within an area, and 3) tracing the silhouettes or photographic images of organisms 

by planimetry or with image-analysis software. In the last method, actual metric areas are then 

converted into percentages to obtain percent cover data. On rare occasions, the cover of a species 

may be calculated by formula based on measurements of selected dimensions, but this method is 
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136

only applicable to species with regular or proportionate shapes and will not be discussed further. 

The first two methods are commonly employed directly in the field while all three methods can 

be used in the laboratory working from 35-mm slides, photographic prints, digital images, or 

video film. 

Field Methods: Visual Scanning. Visual scanning is a commonly used field method that relies 

on an investigator’s ability to accurately estimate the percentage of the planar surface area of a 

plot covered by the species or material of interest. Often, investigators divide plots into 

subsections (Fig. 6-8) to break down cover estimates into smaller, more tractable units (e.g., 

sections representing 10% of the quadrat area) to facilitate estimates and improve accuracy 

(Dethier et al. 1993). When employed by an experienced observer, visual cover estimates can be 

completed rapidly in the field, even under harsh conditions, and result in an accurate taxonomic 

inventory of plot contents. For these reasons, visual scanning might be the preferred assessment 

method if a major goal of the study is to determine species richness. 

Fig. 6-8. Investigators performing cover estimates in plots divided into subsections. The practice 

of dividing plots into subsections is frequently used to facilitate visual estimates. 

Despite its advantages, the visual scanning method generally is considered less accurate than 

other, less subjective methods of determining cover, particularly when plot contents are complex 

(but, see Dethier et al. 1993). Because investigators differ in their levels of experience and their 

inherent ability to visually group together taxa of different sizes, shapes, and distributions, visual 

cover estimates have a high potential for observer error. Moreover, errors produced by visual 
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scanning are unknown because they are largely a property of the investigator and his or her 

taxonomic and visual abilities. For inexperienced observers the absolute error can be high, 

particularly when making estimates of small, spatially scattered taxa (e.g., chthamaloid 

barnacles) or species contributing low cover (e.g., 5 to 10%). Because different observers often 

arrive at different cover estimates under the same circumstances, visual scanning also is the least 

precise or repeatable of the methods commonly used in intertidal assessments (Rivas 1997). 

Accordingly, visual scanning may not be the method of choice in studies where multiple 

investigators repeatedly collect data from one or more sites, or in long-term monitoring programs 

where cover is sampled over a time span likely to transcend the participation of individual 

observers. Lastly, most sampling programs require large numbers of replicates. The repetitive 

use of visual scanning can be mentally demanding, particularly under conditions of high 

biological complexity. For these reasons, errors in visually estimating cover can increase as the 

investigator tires during the later portions of an intensive assessment period. 

To reduce field time, some investigators have adopted the use of grided quadrats and record only 

species presence within individual grids or subsections instead of making actual cover estimates. 

This approach might work well for abundant species but not for most species that provide 

moderate to low cover. This is because sampling error will be increased greatly when grid 

occurrences are summed and converted to quantitative cover values. A likely outcome will be 

unacceptably high sampling errors, particularly for smaller bodied species distributed widely 

throughout plots, which will compromise statistical tests designed to detect changes in 

abundance over space or time. Unless each individual subsection comprises a very small 

proportion of the total plot area, this procedure is not recommended except for surveys where 

only semi-quantitative data are required. If fully quantitative visual cover estimates are believed 

to be impractical, data of higher value and greater utility easily can be obtained with similar 

expenditure of field time by simply using grided intersections as point contacts and listing 

species not contacted by points as simply present in quadrats. For these latter, rare species, an 

arbitrary cover value can then be assigned which is equal to a value less than that possible when 

a species in the quadrat is contacted by only a single point. 

Field Methods: Point Contacts. Besides visual scanning, the most commonly used field 

procedure for estimating the percent cover of intertidal organisms is the point-intercept or pointcontact method. Terrestrial plant ecologists have long used point-based procedures, and much is 

known about the advantages and disadvantages of point sampling terrestrial vegetation (GreigSmith 1983). When using point-based methods, the taxon or taxa subtended by each point 

dropped in the sampling area must be determined and recorded by the investigator (Fig. 6-9). 

Percent cover of a species is then calculated by dividing the number of its point contacts by the 

total number of points distributed within the sampled area or plot. Various means can be used to 

provide point fields using this procedure (Kingsford and Battershill 1998). For example, marks 

(points) can be made on acetate, plastic sheets, or Plexiglas (=Perspex) boards (e.g., Dungan 
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138

1986, Meese and Tomich 1992), rods can be inserted through Plexiglas plates (e.g., Foster et al. 

1991), knots can be tied at random in string attached to a metal bar (Kingsford and Battershill 

1998), and intersecting grid lines can be affixed to plot frames (Kennelly 1987) or provided as 

plastic mesh (Underwood et al. 1991). The use of a double layer for fixing or sighting points can 

reduce parallax errors (Hawkins and Jones 1992, Raffaelli and Hawkins 1996). 

Fig. 6-9. Field researchers making cover estimates using a point contact procedure. Stainless 

steel rods are dropped vertically through holes in a leveled Plexiglas (Perspex) plate used to 

position rods. 

A potential source of error in point sampling stems from the actual diameter of the pin or point 

used to determine contacts (Greig-Smith 1983). Although theoretically the contacts in point 

sampling are to be based on true points, actual sampling is performed using needles, pins, rods, 

cross-wires, grids of line or mesh, knots in string, laser light projections, or other objects that 

only approximate true points. These objects have a finite diameter and contact an area greater in 

size than a true point. An effect of using points with a finite diameter is that percent cover is over 

estimated, particularly when sampling smaller, finely-branched plants (Goodall 1952). 

Points can be distributed randomly or systematically in regular rows and columns. The relative 

merits of using random versus regularly distributed point fields have not been determined for 

sampling intertidal organisms (Dethier et al. 1993). For terrestrial plants, however, 

systematically arranged points yield similar cover values to random point arrays if: 1) the 

distance between points exceeds the size of the individuals or plant clusters, and 2) spacing does 
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not correspond with a repetitive pattern in the vegetation (Tidmarsh and Havenga 1955). If 

points are randomized, a stratified approach should be used in most cases to ensure that points 

are dispersed over the entire area being sampled. This is easily accomplished in the field by 

dividing the sampling apparatus into sections (e.g., quarters) and then randomly selecting points 

from arrays arranged in regular rows and columns. This procedure establishes minimum 

distances between points, ensures that points are dispersed over the entire plot area, and enables 

the observer to easily keep track of assessed points when performing fieldwork. 

A known advantage of point-based sampling procedures is that cover estimates become more 

accurate with increasing point densities (Greig-Smith 1983). This benefit is obtained, however, 

at the expense of the greater time required to process an individual sample. For this reason, the 

investigator should select a point density that yields an ecologically acceptable margin of error, 

and a point field that can be processed within the time constraints of the sampling program. 

Hence, the number of points to be sampled should probably be determined from a pilot study. 

For most intertidal work, however, sampling has been based on history and tradition (Andrew 

and Mapstone 1987) instead of rigorous evaluation, and the densities used in point-contact 

sampling have frequently been selected from previous studies. Although Raffaelli and Hawkins 

(1996) suggest that 30 to 50 points per plot are appropriate for most studies, the majority of 

workers appear to use point fields ranging from 50 to 100 points (Table 6-3). With 50 to 100 

points per plot, the minimum point-generated cover value for a taxon will lie between 2% and 

1%, the case when a single point hits a taxon. Gonor and Kemp (1978) have provided a brief 

discussion of procedures for determining the number of points required to generate cover data 

and Kingsford and Battershill (1998) discuss how binomial sampling theory can inform selection 

of a suitable point field density. 

Table 6-3. A listing of the point densities used in selected intertidal sampling programs. 

The very high point densities required for accurately estimating the cover of species found in low 

abundance (< 5% cover) are rarely, if ever, attained in field sampling programs because of 

sampling-effort limitations. Relying exclusively on point contacts to quantify species presence 
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and cover not only provides poor estimates for species that occur in low abundance but often 

completely excludes rare species from plot assessments (e.g., Carter and Rusanowski 1978, 

Meese and Tomich 1992, Dethier et al. 1993, Rivas 1997). Many species commonly occur in low 

abundance in temperate rocky intertidal systems and, as a consequence, will be missed entirely 

by most point fields. As a result, taxonomic richness is likely to be underestimated in exclusively 

point-based sampling programs, as will diversity measures that are highly sensitive to species 

number. For example, Dethier et al. (1993) observed that a point density of 1 point per 50 cm2 of 

primary substratum failed to include 19% of the species present, with all omitted taxa 

contributing less than 2% cover. Consequently, it is impractical in most cases to attain the 

sampling effort needed to meaningfully measure species richness or detect spatial or temporal 

differences in the cover of rarer species using only point-contact sampling methods. 

Dethier et al. (1993) have argued that cover estimates made using point-contact procedures 

require more sampling time than estimates using visual scanning. This might not be true, 

however, when sampling programs require observers to process many samples in a single field 

day or when plot contents are multilayered and complex. Under these conditions, determining 

the species hit by points results in much less fatigue and accelerates the processing of samples 

when compared with the visual conversion of shapes and patterns into cover values. Studies by 

Rivas (1997), who used simulated species made of paper and cardboard, and personal field 

experience supports the premise that point-contact methods are usually less time consuming than 

visual scanning, particularly when processing many samples. Moreover, the time required to 

process a sample is less influenced by biological complexity when point-contact procedures are 

employed. 

Photographic Sampling 

Density and cover estimates also can be made in the laboratory from photographic methods that 

obtain images in the field using 35-mm, video, or digital cameras. Traditionally, this has been 

accomplished using 35-mm cameras and color (64 or 100 ASA slide) or black and white film, 

although recently portable Hi 8-mm and digital format camcorders and digital still cameras have 

become available. Organisms can be counted and the same visual and point-contact procedures 

for estimating cover in the field can be used on the resulting slides, prints, video film, or digital 

images with most of the same advantages and disadvantages. Photographs or video and digital 

images also can be used in the laboratory to determine the areas of organisms using a hand-held 

planimeter or with the aid of a computer using digitized tracings and image-analysis software. 

Photographic sampling methods offer several advantages over methods that depend exclusively 

on in-situ field assessments but also have significant disadvantages. 

Intertidal studies are almost exclusively performed during periods of low tide so access to the 

shore is limited and investigators encounter field-time constraints that restrict the number of 
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samples that can be collected. Photographic sampling can be completed much more rapidly than 

full field assessments and can increase the number of samples taken per unit field time. Because 

plot-to-plot variation is usually high in intertidal habitats, a large number of samples is often 

needed to obtain the statistical power necessary to detect ecologically meaningful differences in 

species abundances. Photographic sampling also offers the advantage that an essentially 

permanent record of the contents of each plot can be archived and later independently analyzed 

by other investigators or used to visually demonstrate changes in species composition and 

abundances, even to non-scientific audiences. Additionally, in-situ quantification errors resulting 

from investigator mistakes or fatigue, inclement weather, or dangerous surf can be reduced, and 

parallax problems resulting in edge-effect errors can be eliminated by photographic sampling 

(Gonor and Kemp 1978). 

Unfortunately, laboratory-based sampling methods that rely on photographs, video records, or 

digital images also have significant disadvantages. The most important of these is the limits of 

resolution of the film, tape, or digital media which makes it difficult to locate small, “difficult-tosee” taxa or to accurately distinguish morphologically similar species (Gonor and Kemp 1978, 

Foster et al. 1991). Photographic sampling procedures also present problems when applied to 

highly-layered intertidal communities (Gonor and Kemp 1978, Foster et al. 1991, Meese and 

Tomich 1992, Leonard and Clark 1993) because the captured images are only two-dimensional 

views and the entire three-dimensional plot contents cannot be inspected as they can in the field. 

Thus, photographic sampling can be severely compromised in dense seaweed or mussel 

communities where it is impossible to easily move aside upper layers and photograph underlying 

organisms. Photographic techniques work best when sampling simple communities consisting of 

largely two-dimensional populations such as small barnacles, crustose algae, or only the 

overstory fronds of large, canopy-forming seaweeds. Unfortunately, highly layered and often 

seaweed-dominated communities are common throughout the mid- and lower-intertidal zones of 

most temperate coasts. For these reasons, Foster et al. (1991) emphasize the need to substantiate 

identifications and quantification of abundance through on-site fieldwork when using 

photographic sampling methods. Photographic sampling procedures also place constraints on the 

size (and shape) of sample plots; these must be small enough to be photographed at a scale where 

plot contents can be identified and of a shape that conveniently fits within the film frame. 

35-mm Photographic Sampling. 35-mm Single-Lens-Reflex (SLR) cameras have long been 

used to assess species abundances in intertidal sampling programs (Littler and Littler 1985). The 

interested reader can find a discussion of the use of 35-mm cameras in marine sampling 

programs in George (1980). For most applications, photographs are taken of framed quadrats in 

which case the known quadrat dimensions provide a built in linear scale. Rectangular-shaped 

quadrats often are preferred for photographic sampling because their dimensions match those of 

the 35-mm film format (Fig. 6-10). Nonreflective Plexiglas (=Perspex) can be fixed to the 

exterior of the quadrat frame and written on with a wax pencil or lumber crayon to record 

quadrat labels such as date, site, and quadrat number on the film (Littler and Littler 1985). 
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A wide variety of films, cameras, and lenses are available at a range of prices. Usually, 35-mm 

color transparency (slide) film (ASA 64 or 100) is preferred because color offers the best 

opportunity to distinguish intertidal organisms that are variable in coloration and contrast, and 

because the ability to project or digitize transparencies facilitates laboratory assessment. Infrared color film can be advantageous for photographically sampling certain seaweeds, and 

particularly thick cyanobacterial (= blue-green algal) and diatom films that occur on intertidal 

rock surfaces (Littler and Littler 1985). Generally, a 35-mm SLR camera for intertidal work will 

be equipped with a good quality lens and be resistant to damp, salty conditions. The choice of 

lens will depend on the size of the area to be photographed but for many applications a zoom 

lens (e.g., 35 mm to 70 or 80 mm) may be preferred to facilitate framing and focusing. However, 

for most cameras and lens systems, a fixed 35-mm lens will provide greater photographic 

resolution. An easily accessible shoe or PC port that allows the use of a battery-powered, 

electronic strobe is essential because sampling often must be performed in poor light — such as 

Fig. 6-10. Investigators 

using a hand-held 35-mm 

camera equipped with an 

electronic strobe to 

photograph the contents of 

a field plot. The 

photographer has taken a 

position directly above the 

plot so as to photograph its 

contents at an angle as 

close as possible to 90° to 

the plane of the substratum. 

Usually, a second person is 

required to provide 

assistance in positioning 

and securing plots on 

shores where topography is 

heterogeneous and 

irregular.
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at night, in the early morning, or late afternoon. The additional light enables the use of high lens 

ƒ-stops (ƒ8 or greater) to maximize the depth of the field in photographs. Strobe lighting also can 

remove shadows and reduce contrast during well-lit, mid-morning or afternoon hours. When 

high contrast between subjects and shadows are produced by natural lighting conditions, 

photographic quality can be improved greatly by using strobe lighting in conjunction with an 

umbrella or other object to uniformly shade the sample area. Adjustments in film exposure often 

will be required to achieve good results when the photographer moves between intertidal 

communities. For example, barnacle and rock-dominated upper shore plots generally require less 

exposure time (accomplished by an increase of 1 to 2ƒ-stops) than plots harboring darker-colored 

mussels. Strobes should be mounted on a bracket to the side of the camera to avoid reflection 

from wet rocks and seaweeds. A polarizing filter can be used to reduce glare but when used, care 

must be taken to ensure that the filter is set to provide polarization and that appropriate 

adjustments have been made in setting the ƒ-stop or exposure time. 

A significant disadvantage of relying on 35-mm photographs is that it is difficult or impossible to 

later compensate for poor images, and even experienced investigators can have trouble obtaining 

consistently good exposures under the full range of field conditions. Moreover, because 35-mm 

film must be laboratory processed, the quality of photographs cannot be checked before leaving 

the field. To ensure that properly exposed photographic samples are obtained, one or two 

additional photographs can be bracketed around the selected settings by using different lens ƒstops or exposure times. Film is much less costly than the cost (time and effort) required for field 

sampling, so bracketing exposures to ensure usable photographic samples is always a good idea. 

The enclosure of 35-mm SLR cameras and strobes in waterproofed protective cases also might 

be necessary under rigorous field conditions where unprotected cameras and strobes are exposed 

to precipitation, ocean spray, or the possibility of accidental submergence. However, enclosure in 

protective cases requires an added expense and, because cases often are bulky, can make 35-mm 

SLR cameras inconvenient to use. To overcome these problems, most researchers rely on 

underwater cameras (e.g., Nikonos 35-mm series) for sampling under wet field conditions. 

Unfortunately, many underwater cameras, including reasonably-priced Nikonos models, are 

rangefinder cameras that do not frame or focus the subject directly through the lens. This 

increases the probability of framing and focusing errors when rangefinder cameras are hand-held 

and used by inexperienced photographers. Framing and focusing problems with underwater 

cameras can be overcome by mounting the camera on a fixed stand, made for example from PVC 

pipe, that frames the sample and then setting the lens at a predetermined focal distance from the 

subject; single or paired strobes can be mounted at preset lateral positions on the stand to provide 

uniform and angled lighting (Fig. 6-11). Although fixed camera stands are convenient under 

most field conditions, they take field time to assemble and can be difficult or cumbersome to use 

when plots occur on vertically positioned or irregularly angled substrata. 
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144

To partially overcome layering problems in seaweed-dominated communities, both overstory 

and understory photographs of the same plot can be taken and then separately scored in the 

laboratory (Littler and Littler 1985). In performing this procedure, a single photograph of the 

overlying seaweed canopies is first taken and then the understory layer is photographed after 

canopy fronds are nondestructively combed aside. Nonetheless, it is almost always impossible to 

clearly view all plot contents down to the primary substratum using photographs. To better 

interpret plot contents and provide information on “difficult-to-see” taxa, 35-mm photographs 

can be supplemented with field estimates of species cover and notes describing the locations of 

species within plots (Littler and Littler 1985). By constructing data sheets with rows and 

columns that match plot subsections, crude maps of species locations within plots can be 

obtained simultaneously with estimates of subsection cover. Although field notes can add 

important information, if notes are detailed this effort can be time consuming and defeat one of 

the principal advantages of photographic sampling: reduction in the amount of field time 

required to obtain samples. 

Fig. 6-11. Photographer 

standing adjacent to a 

Nikonos camera and an 

electronic strobe 

mounted to a fixed stand 

made of PVC pipe. The 

base of the stand has 

been configured to 

represent the plot 

borders. All photographs 

are taken at the same 

fixed angle and distance 

with respect to the plot 

surface.
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Video Sampling. A few years ago, Whorff and Griffing (1992) introduced a video procedure for 

sampling rocky intertidal populations. This method employed VHS Camcorders to obtain video 

images from which quantitative abundance data were later extracted in the laboratory. Various 

video-based techniques have been used for some time for performing benthic surveys (Harris 

1980, Holme 1984, 1985, Thouzeau and Hily 1986, Leonard and Clark 1993), especially from 

submersibles (e.g., Potts et al. 1987), and sampling fishes in the water column (Kingsford 1998). 

Despite its potential (Whorff and Griffing 1992, Leonard and Clark 1993), video sampling has 

not been used widely in rocky intertidal research, and most photographic methods for sampling 

rocky intertidal populations have relied on 35-mm cameras and film. Nevertheless, video 

technology has improved rapidly in recent years, a trend that clearly will continue in the future. 

Highly portable, battery-operated Camcorders, lighting accessories, and video playing and 

recording systems are now readily available at relatively low cost. Hi 8-mm video film and 

digital video represent significant advances in quality over both VHS and SVHS video media 

and can yield sharp and informative images. 

Video methods provide many of the same advantages and disadvantages as those discussed 

previously for 35-mm photographic sampling. However, the greatest concern when using 

affordable video in place of 35-mm film is image quality. Neither digital nor video film media 

are yet able to offer comparable resolution to 35-mm film. For many purposes, the reduction in 

resolution obtained with video film or digital media may not be crucial, and samples can be 

quantified at levels comparable to those attainable with 35-mm film. However, the higher image 

quality of 35-mm film may be a requirement for many other uses. The use of digital still cameras 

in place of 35-mm SLR film cameras has the same disadvantage: images will still generally be of 

lower resolution than those captured on 35-mm, although with each passing year this gap is 

being closed with improvements in digital technology. 

Video filming also offers advantages and can overcome some of the problems associated with 

35-mm photographic sampling. Because adjustments in filming angles, film exposure, and 

lighting easily can be done in the field, it is possible to quickly take multiple frames of the same 

area to increase the likelihood of acquiring images of needed quality. Additionally, Camcorders 

provide the additional advantage of being able to zoom in and out while filming. Zooming in to 

produce close-ups of small plot sections can help overcome difficulties in identifying “difficultto-see” taxa and increase the amount of information obtained beneath seaweed canopies. Besides 

filming whole plots, Rivas (1997) also filmed smaller areas nested within each larger plot to 

provide supplemental close-up video footage used to help identify “difficult to see” taxa and to 

quantify the understory contents of full plots (Fig. 6-12). Plots (0.3 m x 0.5 m) were divided into 

quarters that were in turn divided into two rows and three columns to produce six subsections. 

After filming each plot quarter, the smaller, understory species in the six subsections were filmed 

sequentially by zooming in the lens while holding the camera steady and perpendicular to the 

substratum. 
Final Study Report – Murray et al. 

146

Fig. 6-12. Videographer filming plot contents in the field with a Camcorder equipped with a 

battery-operated light source. Filming procedures include taking plot views at different scales 

ranging from full plot photos to macrophotos of small plot sections. 

Laboratory-Assessment of Photographic Samples. Visual observations of photographic records 

can be used in the laboratory to list species, count individuals, or visually estimate percent cover. 

For most layered intertidal communities with well-developed seaweed canopies, small or cryptic 

species and low-abundance taxa are often difficult to identify or count based only on information 

contained in photographic samples. Hence, photographic records rarely can be used alone to 

obtain full taxonomic inventories or to determine the densities of most species. On the other 

hand, 35-mm color slides often have been used for laboratory determinations of the cover of 

intertidal species using visual (e.g., Lubchenco and Menge 1978) or point contact (Bohnsack 

1979, Littler and Littler 1985, Foster et al. 1991) methodologies that also can be transferred 

readily to a video-based or digital platform. 

Usually, 35-mm film is processed to produce color slides or transparencies that can be projected 

onto a screen or viewed directly using a dissecting microscope. Alternatively, 35-mm film can be 

scanned to produce digital images for enhancement or to enable quantification using computer 

software. Slides can be projected directly onto a point grid or a sheet of acetate and percentcover estimates made using point contact or other methods (Fig. 6-13). For example, Littler and 

Littler (1985) describe a procedure where 35-mm color slides are projected and focused onto a 

sheet of fine-grained, white paper containing a grid of points arranged at 2-cm intervals. The 
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organisms subtended by each point are then identified and tallied by the investigator with help 

from written maps and data sheets or tape-recorded field notes. Alternatively, the intersections of 

grid lines in a standard ocular graticle (e.g., 10 x 10) can be used as points to score 35-mm slides 

or photographic prints viewed with a dissecting microscope. 

Fig. 6-13. Slides being scored in the laboratory using field notes. A 35-mm color slide of a field 

plot has been projected onto a piece of paper containing a grid of points. The grid is taped to a 

glass panel and the slide is projected from a position on the opposite side of the panel to 

eliminate shadowing.

Although labor intensive, the photographic sampling program described by Littler and Littler 

(1985) includes most of the attributes of both field and photographic data acquisition. In this 

procedure, cover was determined for the more abundant and easy to discriminate species in the 

laboratory based on point-contact scores obtained from 35-mm color slides. However, for the 

smaller, “difficult-to-see” taxa and understory species hidden in photographs, for example, final 

cover values were based on field estimates because these could not be quantified with accuracy 

solely using photographs. 

Similar methods can be used to process the contents of video samples. First the film is reviewed 

on a high-resolution monitor perhaps using a player/recorder equipped with an editing box or 

computer software that allows frame-by-frame scrolling. Video frames containing good images 

of each quadrat can then be selected and frozen on the monitor or digitized from film using a 

computer equipped with a video capture card. Digital photographs taken with still or video 

cameras eliminate the need to use a capture card to digitize film. Captured digital images can be 
Final Study Report – Murray et al. 

148

labeled, stored on disks or other media in various formats (e.g., as TIFF files), until analyzed. 

Rivas (1997) describes a procedure where video frames were captured and stored as TIFF files, 

and then opened in Adobe Photoshop where TIFF images were framed and enhanced, if 

necessary. Images were then transferred to NIH Image, an image-analysis program that can be 

downloaded from the NIH web site (http://rsb.info.nih.gov/nih-image). Rivas then employed a 

custom-designed macro program, embedded in NIH Image, to display a prescribed number of 

randomly dispersed points over the image surface. The points generated by the macro were used 

to determine percent cover of filmed species using the point-contact procedures described 

previously. In lieu of using NIH Image or a comparable image-analysis program, a sheet of clear 

acetate containing a point grid can be superimposed on the high-resolution monitor or the 

computer screen to process the video samples. Either field notes or close-up video of plot 

sections can be used to facilitate identification of taxa. If video close-ups of plots are available, 

these can be played back simultaneously on an adjacent monitor to identify small “difficult-tosee” species and to obtain other views of species lying beneath layered seaweed fronds. 

In addition to the above procedures, photographs or video records can be used to make area 

determinations of crustose or thick, coarse taxa by tracing perimeters with a planimeter. 

Alternatively, 35-mm film or video images can be digitized and tracings can be performed using 

computer-based image-analysis programs such as NIH Image. However, planimeter or digitalbased estimates of occupied areas are really only feasible for larger, coarsely branched seaweeds 

or crustose algae and animals because of difficulties in accurately tracing finely-branched or 

small, irregularly-shaped forms. 

Summary 

Abundance data are routinely collected to describe the status and dynamics of rocky intertidal 

populations and communities and, therefore, form the foundation of most rocky intertidal 

sampling programs, including monitoring and impact studies. How to collect abundance data 

becomes an important sampling consideration, and, as with decisions on sampling design and 

sampling units (see Chapters 4, 5), the selected procedures must be carefully matched with the 

goals of the sampling program. 

Qualitative indications of species abundances can be made using arbitrary categories or 

numerical scales during quick surveys, but these data will be of limited comparative value, 

particularly in time-series monitoring programs, because of difficulties in standardizing observer 

estimates. Point sampling along transect lines is a relatively quick method for estimating cover in 

rapid survey work, provides better precision by reducing subjectivity, and should be preferable to 

strictly qualitative procedures for most purposes. Although other plotless procedures besides line 

and point techniques are available, these are used less often than plot-based methods in most 

rocky intertidal studies.
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Abundance data are usually collected in the field by counting individual organisms or by 

estimating percent cover visually or through the use of point contact methods. Usually, these data 

can be accurately obtained using nondestructive sampling procedures, except in certain highly 

layered communities such as mussel beds. Density data can be obtained only for species with 

discreet individuals, and cannot be consistently collected for most seaweeds and many colonial 

invertebrates. For these species, and also for abundant, sessile invertebrates such as barnacles, 

percent cover is commonly used to express abundance in terms of space occupancy. Cover 

values for mobile invertebrates, most of which occur in much lower densities than barnacles, 

have little ecological meaning and are difficult to interpret. Because of the inability to count most 

seaweeds and the ecological meaning of cover values for mobile invertebrates, most community 

level studies do not rely on one abundance parameter but instead rely on cover data for seaweeds 

(and often sessile invertebrates) and density data for mobile invertebrates. 

Edge effects present problems in plot-based sampling and can become an important source of 

error when estimating species abundances. This problem can be enhanced by observer parallax 

and requires that efforts are made to reduce bias during the quantification of plot contents. 

Layering at larger (e.g., algal canopies) and smaller (e.g., epibiota) scales also present significant 

sampling problems and generally result in >100% plot cover, particularly in seaweed-dominated 

intertidal communities and mussel beds. 

Field data collection provides the best opportunity for recording the presence of species in 

sampling units and also for quantifying the abundances of “difficult to see”, morphologically 

similar, and rare taxa. Visual cover estimates collected by an experienced observer should result 

in an accurate inventory of plot contents and can be completed rapidly. However, visual cover 

estimates are often less accurate and are less repeatable than more objective point-contact 

methods; visual estimates also have unknown sampling errors that are largely the property of the 

taxonomic and visual abilities of the observer. For these reasons, visual methods should not be 

used in long-term monitoring programs where multiple observers collect data at one or more 

sites over a lengthy time span. Grided plots, where cover estimates are derived from the presence 

or absence of species within grid units, might be satisfactory for sampling abundant species but 

generally are not recommended where the goal is to determine statistical changes in species 

cover. Point contact procedures have long been used in sampling terrestrial vegetation and also 

have been widely used in rocky intertidal sampling programs. Point-based procedures are easy to 

apply and become more accurate with increasing point densities meaning that an investigator can 

adjust the number of points to obtain the desired margin of sampling error. Point methods also 

are more repeatable and can be less tiring and time consuming than visual procedures, 

particularly where biological complexity is high. Hence, point contact approaches are preferred 

over visual cover estimates in monitoring programs or other time-series sampling studies where 

it is important to reduce sampling error and where multiple observers participate in data 

collection. 
Final Study Report – Murray et al. 

150

Photographic sampling procedures, using 35-mm, video, or digital cameras, reduce the field time 

required per sample, eliminate parallax problems, and yield permanent records that can be 

archived or inspected by other investigators. These are valuable attributes for long-term 

monitoring programs. However, the ability to count individuals, to discriminate among 

morphologically similar species, and to resolve “difficult-to-see” taxa present significant 

disadvantages, particularly in highly layered intertidal communities. Methods for extracting data 

from photographic samples in the laboratory are well established but generally are as time 

consuming as collection of the same data in the field. However, laboratory analyses can be 

completed over a much longer time schedule, under comfortable conditions, and at the 

convenience of the investigator. Photographic samples also are excellent tools for reconstructing 

time series changes and, therefore, are valuable components of any long-term intertidal 

monitoring program, either for data collection or for providing archivable visual records of 

sample contents. 

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Chapter 7. 

Quantifying Abundance: Biomass 

By 

Steven N. Murray 

 Crystal Cove State Park, California 
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Introduction 

Abundances of rocky intertidal organisms are generally expressed as numerical density or counts 

and as cover. Occasionally, however, the goals of a sampling program might require that the 

biomass of rocky intertidal organisms be determined and used to express abundance. Biomass is 

defined as the mass of living organisms in a population at the time of sampling (Poole 1974). 

Biomass data usually are expressed as wet, dry, or ash-free dry weight per unit area, but also can 

be converted to calories, carbon, or other units. Generally, these conversions are made using 

mathematical relationships between biomass and the metric (e.g., calories) of interest. Previous 

discussions of procedures for sampling for biomass can be found in Gonor and Kemp (1978), 

Kanter (1978), Littler (1980), and DeWreede (1985). Brinkhuis (1985) also offers particularly 

good advice on how to treat algal samples during weight determination. 

Biomass data represent the standing stock or the quantity of living material obtained at the time 

of sampling. Unlike density determinations, which require the ability of the investigators to 

distinguish individuals, biomass can be measured for all seaweeds and invertebrates. Collecting 

biomass data usually requires destructive sampling because organisms generally are removed 

from the habitat and returned to the laboratory to be weighed. Although as a rule sampling for 

biomass is destructive, the collected data can be of great value. For example, biomass data can be 

used as the common metric for reporting the abundances of all populations in a rocky intertidal 

community. As discussed in Chapter 6, it is often impossible to distinguish discreet individuals 

when sampling most intertidal seaweeds and invertebrates such as sponges and colonial 

ascidians. Since investigators are generally unable to make counts of these populations, cover 

data are usually obtained to express the abundances of seaweeds and colonial invertebrates. In 

contrast, density, not cover, is the preferred metric for quantifying the abundances of mobile 

invertebrates. Consequently, biomass data can be used to express the abundances of all seaweeds 

and invertebrates in a community. This allows all sampled macroorganisms to contribute to 

community-level analyses dependent on diversity indices or multivariate methods based on 

similarity matrices. 

Compared with cover estimates, biomass data will generally better reflect the true abundances of 

most macrophytes and certain invertebrates in rocky intertidal communities. This is because 

cover is a two-dimensional (area-based) parameter that has limited ability to capture the quantity 

of plant or animal material that during high tide extends up from the substratum. Hence, biomass 

data generally best enable estimates to be made of resource availability between trophic levels. 

Biomass data (g m-2) also can be used alone (e.g., Bellamy et al. 1973) or together with biomassbased measurements of photosynthesis (e.g., Littler and Murray 1974, Littler et al. 1979) to 

calculate the contributions of seaweed and seagrass populations to the community primary 

productivity. If productivity values are available, biomass data also can be used to calculate 
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Production-to-biomass ratios for a population or community. Biomass sampling can also increase 

the information obtained in biodiversity studies because inconspicuous species that might be 

difficult to see in the field can be encountered and inventoried during laboratory sorting. As a 

result, destructive biomass sampling usually results in more species determinations (and higher 

estimates of biodiversity) than nondestructive field sampling programs. 

Using biomass data to estimate abundances of intertidal organisms also has several 

disadvantages (Gonor and Kemp 1978, DeWreede 1985). First, biomass sampling usually 

disturbs the study site because organisms almost always must be removed from the substratum 

and returned to the laboratory to be weighed. The destructive collection of biomass samples can 

affect future work, particularly in monitoring or other research programs that require repeated 

assessments of large, long-lived species with limited recruitment (Gonor and Kemp 1978). 

Although often difficult to detect, changes in the densities of opportunistic algae or mobile 

herbivores and predators following biomass harvesting can significantly influence community 

composition in areas adjacent to cleared plots. Hence, when repeated assessments of biomass are 

planned, the study area must be large enough to avoid reharvesting the same plots, and newly 

harvested sites must be spread at distances great enough to avoid the effects of prior sampling. 

These issues must be given careful consideration when designing long-term monitoring 

programs since there are no guidelines for arriving at “safe” distances between plot distances. 

Moreover, if the study area must be expanded to accommodate the demands of destructive 

sampling, then statistical comparisons of the collected data might be compromised by the 

environmental differences likely to occur as samples are distributed over more intertidal habitat 

(DeWreede 1985). 

Besides altering community composition in the harvested plots, biomass determinations usually 

are very time consuming and costly due to the need for extensive laboratory processing. For 

example, a single 0.3 m x 0.5 m sample harvested in a dense, heavily epiphytized coralline algal 

turf can take 40 or more hours of laboratory work to sort seaweeds and invertebrates to species 

and perform wet and dry weight determinations. For this reason alone, biomass sampling is not 

suitable for low-cost sampling programs or survey work involving multiple sites. 

Because of the destructive nature and high cost, biomass-sampling programs should be carefully 

planned and designed (Fig. 7-1). Careful consideration must be given to site selection (Chapter 

2) and in choosing the specific area within the site to be delineated for study. Biomass estimates 

must be normalized by area for use as abundance data requiring that plots or quadrats be used as 

sampling units. After selecting the plot size and shape, a strategy must be developed for locating 

samples within the study area. Considerations for distributing samples and for selecting plot sizes 

and numbers have been discussed by DeWreede (1985) and are addressed in Chapters 4 and 5. 

Gonor and Kemp (1978) suggest that information should be obtained on the composition of each 

plot prior to extracting organisms. 
Final Study Report – Murray et al. 

158

Fig. 7-1. Decision-tree for destructive biomass sampling. 

This can be done by taking 35-mm or digital photographs, making video records, or taking notes 

that describe species cover, and by counting individuals and measuring a selected morphometric 

parameter to obtain size (e.g., maximum shell length). Complete nondestructive sampling for 

density or cover (see Chapter 6) can be performed prior to removing organisms for biomass 

determination. If cover or density and size data have been taken prior to biomass determination, 

then biomass can be estimated from these data when implementing future nondestructive 

sampling programs. This can be accomplished, for example, by establishing mathematical 

relationships using the pairs of cover and biomass data gathered for each species from the 

harvested plots. However, such relationships require assumptions (e.g., minimal spatial and 
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temporal variation) and should be used with caution. Strongest mathematical relationships should 

occur between cover and biomass for seaweed species with small fronds that generally do not 

show layering or extensive vertical growth and for largely two-dimensional invertebrates such as 

barnacles and sponges. For canopy-forming seaweeds, best cover-biomass relationships should 

be achieved when the cover exceeds 5-10% but is less than 80-90%. This is because a larger, 

nondestructive, sampling error is expected when cover is low or approaches 100% when fronds 

are layered and lie on top of one another. Littler (1979a,b) reported significant geometric mean 

regressions for wet and dry weight as a function of percent cover and the ratios of ash-free to dry 

biomass for most of the common southern California intertidal seaweeds and many 

macroinvertebrates. Density data alone are much less likely to show significant mathematical 

relationships with biomass because of strong spatial and temporal variation in population size 

structures. Therefore, measurements of morphological features correlated with body size also 

should be taken and used together with density data to estimate biomass. Good mathematical 

relationships should exist between size-related morphometric parameters and biomass for 

barnacles, mussels, limpets, turban snails, anemones, sea stars, and urchins. 

Harvesting Procedures 

Because biomass data are obtained from plots, the problems discussed in Chapter 6 concerning 

parallax and the determination of plot boundaries also apply during harvesting. As described 

previously, rules regarding the fixing of boundaries and the handling of organisms positioned on 

plot borders must be established a-priori to avoid a potentially important source of sampling 

error (Fig. 7-2). Similar to density determinations, only those sessile organisms and seaweed 

thalli attached within plot boundaries should be harvested to ensure that quantification reflects 

the amount of biomass anchored to the prescribed area of substratum. This means that fronds of 

larger seaweeds that lay over the surface of a plot should not be harvested unless the holdfast is 

determined to lie within plot boundaries. For mobile invertebrates, determinations of whether to 

harvest an organism should follow the same rules as those described for obtaining density data. 

In mussel beds, or at times in layered, foliose algal communities, care must be taken to retain 

crabs and other mobile invertebrates that can move out of plots during sample collection. When 

necessary, vertical sides made of metal or wood with a flexible material such as foam neoprene 

or foam plastic can be affixed to quadrat frames and pressed down onto the substratum to prevent 

mobile animals from leaving plots during harvesting (Gonor and Kemp 1978). Gonor and Kemp 

(1978) have suggested using a chemical agent such as ethylene chloride, diethyl ether, alcohol, 

acetone, or a mixture of either alcohol or acetone and dry ice, in conjunction with such frames to 

kill or narcotize mobile animals. Investigators also have used hot formalin seawater (Glynn 

1965) for this purpose. However, formalin poses obvious safety hazards and killing effects can 

easily spread beyond the intended area. Other chemicals designed to improve the collection of 

mobile organisms should be fully assessed for these considerations prior to their use. 
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Fig. 7-2. Procedure for harvesting large seaweeds and macroinvertebrates from field plots. 

For sessile animals and seaweeds, only individuals attached within plot boundaries should be 

removed for most applications. For mobile animals, location at the time of sampling should 

determine whether or not an individual is in or outside plot boundaries. Rules for including 

organisms within plots should be established prior to field sampling. For example, if it is 

decided a-priori that organisms will be harvested when 50% or more of the individual is 

determined to occur within plot boundaries, then seaweeds i and ii should be harvested but iii 

should not. The holdfast for seaweed i is located entirely inside the plot whereas the holdfast 

for seaweed iii is located entirely outside plot boundaries. Seaweed ii is harvested because 

more than 50% of the holdfast is within the plot. In contrast, if harvesting rules include all 

organisms touching or occurring within the boundaries of two (upper and right) of the four 

sides of a rectangular or square plot, then sea stars a and b should be harvested but c should 

not. Sea stars a and b are located on the border of the two sides designated for inclusion 

whereas sea star c is located on the border of a non-designated plot edge. 
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Because seaweeds and sessile animals are attached to the substratum, these organisms usually 

must be removed using a flattened scraping tool such as a diving knife, a “putty” knife, or even a 

standard kitchen knife (Fig. 7-3). The swiftly executed placement of a flexible, thin-bladed butter 

knife is usually effective for removing limpets, chitons, and other invertebrates that hold fast to 

the substratum. Organisms should be placed in labeled bags or containers immediately following 

their removal from plots. If making biomass determinations on most or all species, harvested 

individuals should be quickly presorted in the field using separate plastic bags for each species or 

species group (Fig. 7-4). Although difficult to use in the subtidal, inexpensive plastic bags are 

generally more efficient than buckets, cloth bags, nylon nets, or other containers for collecting 

harvested seaweeds and invertebrates, because bags for individual species can be placed into 

larger bags that contain the contents of specific plots. Also, plastic bags facilitate transportation 

to the laboratory and storage. However, if specimens are to be analyzed for chemical constituents 

(e. g., petroleum hydrocarbons or trace metals), or used for other purposes, the choice of 

harvesting tools and procedures and the composition of storage containers — bags, vials, jars, or 

other vessels — should be carefully selected to avoid contamination. 

A strong disadvantage of destructive sampling programs is that harvested material usually must 

be stored prior to final laboratory sorting and weighing, which requires some form of sample 

preservation. For biomass determination, preservation can be accomplished using chemical 

preservatives such as formalin (commercial formalin = 37% Formaldehyde) buffered with 2 to 3 

tablespoons (ca. 0.06 L) of borax per 3.8 L formalin is an excellent preservative but requires 

caution: the use of gloves and eye protection when preserving and handling material, fume hoods 

when sorting or drying samples, and controlled disposal of both liquid and solid wastes. Also, 

personnel should be educated in how to handle spills. Generally, investigators use a 5-10% 

formalin-seawater solution (commercial formalin treated as 100%) for invertebrates (Smith and 

Canton 1975) and a 3-5% solution for seaweeds (Tsuda and Abbott 1985). Seaweeds stay well 

preserved in formalin-seawater and can be held for long periods without losing color if stored in 

the dark. Transferring invertebrate specimens to alcohol (70-95%) is preferred for longer storage, 

particularly if retaining specimens as vouchers. It might be necessary to first anesthetize delicate, 

soft-bodied invertebrates or shelled gastropods with tightly closing opercula in magnesium 

chloride (73 g MgCl2 • 6 H2O per L of tap water) to prevent contraction and ensure complete 

fixation (Gonor and Kemp 1978). 

A viable alternative to the use of chemical preservatives is to freeze algal and invertebrate 

samples until laboratory processing. Most seaweed thalli and invertebrates respond reasonably 

well to freezing when the aim is biomass determination, although freezing often negates the use 

of specimens for detailed taxonomic study or for retention as voucher specimens. Weights of 

frozen and then thawed specimens, however, will differ from fresh wet weights, particularly for 

seaweeds or animals whose thalli or bodies begin to show structural breakdowns when defrosted. 
Final Study Report – Murray et al. 

162

Fig. 7-4. Field sorting of the contents of harvested plots. Harvested species are 

bagged separately where possible to facilitate laboratory sorting and reduce 

laboratory processing time. 

Fig. 7-3. Field 

harvesting of plot 

contents. Species are 

scraped from the 

substratum using a 

knife or other 

flat-bladed tool.
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Because of its simplicity and the ability to avoid using and working with chemical preservatives, 

freezing is probably the method of choice for most destructive sampling programs if harvested 

organisms can be returned from the field prior to undergoing spoilage and breakdown. Freezing 

also generally maintains specimens in a condition suitable for later chemical analyses while 

chemical preservation usually compromises their use for these purposes. Hence, if harvested 

organisms are to be analyzed for chemical constituents, specimens should probably be frozen and 

stored in laboratory freezers prior to analysis. 

Biomass Determination 

Wet Biomass 

Following the laboratory sorting of harvested material to the desired level of taxonomic 

discrimination, weights must be determined to obtain biomass data. Ideally, wet weight is the 

mass of a fully hydrated organism after removing all superficial water adhering to its surfaces or 

contained inside or between shells, plates, or other structures. Conceptually, wet weights of 

organisms are simple to determine and require the least processing time. However, because of 

difficulties in standardizing the degree of hydration and removal of superficial water, wet 

weights present the greatest potential for measurement error. Consequently, wet weight is usually 

not recommended for expressing biomass of invertebrates or seaweeds (Gonor and Kemp 1978, 

Brinkhuis 1985, DeWreede 1985). 

For calcareous seaweeds and most invertebrates, wet weights taken of the whole organism will 

be strongly affected by the weights of calcified walls or tubes, plates, tests, or shells. Moreover, 

wet weights can yield values of little ecological importance for organisms like anemones, where 

water retention can vary greatly under different conditions, or species that characteristically have 

very high water contents and very little usable organic material (Gonor and Kemp 1978). 

Animals can be removed from their shells, tubes, or plates prior to weight determinations to 

exclude external inorganic hard parts that make little, if any, energetic contribution to higher 

trophic levels. Dissection might be required to separate the soft body parts of many species; for 

some invertebrates, removal from external shells, tubes, or plates can be facilitated by first 

relaxing animals in a magnesium chloride solution. In some species, placing animals in an acidic 

dilute formalin solution [(15 mL concentrated glacial acetic acid, 15 mL diluted acetic acid 

(= commercial vinegar), and 10 mL 10% formalin-seawater)] for several days also can slowly 

dissolve calcified shells. For calcareous seaweeds, Brinkhuis (1985) suggests dissolving CaCO3 

walls of seaweeds by applying HCl (5-10% v/v) or by holding specimens in a saturated solution 

of EDTA (e.g., Na2 • EDTA = disodium salt of Ethylenediaminetetraacetic acid), kept fresh by 

daily replacement, to remove CaCO3 by chelation. 
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Weight-contributing epibiota and sediments must be removed prior to weight determination and 

frozen specimens must be treated carefully during thawing to reduce loss of slimy secretions. 

Preserved samples are usually rinsed with tap water to reduce fumes and remove excess formalin 

or alcohol before sorting. For some species, significant weight changes can occur during storage 

in formalin or alcohol, so attempts should be made to process samples within a standardized 

period to reduce sample-to-sample variation resulting from the effects of preservatives. It is 

particularly difficult to obtain accurate wet weights of shelled gastropods that can hold unknown 

amounts of water inside their shells, and organisms such as barnacles that are difficult to remove 

from rocks without losing organic material during collection, storage, or sorting. After ensuring 

that tissues are fully hydrated and have not desiccated, organisms are blotted to remove surface 

water and weighed, usually to no more than ± 0.1 g on a top-loading balance. When laboratory 

sorting takes a long time, samples can be occasionally sprayed with seawater mist or kept moist 

with wet paper towels to ensure that tissues are hydrated prior to blotting. If necessary, larger 

organisms can be rehydrated by submersing them directly in seawater for a few minutes. 

Different techniques have been used to remove the exterior film of surface water from seaweeds, 

including twirling specimens in mesh bags (Brinkhuis 1985) or in salad spinners. However, 

repetitive hand blotting with paper towels until no water appears to be transferred to the paper is 

probably the simplest technique for removing excess surface water from most specimens. 

Dry Biomass 

Dry biomass is the weight of tissue remaining after removing all water (Brinkhuis 1985, 

DeWreede 1985). To obtain dry weights, samples should be cleaned of sediments and epibiota, 

rinsed quickly in tap water to remove sea salts, placed in preweighed (tared) labeled weighing 

containers, and put into a drying oven where they are held at a specified temperature until 

constant weight is achieved. Depending on the purpose of the study, walls, tubes, plates, tests, or 

shells made of inorganic material can be removed prior to drying calcareous seaweeds and 

invertebrates as described previously. Aluminum weighing boats available commercially make 

good weighing containers. Where samples are too large to fit into standard weighing boats, 

aluminum foil can be molded around beakers or other objects to make custom-sized weighing 

containers. Drying can be achieved by heating samples to drive off water or by lyophilization 

(= freeze drying). The latter procedure is more time consuming than oven drying and prevents 

significant changes in chemical constituents of specimens during the drying process (Brinkhuis 

1985). However, for most applications, drying specimens in a drying oven is recommended. 

Complete sample dryness is difficult to define although the goal is to dry the sample to constant 

weight under the conditions employed. The procedures and temperatures used vary greatly 
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among investigators and must be clearly specified. Brinkhuis (1985) reports the use of drying 

temperatures ranging from around 20°C to greater than 110°C to achieve dry biomass values for 

seaweeds. Low drying temperatures often are employed when large amounts of material are 

dried in the open air; however, Brinkhuis (1985) recommends against air drying samples because 

of difficulties in repeating temperature, humidity, and other conditions that affect dry weight. 

Gonor and Kemp (1978) have recommended using temperatures of 70°C for drying samples of 

intertidal organisms, but the most commonly used drying temperature is probably 60°C. This 

temperature is conveniently achieved in a variety of drying chambers, including hand-made 

containers that rely on heating from light bulbs. Drying temperatures of 100°C to 110°C will 

accelerate the drying process and are commonly used for obtaining dry weights of terrestrial 

plants. Although drying at 100°C to 110°C drives off all water (except for bound water and water 

of crystallization), samples also undergo chemical changes and lose volatile compounds (Brower 

et al. 1998). Hence, if dried samples are to be analyzed for chemical constituents, drying 

temperatures should not exceed 60°C (Brinkhuis 1985). Regardless of the method used, samples 

should be dried long enough to obtain constant weight and drying and weighing methods should 

be fully reported. 

Brinkhuis (1985) notes that dry seaweeds, and probably other marine specimens, are very 

hygroscopic and quickly absorb water (and weight) from surrounding air humidity and even 

desiccant. Consequently, samples should be transferred to desiccators charged with fresh 

desiccant immediately after their removal from drying ovens to protect against weight changes 

resulting from the absorption of water vapor. After cooling to room temperature under desiccant, 

samples should be weighed to ± 0.001 g using a precision balance. A small beaker with fresh 

desiccant can be stored in the corner of the weighing chamber to obtain stable weights by 

preventing specimens from absorbing water vapor during the weighing process. 

Ash-Free Dry Biomass 

Dried organisms also can be ashed to determine ash-free dry biomass or organic dry biomass. 

Ash-free dry weight is the dry weight of organic material in the absence of inorganic materials 

and is obtained by subtracting the weight of ash (inorganic material) from the dry weight of the 

sample (Brinkhuis 1985). Intertidal invertebrates and seaweeds have different body compositions 

and will retain different concentrations of inorganic salts and minerals in their soft tissues after 

drying, even after the removal of shells, plates, tubes or other inorganic structures. Biomass data 

are perhaps best expressed as organic or ash-free dry biomass per unit area because these data 

provide a common (organic matter only) basis for describing the standing stocks of all 

macrophyte and macroinvertebrate populations. However, this means that additional work will 

be required to determine the contribution of inorganic ash to the dry weight of each sample. 
Final Study Report – Murray et al. 

166

Ash weights of specimens are obtained by combusting known dry weights of samples in a muffle 

furnace, usually at 500°C to 550°C, for at least three to four but usually as long as six or more 

hours to determine inorganic ash content (Brinkhuis 1985). The specific time needed to oxidize 

all organic material will vary depending on the temperature and the type and amount of the 

sample and should be worked out. This is done by re-ashing and re-weighing samples until stable 

ash weights are obtained. Ashing should be considered incomplete if black charcoal deposits 

remain in samples (Brower et al. 1998). Oven temperatures should not exceed 550°C to prevent 

volatilization of sodium and potassium and carbonate combustion (Brinkhuis 1985, Brower et al. 

1998). 

Fig. 7-5. Glass weighing jars and ceramic crucibles containing dried algal powder loaded on the 

shelf of a muffle furnace prior to ashing. 

If shells, plates, tubes, or other inorganic structures are present, these should not be placed in the 

muffle furnace but should be carefully removed as described previously, scraped to remove 

organic residues, and dried and weighed separately. Aliquots (0.5 g to 2-4 g) of dried seaweed or 

invertebrate material should then be broken into small pieces, or preferably ground to a powder 

in a grinding mill, and placed uniformly over the bottom of acid-cleaned and preweighed 

ceramic crucibles or small, glass weighing jars (Fig. 7-5). The dried material or powder should 

be weighed together with the crucible or jar to at least 0.0001 g using a precision balance noting 

the weighing precautions described previously. Brinkhuis (1985) notes that crucibles or jars 

should not be placed directly into a hot furnace but should be added when temperatures are less 

than 200°C to avoid rapid ignition and the loss of inorganic material. Combustion time should 
 Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 

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begin when the furnace has reached the designated temperature. Samples should then be 

removed from the furnace using tongs, carefully placed in a desiccator to cool, and weighed. 

Summary 

Clearly, biomass methods of measuring abundance require more laboratory and field time and 

carry more costs for supplies and materials than nondestructive methods. Biomass data better 

characterize trophic resource availability than density or cover data and provide a uniform, 

comparable means of expressing the abundances of both seaweeds and invertebrates. However, 

biomass determination usually requires that organisms be harvested resulting in the need to 

disturb the study site during sampling. It is difficult to envision a case where destructive biomass 

sampling would be preferred for studies of small, ecologically-sensitive habitats or for 

performing long-term monitoring programs that require repeated assessments of the same study 

site. If biomass data are required, costs can be reduced and habitat damage lessened by 

subsampling species of interest to establish relationships between nondestructive sampling 

parameters such as cover or size plus density and biomass. Similarly, relationships can be 

established for each species and used to calculate dry from wet weight or ash from dry weight to 

save time and money. However, caution should be exercised in using such mathematical 

functions because of spatial and temporal variations in the established relationships. Because 

biomass sampling is costly and usually results in habitat disturbance, the investigator should 

ensure that biomass data are required before initiating a destructive, biomass sampling program. 

Consequently, destructive sampling for biomass should be carried out only when necessary to 

achieve the goals of the study and when nondestructive procedures cannot provide the required 

information. 

Literature Cited 

Bellamy, D. J., A. Whittick, D. M. John, and D. J. Jones. 1973. A method for the determination 

of seaweed production based on biomass estimates. Pages 27-33 in A guide to the 

measurement of primary production under some special conditions. UNESCO, Paris, 

France. 

Brinkhuis, B. H. 1985. Growth patterns and rates. Pages 461-477 in M. M. Littler and D. S. 

Littler, editors. Handbook of phycological methods. Ecological field methods: 

macroalgae. Cambridge University Press, Cambridge, UK. 

Brower, J. E., J. H. Zar, and C. N. von Ende. 1998. Field and laboratory methods for general 

ecology, fourth edition. WCB/McGraw-Hill, Boston, Massachusetts, USA. 
Final Study Report – Murray et al. 

168

DeWreede, R. E. 1985. Destructive (harvest) sampling. Pages 147-160 in M. M. Littler and D. S. 

Littler, editors. Handbook of phycological methods. Ecological field methods: 

macroalgae. Cambridge University Press, Cambridge, UK. 

Glynn, P. W. 1965. Community composition, structure, and interrelationships in the marine 

intertidal Endocladia muricata - Balanus glandula association in Monterey Bay, 

California. Beaufortia 12: 1-198. 

Gonor, J. J. and P. F. Kemp. 1978. Procedures for quantitative ecological assessments in 

intertidal environments. U.S. Environmental Protection Agency Report. EPA-600/3-78-

087. 

Kanter, R. 1978. Mussel communities. Report 1.2, Volume III. Intertidal study of the Southern 

California Bight. Bureau of Land Management, U.S. Department of the Interior, 

Washington, D.C., USA. 

Littler, M. M. 1979a. Geometric mean regression, product moment correlation coefficient 

equations for wet and dry weight as a function of per cent cover for biota throughout the 

Southern California Bight during 1975-78. Volume IV. Appendix B. Pages 1-23 in M. M. 

Littler, editor. The distribution, abundance and community structure of rocky intertidal 

and tidepool biotas in the Southern California Bight. Southern California Bight Baseline 

Study. Intertidal, Year three. Bureau of Land Management, U.S. Department of the 

Interior, Washington DC, USA. 

Littler, M. M. 1979b. Mean ratio of ash-free to dry biomass for dominant macrophytes and 

macroinvertebrates with high ash content at sites sampled utilizing the disturbed method 

in 1977-78. Volume IV. Appendix C. Pages 1-5 in M. M. Littler, editor. The distribution, 

abundance and community structure of rocky intertidal and tidepool biotas in the 

Southern California Bight. Southern California Bight Baseline Study. Intertidal, Year 

three. Bureau of Land Management, U.S. Department of the Interior, Washington, D.C., 

USA. 

Littler, M. M. 1980. Southern California rocky intertidal ecosystems: methods, community 

structure and variability. Pages 565-608 in J. H. Price, D. E. G. Irvine, and W. F. 

Farnham, editors. The shore environment. Volume 2: Ecosystems. Academic Press, 

London, UK. 

Littler, M. M. and S. N. Murray. 1974. The primary productivity of marine macrophytes from a 

rocky intertidal community. Mar. Biol. 27: 131-135. 
 Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 

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Littler, M. M., K. E. Arnold, and S. N. Murray. 1979. Seasonal variations in net photosynthetic 

performance and cover of rocky intertidal macrophytes. Aquat. Bot. 7: 35-46. 

Poole, R. W. 1974. An introduction to quantitative ecology. McGraw-Hill, New York, USA. 

Smith, R. I. and J. T. Carlton, editors. 1975. Light’s manual: intertidal invertebrates of the central 

California coast, third edition. University of California Press, Berkeley, USA. 

Tsuda, R. T. and I. A. Abbott. 1985. Collection, handling, preservation, and logistics. Pages 67-

86 in M. M. Littler, and D. S. Littler, editors. Handbook of phycological methods. 

Ecological field methods: macroalgae. Cambridge University Press, Cambridge, UK. 
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Chapter 8. 

Individual-Based Parameters: Age-Determination, 

Growth Rates, Size Structure, and Reproduction 

By 

Steven N. Murray 

 Outer northwest coast, San Clemente Island, California circa 1972
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Introduction 

Most rocky intertidal monitoring and impact studies are designed to determine the status of 

sampled populations solely in terms of abundance. This approach can present two major 

problems. First, abundance data alone do not adequately describe a population in a way that 

depicts its dynamics. Population density is a result of what Chapman (1985) has referred to as 

primary and secondary population parameters. Primary population parameters include natality, 

mortality, immigration, and emigration. Secondary population parameters, such as size and age 

class distribution and sex ratios, are end products of population dynamics, but also provide a 

sharper picture of existing structure compared with density data alone. Data on primary and 

secondary population parameters offer a measure of population status superior to abundance data 

and provide the information required to compare population growth and structure among sites or 

over time. Moreover, data on primary and secondary population parameters provide the basis for 

developing models predicting the future status of populations, including the time-course for 

recovery following an oil spill or other catastrophic event. A second problem involves the high 

“noise to signal” ratio because of the usual high variation obtained when sampling for abundance 

data or other population-based parameters. In contrast, individual-based parameters, such as size, 

growth rate, and gonadal production, yield greater statistical power because of lower variability 

and greater effect size (Osenberg et al. 1996). 

The value of primary and secondary population parameters underscore the importance of 

extending studies beyond the determination of abundance if the goal is to compare the status of 

populations over spatial or temporal scales. However, studies of primary parameters include 

assessments of population additions from natality and immigration (in animals) and subtractions 

from mortality and emigration (in animals). Because most benthic intertidal animals are either 

sessile or have low mobility, emigration and immigration often are of little importance and can 

be ignored. Natality and mortality measurements, however, are difficult and costly to make 

because most rocky intertidal organisms have small planktonic larvae or spores that are 

transported over scales ranging from meters to tens of kilometers. Usually new individuals are 

first identified as entering a rocky intertidal population when they settle onto benthic substrata 

and their appearance is usually used as a substitute for natality in demographic studies. 

Unfortunately even studies designed to determine recruitment or mortality rates of early benthic 

recruits are difficult to perform. Moreover, the best means of measuring mortality in most rocky 

intertidal populations is through the long-term monitoring of marked individuals. Thus, despite 

their importance, demographic studies dependent on primary population parameters are almost 

never incorporated into monitoring programs or environmental impact studies of rocky intertidal 

populations. 
Final Study Report – Murray et al. 

172

Studies of secondary characteristics, such as size or age class distribution and reproductive 

condition, provide more complete ecological comparisons of population status than those where 

only abundance data are collected, and usually are simpler to perform than recruitment and 

mortality studies. Unfortunately, data describing secondary population parameters are seldom 

collected and little is known about individual-based parameters such as age, size, or reproductive 

output for most rocky intertidal populations. The purpose of this chapter is to describe and 

discuss selected approaches for measuring secondary population parameters in rocky intertidal 

organisms (Fig. 8-1). Emphasis has been placed on procedures used to determine age and size 

class distributions, growth rates, sex or phase ratios, and reproductive condition in seaweeds and 

benthic invertebrates. 

Fig. 8-1. Basic approaches for studying secondary population parameters in rocky intertidal 

macrophytes and macroinvertebrates. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 173

Seaweeds 

Growth Rates and Age Determination 

We know very little about the maximum ages of individual thalli or the age structure of most 

seaweed populations (Chapman 1985, 1986). In many invertebrates, growth continues over time 

in a predictable allometric pattern and, by knowing the rate of growth, the size of certain 

anatomical features can be used to estimate age. In seaweeds and surfgrasses, however, overall 

growth patterns rarely proceed exclusively along single, definable axes, and few species exhibit 

morphological features that consistently coincide with thallus age. Instead, most seaweeds have 

highly plastic morphologies shaped by the initiation, growth, and development of multiple 

modular units consisting of primary and secondary axes. In many species, the irregular 

production of adventitious and secondary lateral branches also can increase “bushiness” and 

modify thallus appearance. In addition, seaweed morphologies can vary with exposure to light, 

wave action, herbivory, or any other parameter that affects axis growth rates and longevity and, 

therefore, thallus size and shape. 

Growth Rates. Seaweed growth rates can be determined in the field or in the laboratory where 

plants can be held in culture. The various methods for measuring seaweed growth rates have 

been thoroughly reviewed by Brinkhuis (1985) and will only be discussed briefly here. The most 

commonly employed approaches involve measurements of changes in seaweed length, weight, or 

area. Procedures for making wet weight determinations of seaweeds are discussed in Chapter 7. 

As pointed out by Brinkhuis, weighing individual seaweeds in the field presents problems unless 

thalli can be detached, weighed, and re-attached such as when plants are clipped to pipes, ropes, 

or nets and grown in field pens or aquaculture tanks. Consequently, most field measurements of 

seaweed growth are made from length or area measurements and must be made without 

detaching plants using non-destructive methods. Generally, this is done by repetitively 

photographing seaweed axes or whole thalli with a ruler or other item of known dimensions for 

use as a scale. Measurements are then made on photographic records in the laboratory with 

rulers, calipers, planimeters, or image analysis software (see Chapter 6 for discussions of 

photography and computer processing of images). 

Because growth of most seaweeds is “plastic” and can proceed in multiple planes, the best 

candidates for in-situ growth studies are highly differentiated species that grow principally along 

identifiable axes. Examples include certain kelps, such as Laminaria spp., where the linear 

elongation of blades can be measured (e.g., Lüning 1979; Mann and Mann 1981) by following 

the migration of holes punched above the localized intercalary blade meristem (Fig. 8-2). 
Final Study Report – Murray et al. 

174

Fig. 8-2. Measuring growth in Laminaria saccharina by punching a series of small holes (< 5 

mm in diameter) at fixed distances of 10 cm along the blade. L. saccharina blades at time of 

initial hole punching (t = 0) and later (t = 1). At each measurement interval, the number of holes 

remaining, the blade length, the stipe length, and the distance from the base of the blade to the 

basipetal hole are recorded. (After procedures described by Brinkhuis ,1985.) 

Age Determination. The life spans of seaweeds and surfgrasses vary greatly among species and 

habitats. Some seaweeds, including opportunistic green algae and the summer brown annual 

Leathesia difformis (Chapman and Goudey 1983), are known to have life spans measured in 

weeks or months. In other species, e.g., the kelps Laminaria saccharina (Parke 1948) and 

Pelagophycus porra (Coyer and Zaugg-Haglund 1982), very few individuals survive for more 

than two years. Life spans of 2.5 to more than 8 years have been described for Atlantic (Pelvetia 

canaliculata and Fucus spp.) and Pacific (Silvetia compressa as Pelvetia fastigiata) rockweeds 

(Knight and Parke 1950, Subrahamnyan 1960, 1961, Niemeck and Mathieson 1976, Gunnill 

1980). Another relatively long-lived seaweed is the giant kelp Macrocystis pyrifera, where the 

life expectancy of established plants in a southern Californian population has been reported 

(Rosenthal et al. 1974) to exceed 7 years. Some species of seaweeds may have even longer life 

spans. For example, David (1943) estimated a 15-year half-life for the Atlantic fucoid 

Ascophyllum nodosum. Moreover, in certain species of red algae with well-developed 

heterotrichous basal systems individual genets may persist for decades, or maybe even 

indefinitely by periodically producing new erect axes from basal holdfasts. For instance, Dixon 

(1965) concluded that a Pterocladiella capillacea (as Pterocladia capillacea) clone was at least 

40 years old and hypothesized that one clone of Pterosiphonia complanata might be 130 years 

old. In southern California, the ages of articulated coralline algal genets that produce thick, 

intertidal turfs from well-developed heterotrichous, crustose basal systems are probably very old, 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 175

easily exceeding 10 years (Murray, personal observation). Crustose algae also may have long life 

spans under certain conditions. A case in point is the crustose red algal tetrasporophyte phase of 

Mastocarpus (Petrocelis middendorfii) where the age of an individual crust has been estimated 

(Paine et al. 1979) to be as great as 100 years. 

For most macrophytes, it is impossible to directly determine age without tagging and following 

the survivorship of marked individuals. This requires the use of non-destructive marking 

procedures, followed by the maintenance of marks or tags over the life span of each marked 

individual. Unfortunately, direct tagging is impossible for most seaweeds because of their soft, 

fleshy thalli (Chapman 1985), and the direct application of tags usually is avoided because of the 

high probability of losing both tags and injuring or losing thallus parts during the course of 

study. Hence, direct tagging mostly has been restricted to larger, tougher species such as kelps 

(Foster et al. 1985). However, even for kelps, where it is possible to non-destructively tag the 

thick and tough stipes and holdfast haptera, Foster et al. recommended using double tags — one 

on the seaweed and one affixed to the substratum immediately adjacent to the holdfast — to 

increase the likelihood of tag retention. In place of tags, larger, nonturf-forming macrophytes can 

be relocated by fixing epoxy, bolts, nails, or other reference marks into the substratum adjacent 

to their holdfasts. In addition, plant relocation can be accomplished by triangulation using 

transect tapes and two fixed reference points. Differential measurements made with Global 

Positioning Satellite instrumentation also may be useful for obtaining the approximate positions 

of scattered, conspicuous thalli in heterogeneous intertidal landscapes. 

In a very few cases, it is possible to directly determine age by performing measurements on 

collected plants. For example, in some kelps, including Laminaria spp. (Kain 1963, 1971, 

Klinger and DeWreede 1988) and Pterygophora californica (DeWreede 1984, 1986), age can be 

determined with some degree of confidence by counting annual growth lines found in the stipe. 

This procedure requires destructive sampling, however, because stipes must be sectioned to 

inspect growth rings. Non-destructive estimates of thallus age can be made for species such as 

the subtidal red seaweed Constantinea subulifera, by counting the stipe scars remaining from 

annual cycles of blade production (Powell 1986). Age estimates also can be made on field plants 

of the Atlantic fucoid, Ascophvllum nodosum, where a single air bladder forms each year on 

growing, upright axes following the first year of development (Baardseth 1968). However, this 

method is not fool proof, because, as pointed out by Cousens (1981), axes of this brown seaweed 

often are broken and the number of bladders produced can be used only to calculate a minimum 

age. 
Final Study Report – Murray et al. 

176

Population Size Structure

Instead of calendar age, a more meaningful approach for studying the population structure of 

plants is to use size or developmental stage as the incremental unit; in this procedure, individual 

plants are assigned to size or developmental categories based on a combination of quantitative 

and qualitative parameters (Hutchings 1986). Not only is this approach usually more feasible for 

terrestrial flowering plants that also are difficult to age, but it has been argued (Werner and 

Caswell 1977) that population models based on size or developmental stage are more 

informative than models based on calendar age for at least some species. As pointed out by 

Harper (1977) for forest trees, however, a consistent relationship between the size of a plant and 

its age should not be assumed and small-sized individuals can be of any age. 

Categorization by size or stage is an attractive alternative for studying population structure in 

macrophytes because, as discussed, few species have morphological or developmental 

characteristics that consistently enable age determination. Except for many of the 

morphologically complex kelps, rarely do seaweeds and surfgrasses show growth patterns that 

enable their assignment even to specific developmental stages. This means that size must be used 

to categorize individuals when performing analyses of population structure. Although 

demographic events are probably better described by size than by age in seaweeds, this has yet to 

be unequivocally demonstrated (Ang and DeWreede 1990). 

The morphologies and growth characteristics of many macrophytes can confound the 

development of size structure classifications and may dictate the use of several morphological 

parameters to obtain a meaningful system of size categorization. Models for following size 

classes over time also can be difficult to employ because unlike unitary invertebrates, seaweeds 

and surfgrasses can readily decrease in size due to axis loss or breakage. Therefore, between 

measurement periods, seaweeds can move both backwards and forwards through size-based 

categories unlike age-based categorization. For these reasons, the population structures of 

seaweeds and surfgrasses are much more difficult to study than invertebrates and information on 

size, age distribution, or other secondary population parameters exists for only a few species. 

Axis length is the most common thallus parameter used to establish size classes for demographic 

analysis of seaweed populations. The lengths of individual axes can be determined directly in the 

field for many species without destructive removal from the substratum. The best candidates for 

studies of population size structure are fucoids, kelps, and other large, conspicuous macrophytes 

where distinct individuals can be recognized and major axes easily identified and measured. For 

example, Ang et al. (1996) used maximum axis length to group plants by size class in his 

analysis of variations in the structure of populations of the economically important Atlantic 

seaweed Ascophyllum nodosum at sites with different harvesting histories. Similarly, Denis and 

Murray (unpublished data) used maximum axis length to describe changes in the structure of 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 177

Silvetia compressa (= Pelvetia compressa) populations following the application of experimental 

trampling treatments (Fig. 8-3). Like most seaweeds and surfgrasses, however, thalli of 

Ascophyllum and Silvetia have numerous axes of varying lengths. For these reasons, the length of 

the longest axis is usually recorded and used to represent thallus size and to place individual 

macrophytes into size classes. 

 

Unfortunately, maximum axis length may not always be a good correlate of size, particularly if 

size is being used to represent thallus biomass. This is particularly true for species with plastic 

morphologies where the relative lengths and numbers of major and minor axes are known to vary 

considerably among populations or over time. Populations of these kinds of seaweeds growing in 

Fig. 8-3. Effects of two levels of

trampling treatment on 

population size-structure in 

Silvetia compressa at Monarch 

Bay, California. Depicted is the 

proportion of the biomass 

obtained for each size class 

interval for all thalli harvested 

from control plots (0 steps) and 

plots receiving monthly 150, and 

300 step trampling treatments.

Size classes based on maximum 

axis length. Thalli were pooled 

from 0.5 m x 0. 7 m replicate 

plots (n = 5) for controls and for 

both trampling treatments.
Final Study Report – Murray et al. 

178

different sites, or even different habitats within a single site, will generally show much 

morphological variation and exhibit different thallus length to biomass ratios. Hence, for most 

purposes it is advisable to work out and report relationships between maximum axis length and 

biomass when comparing the structure of seaweed populations if the analysis is to represent the 

structure of the standing stock. However, a disadvantage of obtaining length to biomass data is 

that biomass determinations almost always are difficult to perform in the field (Brinkhuis 1985) 

and require destructive harvesting (see Chapter 7). 

Sex or Phase Ratios 

Most of our knowledge of spatial or temporal variation in patterns of macrophyte reproduction 

has been gained from largely qualitative phenological studies where the presence or absence of 

reproductive organs is noted during field surveys or from laboratory inspection of herbarium 

specimens. Except for obviously fertile specimens, it is usually very difficult to determine even 

the sex or phase of most seaweeds without the benefit of detailed microscopic examination. This 

is because seaweed reproductive structures are small and cryptic, often found beneath the surface 

where they are concealed inside thallus tissues. Although surfgrasses produce flowers, frequently 

these are absent in local populations during most of the year and are difficult to observe even 

when present. Unlike surfgrasses that produce dioecious flowers, the gametangial phases of 

seaweeds may be either monoecious or dioecious depending on the species. However, even when 

male and female thalli occur separately they are almost never sexually dimorphic except for 

species of the red algal Order Palmariales where dimorphic gametangial thalli characterize the 

group. 

In a few red algal genera, including most species of Rhodymenia and Porphyra, fertile male 

thalli can be distinguished readily in the field because visible white or light colored male son 

develop on thallus surfaces. In contrast, male thalli may not be detected easily in those species 

where male gametangia are scattered over the thallus or develop only within narrow time 

windows. Female thalli also are difficult to detect in most red seaweeds except following 

fertilization because female gametangia cannot be seen without microscopic examination (and 

often laborious specimen preparation). However, following fertilization, carposporophytes 

develop from zygotes as dense filamentous aggregations that often are visible to the unaided eye. 

In many of these species, the carposporophytes become surrounded by gametangial tissues and 

form visible, berry-like structures called cystocarps, embedded below or projecting from the 

thallus surface, that form dark spots ranging in size from 1 to 5 mm in diameter (Santelices 

1990). In contrast, gametangia usually are not highly differentiated in green seaweeds, and true 

male and female gametes and phases do not occur. This is also the case in many brown algae, 

except gametangia usually can be differentiated from vegetative cells. Male and female 

gametangia, however, occur in only certain orders, including the Desmarestiales, Laminariales 

(kelps), Fucales, and Dictyotales. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 179

Unfortunately, seaweeds often are sterile when collected or encountered in the field and show no 

apparent signs of either gametangia or sporangia. Except for many of the red algae that belong to 

the Gigartinaceae, phase identification in these cases is almost impossible without laboratory 

measurements of ploidy level. In many gigartinacean red algae, gametangial and tetrasporangial 

thalli can be distinguished in the field, even when thalli are sterile. This is done by testing for 

differences in wall chemistry that occur between gametangial and tetrasporangial phases by 

adding resorcinol to test tubes containing small thallus pieces and inspecting resultant color 

changes (Garbary and DeWreede 1988). 

Phase determination is most easily made in seaweeds with heteromorphic life histories, such as 

the kelps, where gametangial and sporangial plants differ greatly in appearance. In contrast, 

reproductive structures almost always must be found to make phase determinations in seaweeds 

with isomorphic gametangial and sporangial phases without resorting to arduous laboratory 

determination of chromosome number or measurements of relative nuclear fluorescence (see 

Murray and Dixon 1992). 

In the red algae, sporangial plants can be distinguished from gametangial thalli when 

tetrasporangial structures or son are present but rarely without microscopic inspection. In the 

Laminariales (keips) and Desmarestiales, the life history consists of heteromorphic phases, and 

the male and female gametangial thalli are composed of only a few cells and cannot be detected 

without great effort in the field. This means that all large, conspicuous kelp plants are sporangial 

thalli or sporophytes. In contrast, the gametangial and sporangial phases in species belonging to 

the Dictyotales are isomorphic and the phase or sex of unfertile specimens cannot readily be 

determined. When fertile, however, male, female and sporangial thalli can be discriminated with 

the unaided eye or with the aid of a hand lens based on subtle differences in the appearance of 

their reproductive organs. Male gametangia occur inside light colored son on the thallus surface, 

whereas oogonial sori are brown and sporangial son have a speckled brown and white 

appearance due to a mixture of brown sporangia and numerous white sterile hairs. The life 

history of members of the Fucales does not include gametangial and sporangial phases but 

instead consists of only a diploid phase upon which male and female gametangia are produced 

inside pit-like structures called conceptacles. In monoecious species, the sex of a specimen 

usually must be determined by microscopic examination although eggs or packets of male 

gametes may be observed adjacent to conceptacles immediately following their discharge. 

Reproductive Output 

When fertile, seaweeds can produce very large numbers of reproductive propagules. For 

example, Laminaria digitata sporophytes inhabiting 1 m2 of rocky habitat can produce more than 

20 x 109 spores (Chapman 1984), and enough spores can be released from plants in a Laminaria 

hyperborea forest to accumulate 3.3 x 106 spores mm-2 of benthic surface (Kain 1975). Because 
Final Study Report – Murray et al. 

180

of the high production of reproductive propagules and difficulties in identifying fertile seaweed 

tissues, quantitative determination of reproductive production (e.g., spore or gamete output) or 

the amount of resources allocated to reproduction can be very difficult in seaweeds (Santelices 

1990). Among the best candidates for measuring reproductive effort are brown algae belonging 

to the Fucales. These seaweeds, (e.g., Fucus, Silvetia, Hesperophycus, Halidrys, and Cystoseira)

have simple life histories where the only morphological phase is the diploid, gamete producing 

plant. Moreover, the gametangia are confined to conceptacles or pits that occur only on 

conspicuous, swollen branch tips called receptacles (Fig. 8-4). Thus, it is relatively easy to note 

receptacle presence on plants in the field and to obtain harvested specimens to determine the 

ratio of receptacle to vegetative biomass. 

As pointed out by Chapman (1985), the reproductive effort of a seaweed can be determined by 

measuring the proportion of the total thallus biomass allocated to reproductive functions or to 

gamete production alone. Unfortunately, few such studies have been performed, and these have 

produced variable results (Santelices 1990). In kelps, where reproductive structures are 

Fig. 8-4. Swollen 

terminal 

receptacles of 

Fucu gardneri. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 181

concentrated in fertile sori, estimates of resources allocated to reproductive tissues have varied 

from about 4% in Macrocystis pyrifera to 2-30% in Laminaria, and 10-20% in Ecklonia radiata 

(Santelices 1990). Higher estimates have been made for the fucoid Ascophyllum nodosum (40-

60%), the crustose red alga Lithophyllum incrustans (10-55%), and the green seaweed Ulva 

lactuca (20-60%) (Santelices 1990). 

In estimating the amount of resources allocated to reproduction in fucoids, receptacle tissues 

usually are assigned a reproductive function. Using this approach, the percentage of reproductive 

biomass has been found (Cousens 1981, 1986, Robertson 1987, Back et al. 1991, Ang 1992, 

Mathieson and Guo 1992, Brenchley et al. 1996) to vary seasonally and among fucoid species. In 

addition, Russell (1979) suggested that differences in ratios of receptacle to vegetative mass in 

Fucus vesiculosus populations from sheltered and exposed shores might result from adaptations 

to habitat conditions. 

Estimates of reproductive effort can be made by calculating the ratio of receptacle to total 

biomass. For example, Brenchley et al. (1996) determined that mature receptacles accounted for 

more than 40% of the dry weight of a Fucus serratus population during the reproductive season, 

but made up less than 10% of the dry biomass during non-reproductive winter periods. In 

contrast, Brenchley et al. reported that mature receptacles amounted to more than 90% of the dry 

biomass in a population of Himanthalia elongata, a species with only a single reproductive 

event. If required, gamete weights also can be estimated using approaches described by Vernet 

and Harper (1980) and Chapman (1985). Interestingly, estimates of the proportion of total body 

weight allocated to gametes ranged from 0.1 to 0.4% in three species of Fucus, values two orders 

of magnitude below calculations of reproductive allocation based on receptacle mass (Vernet and 

Harper 1980). 

Receptacles also can be used to estimate the seasonal reproductive effort or to obtain estimates of 

the number of eggs produced in a fucoid population (see Vernet and Harper 1980). This can be 

accomplished by first determining in the field the mean number of receptacles or the receptacle 

mass per unit area of substratum, and then estimating the conceptacle density per individual 

receptacle or per receptacle mass. Mean conceptacle densities can be determined by counting the 

number of conceptacles on randomly selected receptacles using transmitted light and a dissecting 

microscope. The number of eggs per conceptacle can be determined by dissecting out a number 

of randomly selected conceptacles, carefully squashing the conceptacles on a microscope slide, 

and counting the number of mature eggs using a compound microscope. Using the described 

procedures, Aberg and Pavia (1997) calculated egg production for eastern North Atlantic 

populations of Ascophyllum nodosum to be as high as 2.5 x 109

 eggs m-2 during the reproductive 

season. Using similar approaches, Koehnke and Murray (unpublished data) estimated seasonal 

variations in receptacle and conceptacle production for a southern California population of 

Silvetia compressa (Fig. 8-5). 
Final Study Report – Murray et al. 

182

Macroinvertebrates 

Growth Rates 

The growth rates of intertidal invertebrates can vary considerably among sites and over time due 

to changes in food availability or environmental conditions such as temperature. Growth rate 

studies can be used to estimate the age of intertidal invertebrates by fitting growth rate data to a 

mathematical function. This is probably the most common method for estimating the ages of 

most rocky intertidal invertebrates because most species lack annuli or other time-specific shell 

or anatomical markings that can be used directly for age estimation. 

Fig. 8-5. Temporal variation 

in receptacle and conceptacle 

production in a Silvetia 

compressa population from 

Crystal Cove State Park in 

southern California. Top 

Panel. Number of receptacles 

m

-2. Middle Panel. Receptacle 

wet biomass m-2. Lower 

Panel. Number of 

conceptacles m-2. Data are 

means (+ 1 SE) for 10 

replicate 0.25 m x 0.30 m 

plots in habitat containing a 

minimum of 95% S. 

compressa canopy cover. 

Conceptacle estimates 

extrapolated from receptacle

numbers and determined from 

counts of a minimum of 30 

receptacles per sampling 

period.
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 183

Because macroinvertebrates of different size grow at different rates, animals of similar size 

should be selected for comparative growth rate studies. Smaller animals grow at faster rates and 

should yield measurable changes in biomass, shell size, or dimensions of selected anatomical 

features in a shorter period of time. On the other hand, if the study goal is to age animals based 

on growth rates, then animals ranging widely in size are selected for study in order to obtain the 

size-related differences required for use in equations describing size-age relationships. In either 

case, growth rate studies require that the investigator follow marked animals to record changes in 

measured parameters over time. 

Marking Animals with Tags. Because growth rates of animals are determined by making 

repetitive (at least two) measurements on the same individual, marks must allow for the 

identification of different animals in the field and remain in place for the length of the study. 

Keeping marks on invertebrates for the period (usually > 6 months) needed to obtain measurable 

growth increments is often difficult, particularly in rocky intertidal habitats strongly influenced 

by wave action or sand scour. To prevent tag loss, double and even triple marking is 

recommended, and frequent tag maintenance and remarking may be necessary. For sessile 

animals, the relocation of marked animals can be facilitated by triangulation from reference 

screws or bolts put into the substratum, and previously marked individuals often can be 

identified by their positions even following tag loss. In contrast, the movements of mobile 

invertebrates will be much more difficult to track, and the recovery of marked individuals may 

be low. Hence, consideration should be given to affixing multiple marks to tagged animals, and 

to marking extra animals in order to accommodate projected losses of marked individuals during 

the study. 

Much attention has been given to the development of tagging methods for fishes and various 

approaches have been compiled and discussed by Nielson (1992). Benthic invertebrates belong 

to many phyla, however, and because of different morphological features, require different 

tagging strategies. Molluscs and barnacles with calcareous hard parts (e.g., shells or plates) 

usually can be marked without injuring the animal. Numbered tags can be inserted through a 

thick portion of the carapace to mark large crustaceans such as crabs and lobsters. The chitinous 

exoskeletons of smaller juvenile crustaceans, such as shore crabs, can be marked with paint. 

However, as pointed out by Ju et al. (1999) because marks on the exoskeleton will be lost during 

molting, crustaceans are particularly difficult to tag. Echinoderms, such as urchins and sea stars, 

and most soft-bodied animals, such as anemones, are much more difficult to mark because tags 

usually cannot be securely affixed to their external surfaces without causing injury (but see Joule 

(1983) for marking soft-bodied polychaetous annelids). 

Marking benthic invertebrates with calcareous shells or plates usually has been accomplished in 

two ways: 1) using colored dot patterns made with enamel paint, nail polish, or epoxy, and 2) by 

etching or affixing numbered tags. Individual molluscs can be distinguished using color coded 

dots painted on their shells, a commonly used technique that has been employed to mark even 
Final Study Report – Murray et al. 

184

very small (< 1 mm) juvenile gastropods (Gosselin 1993). For example, under a dissecting 

microscope Gosselin used six different paint colors to mark Nucella emarginata shells with three 

dot color combinations, a procedure that can generate up to 186 different color codes if two 

consecutive dots are never the same color. Numbered tags also can be fixed to shells using either 

“superglue” containing cyanoacrylate ester or epoxy cement. Tags, however, either should be 

coated with clear acrylic or be of a material that can withstand repetitive emersion, submersion, 

and sand scour to prevent code loss. Tags used for wires (e.g., manufactured by W.H. Brady Co., 

Milwaukee, WI, sock WM 67-69, Tape B-500+), to label bivalves (Hallprint, Holden Hill, South 

Australia), or to label insects such as bees (Chr. Graze; 71384 Weinstadt, Germany) all have 

been used to successfully mark benthic marine invertebrates (Fig. 8-6). 

Fig. 8-6. Limpets (Lottia gigantea) affixed with multiple tags. 

Recently, decimal coded wire tags (DCWTs) with individual electronic codes that can be 

recorded with a scanning instrument (Northwest Marine Technology, Inc., PO Box 427, Ben 

Nevis Loop Road, Shaw Island, WA 98286; http://www.nmt-inc.com/products/cwt/cwt.html) 

have been used to tag fishes and invertebrates. For mobile animals where tagging cannot be done 

on soft tissue surfaces, an option is to place the DCWTs in the body cavity if size and anatomy 

allow. DWCT tags also can be used to mark shelled invertebrates by gluing the tags to the shell 

where they are visible in the field. Because of their size and construction, DCWTs can be used 

with little difficulty, have very large numerical capacity, and are inexpensive. A disadvantage of 

using DCWTs is that scanning equipment can be costly (although portable scanning wands are 

available) and, in many applications, tags must be excised, if implanted, prior to being read. The 

use of DCWTs has worked well for marking crabs (Van Montfrans et al. 1986), lobsters (Krouse 

and Nutting 1990, Uglem and Grimson 1995) and sea stars (Robles, personal communication), 

and has been used successfully for many applications with fish. However, DCWT marked 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 185

organisms can be difficult or impossible to relocate if animals are not also marked with 

externally-visible tags. Without a second conspicuous tag, it may be difficult to determine tag 

loss and much field time will be spent testing animals encountered in the habitat for the presence 

of DCWTs, particularly if only a small proportion of the individuals in a population have been 

marked. 

Measuring Growth. Invertebrate growth rates can be determined non-destructively by repeatedly 

measuring biomass or increments in the length, width, or maximal diameter of selected 

anatomical features. If the goal is to compare growth rates at different sites or times, then 

animals of comparable size should be studied because smaller animals generally grow at faster 

rates than larger ones. Representative animals within the required size range should be selected 

at random from the population being studied, and either marked in place or carefully removed, 

tagged, and then returned to their habitats. Growth rates can be determined by first establishing a 

reference mark on an animal’s growing surface using dyes or a mark etched into a hardened 

growing structure such as a shell. For example, in shelled invertebrates, the distance from 

reference marks etched into the shell at a specific point of growth can be used to measure shell 

growth rates. This is commonly done for molluscs by etching a fine cross-hair into the shell 

surface along the axis of maximum growth near the growing edge of the shell. For trochids and 

other coiled snails, this would be the outer or abaxial rim of the shell aperture [but see Vermeij 

(1980) for a discussion of the complexity of shell growth in coiled gastropods]. In limpets, where 

the growth axis is nearly linear (Vermeij 1980), the mark is probably best made along the 

midplane near the posterior edge of the shell. Measurements of the distance between the 

horizontal line and the shell edge are then made using the vertical portion of the cross-hair to reestablish the measuring angle during assessments. Shells can be etched in the field with 

triangular files, diamond-pointed scribes, strong scalpels, or fine, hand-held battery operated 

inscribing tools. Because chitons are flexible and adopt body positions that fit the contours of the 

substratum, an increase in body length can be difficult to determine without detaching animals. 

Thus, measurements of chiton growth are probably best made using the 4th or 5th intermediate 

valve, perhaps from the valve edge to the point where the jugum intersects with the edge of the 

abutting posterior valve Eernisse, personal communication). 

Animals that lay down calcium carbonate shells, skeletal plates, tests, or spicules also can be 

marked by exposure to substances such as tetracycline or calcein that produce a fluorescent mark 

which can be viewed under blue light. For example, tetracycline has been used to successfully 

mark oysters (Nakahara, 1961) urchin tests (Ebert 1988, Ebert and Russell 1993), and abalone 

(Pirker and Scheil 1993). Calcein (2,4-bis-[N,N’-di(carbomethyl) -aminomethyl] fluorescein: 

Sigma #C 0875; Moran 2000) is believed to be superior to tetracycline, however, because it is 

more readily absorbed and incorporated into calcified structures, shows brighter fluorescence, 

and is less toxic (Rowley and Mackinnon 1995). Marking calcified structures with a fluorescent 

dye lays down a reference mark that can be used later to calculate growth increments but does 
Final Study Report – Murray et al. 

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not allow the distinction of individual animals. Calcein marks can be observed even months after 

removing calcified shells and structures from sacrificed animals. 

As described by Moran (2000), a calcein stock solution is prepared by dissolving 6.25 g calcein 

in 1 L of distilled water, and then buffered to pH 6 with sodium bicarbonate to enhance 

solubility. The concentrated calcein solution is then added to filtered seawater to achieve a 

marking solution of 100 mg calcein L-1. Animals are submersed in the calcein seawater solution 

or injected with sterile calcein solution (ca. 10 mL per kg of body weight). Rowley and 

Mackinnon report very successful results from injection, finding that marks appear within a day. 

For most intertidal species, exposure to calcein is probably best done by submersing animals in a 

well-aerated, calcein-seawater solution for at least 24 hours. However, exposure trials should be 

made to determine the treatment times required to produce detectable calcein marks in the 

animals being studied. Among other invertebrates, calcein has been used as a marker for 

measuring growth in mussels (Lutz and Rhoades 1980), urchins (Ebert cited in Rowley and 

Mackinnon 1995), juvenile snails (Moran 2000), and brachiopods, cockles, and bryozoans 

(Rowley and Mackinnon 1995). 

Marking calcified shells, tests, or other structures with calcein or other fluorescent dyes has 

certain disadvantages that need to be considered when performing growth studies. First, the 

fluorescent mark laid down at the time of calcein or tetracycline exposure can only be viewed 

after cleaning and often cutting open the shell, test or other calcified structure, a process that 

requires sacrificing the marked animal. To view calcein marks, soft tissues are removed (e.g., 

with sodium hypochlorite bleach) and the calcified structure is placed under blue light (470-510 

nm; optimal 497 nm) so that the incorporated calcein fluoresces yellow-green (514 nm) (Rowley 

and Mackinnon 1995). If the structures are small or the marks inconspicuous, observations can 

be made with a fluorescence dissecting microscope, with a standard dissecting microscope using 

epi-illumination and filters (see Moran 2000), or under high intensity blue or ultraviolet light 

using an interference filter (514 nm). Because the fluorescent imprint is not visible in the field, a 

second tagging procedure should be used to avoid collecting both treated and untreated animals 

to find calcein marked organisms. 

A disadvantage of shell-based growth measurements is that the individual animals comprising a 

population may have different shell shapes and thicknesses that might compromise among-site 

growth comparisons based only on single shell attributes. Because shell measurements may not 

always accurately represent body size, animal biomass also has been used to measure size and 

follow growth. If total mass is measured in shell-bearing species, however, the attained weights 

will be dominated by shell mass not by the organic weight of the animal. To more accurately 

obtain measurements of animal mass and eliminate sources of variation due to differences in 

shell shape and thickness, Palmer (1982) developed a non-destructive technique to separate body 

mass from shell mass when working with molluscs. This procedure involves taking the weight 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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of the whole animal (shell and body) when submersed in seawater and then subtracting this from 

the weight of the whole animal (including shell) obtained in air. A correction factor is then 

determined by establishing a regression of immersed shell weight against destructively 

determined shell dry weight and used to calculate true shell weight under submersed conditions. 

In performing this procedure, Palmer notes the importance of removing gas from inside the 

shells and mantle cavities of animals prior to determining their weights in seawater in order to 

avoid significant weighing errors. This is accomplished by completely submersing animals in 

seawater for 24 to 48 hours prior to weight determination and, by pressing the tips of forceps or 

other blunt objects against the operculum in gastropods to push the body back into its shell. 

Although Palmer’s procedure has the advantage of being non-destructive, its use is much more 

time-consuming than simple shell length, width, or diameter measurements, which are more 

commonly used in field studies of molluscan growth. 

Age Determination 

Most rocky intertidal macroinvertebrates are generally impossible to age without following 

marked individuals. Because of their longevity and difficulties in retaining permanent marks, it is 

usually impractical or impossible to follow the survivorship of marked individuals from 

recruitment to death. Hence, ages of intertidal macroinvertebrates are usually determined 

indirectly in one of two ways: 1) calculating age from counts of growth markings or rings; 2) 

estimating age from growth rates. 

Annuli and Growth Rings. Age can best be estimated in those species that produce shells or 

other persistent structures with markings that show variations in growth rate over the course of 

the year. If such growth rings or marks result from seasonal variation, growth increments can be 

calculated from the spacing between markings and age can be determined from counts of marks 

or rings. In some temperate bivalves (Seed 1980), visible shell markings or annular rings (annuli) 

are produced in the winter or at the onset of new spring growth; in certain cold water species 

shell markings can even result from inhibition of growth during summer when temperatures are 

high (Wilbur and Owen 1964). Depending on the species and the structure being examined, rings 

or markings can be viewed and counted and inter-ring distances measured either by direct 

observation or using transmitted light or x-ray photographs. 

Unfortunately, the use of growth annuli or seasonally produced markings is not applicable for 

determining the ages of most rocky intertidal invertebrates because there is no evidence that 

annular or seasonal markings are consistently produced. An exception is Tegula funebralis, 

which along the Oregon and Washington coasts produces annual shell markings along the body 

whorl (Frank 1975). These markings are known to represent periods of interrupted growth; 

however, south of Monterey, annuli cannot be consistently detected in T. funebralis presumably 

because of the absence of regular periods of interrupted growth (Frank 1975). Other types of 
Final Study Report – Murray et al. 

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markings that can be used to age benthic macroinvertebrates include lipofuscin accumulation in 

blue crabs (Callinectes sapidus) and other crustaceans (Ju et al. 1999), ligament scars on the 

oyster Crassostrea virginica (Wilbur and Owen 1964), opercular rings in the gastropods 

Babylonia japonica, Lithopoma undosum (= Astraea undosa) and Turbo setosus (Wilbur and 

Owen 1964, Sire and Bonnet 1984, Cupul-Magaña and Torres-Moye 1996), and lines on the 

plates of the chiton Chiton tuberculatus (Wilbur and Owen 1964). 

Age Calculation from Growth Rates. By following marked animals over time, either by 

measuring increases in length, width and diameter of shells and tests or changes in biomass, rates 

of growth can be used to predict age based on animal size. Analysis of growth increment data, 

however, can be complicated because animals of different size grow at different rates. Under 

most conditions, smaller and younger animals grow much faster than larger and older animals. 

Additionally, growth often differs over the various parts of the body so that relative body 

proportions (i.e., the allometry of the individual) can change over time. In order to develop 

mathematical relationships that translate the size of an individual into an estimated age, growth 

data usually need to be obtained from animals that encompass the full range of sizes in the 

population. Therefore, at the outset of the study, consideration should be given to selecting 

animals that represent all size classes in the population. Animals are then marked or tagged, the 

growth parameter selected (e.g., shell length, width or diameter) and measured at time t, and then 

returned to their natural habitat. After a sufficient period of time (t + 1), for example 6-12 

months for many intertidal invertebrates, tagged individuals are recovered and a second 

measurement made to obtain the growth increment over time (e.g., weeks or months) or the 

average growth rate. In most cases, measurements would need to be made at more frequent 

intervals if the goal of the study was to determine seasonal growth rates. Growth functions can 

then be used to calculate relationships between size and age. Although several growth functions 

are available, three are probably the most commonly employed: 1) the von Bertalanffy curve, 2) 

the logistic equation, and 3) the Gompertz function. Detailed discussions of these growth 

functions are available in Ebert (1999) and will be discussed only briefly here with emphasis on 

the von Bertalanffy function, which has been applied to limpets (Balaparameswara Rao 1976, 

Branch 1981). 

Following procedures outlined by Balaparameswara Rao (1976) for the limpet Cellana radiata, 

the growth increment (shell length) data are first plotted as length at time t + 1 and length at time 

t to create a Ford-Walford plot. The regression equation for these data is then calculated: 

where, St = size or shell length at time t; St+1 = size at time t + 1; m = the slope; and i = the 

intercept. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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The parameters in Equation 1 are needed to calculate S∞ = the theoretical maximum size attained 

by members of the population based on the obtained growth data. 

Many of the most widely used growth curves, including the von Bertalanffy function, are based 

on the premise that the growth of individuals in the population is determinate and reaches some 

maximum size (e.g., S∞). The slope derived from Equation 1 is then used in Equation 3 to 

calculate K = the growth coefficient: 

K is then used in the von Bertalanffy Growth Equation (Equation 4) to determine the size-age 

relationship for the population where t0 is the theoretical age at which size is zero: 

Of course, age estimates made from growth equations are only as reliable as the growth function 

itself, and several assumptions are made by the von Bertalanffy equation besides determinate 

growth leading to a maximum theoretical body size, including extrapolation of the age at which 

size is zero. Using these procedures, Balaparameswara Rao (1976) estimated that the largest C. 

radiata on Indian shores have survived for 3 to 4 years. Similarly, Kido (2000) determined that 

the ages of the largest individuals in an open rock population of the exploited owl limpet (Lottia 

gigantea) exceeded 8 years in southern California. Excellent discussions of growth functions and 

their applications can be found in Ebert (1999). 

Population Size Structure 

Size-Frequency Profiles. Since the ecological functions performed by intertidal invertebrates are 

probably best correlated with size, comparisons of size frequency profiles among sites or over 

time are more informative than abundance data alone. Size frequency profiles also can be used to 

gain insight into important population features such as age structure and recruitment patterns, 

and can provide the basis for estimating survival, growth rates, and for building population 

models (Cerrato 1980, Ebert 1999). Size-frequency profiles also can form the basis for 

determining recovery time following an oil spill — not just of population numbers but also of 

population structure and the ecological functions tied to structure. 

Size frequency profiles are constructed by taking measurements of size-informative parameters 

for individuals in a population. To be of greatest value, the parameter selected for size 

measurement will have a strong positive relationship with growth and reflect size-related 
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190

ecological roles of the organism. Besides biomass, such parameters include, for example, shell 

length, height, width, or maximum diameter in molluscs, test diameter in urchins, longest arm 

length or greatest tip-to-tip span in sea stars, and carapace width in crabs. Choosing the length or 

appropriate parameter for measuring shell size in molluscs must be given careful consideration. 

For limpets, the maximum shell length along the anterior-posterior axis has routinely been used 

to represent size. However, the allometry of coiled gastropods (Vermeij 1980) can present 

problems in determining shell height, which is measured along the axis of coiling. In addition, 

shell apices often become eroded making length measurements inaccurate. Consequently, shell 

width (= distance at right angles to the shell axis) is often used to indicate shell size in coiled 

gastropods. 

Excellent discussions of techniques for deducing attributes of molluscan populations from 

analyses of shell parameters can be found in Cerrato (1980) and Ebert (1999). To build sizefrequency profiles of macroinvertebrate populations, individuals are randomly sampled from the 

selected population, and accurate measurements made on the anatomical parameter chosen to 

represent size. Care must be taken to ensure that smaller, less conspicuous members of the 

population are not overlooked during sampling and, that if juveniles and adults occupy different 

microhabitats, this is taken into account. Digital calipers can greatly increase the rate at which 

size measurements of most common intertidal invertebrates can be made in the field and reduce 

errors, particularly when multiple investigators perform measurements (Fig. 8-7). For some 

invertebrates, such as barnacles, measurements must be made on animals fixed to the substratum, 

but it is best to leave even animals such as limpets and chitons in place when performing 

measurements to avoid injury. For other invertebrates, such as turban snails and littorines, 

animals can be picked up, measured, and then returned to the location from which they were 

collected. When substratum topography or the presence of other organisms prevents the direct 

use of calipers, measurements can be taken on dimensions obtained with dividers that can more 

easily be manipulated around animals in the field. 

Following measurement, animals are then sorted into size classes and the percentage or 

proportion of individuals in the sampled population that occur within each size class is 

determined (Fig. 8-8). The number of size classes and the size range within each size class are 

selected by the investigator so as to best represent the structure of the population. Cerrato (1980) 

reports that sizes ranging from 1 to 5% of the maximum size found in the population are mostly 

used to define size-class intervals and suggests that this size range generally provides the number 

of intervals needed to resolve size classes in the population. Ebert (1999) indicates that at least 

15 and preferably 20 or more size classes should be used for some analyses of size structure data. 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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Fig. 8-7. Performing size measurements of owl limpets in the field. 

Three approaches are commonly used to compare size structures between and among sites or 

over time. 1) mean sizes can be compared using standard univariate procedures such as analysis 

of variance or two-sample tests; 2) size distributions can be compared using the KolmogorovSmirnov procedure or, if the data allow, two-parameter gamma curve-fitting can be used to 

compare profile means and distributions; and, 3) the χ

2 test can be used to compare the sizefrequency distributions. Regardless of the approach, however, caution must be taken when 

interpreting differences in size frequency profiles. For example, size frequencies may differ 

greatly among sites where recruitment and growth rates vary with local conditions. Moreover, 

the size structure of a population even can vary considerably within a site, such as when different 

microhabitats are occupied (Kido 2000), or when mobile invertebrates settle at one end of their 

vertical range and migrate to the other. Therefore, it may not be possible to extrapolate 

population structures measured at one site to another. 

Growth Rates from Size Frequency Profiles. Size-frequency data collected for the same 

population over a series of time intervals can be used to estimate certain demographic parameters 

including the growth rates of intertidal invertebrates (Seapy 1966, Ebert 1999). The series of 

modes obtained from the size frequency profiles determined for each sampling period are 

presumed to represent different age classes. Growth rates for different age classes are then 

estimated by calculating the shift in modal length of an age class as it has progressed from one 

measurement period to the next. Usually, large sample sizes are required to provide distinct age 

classes for this procedure. As pointed out by Wilbur and Owen (1964), best results are obtained 

when populations show seasonal growth and each year’s recruitment class is represented by a 

tightly-defined size group. Estimation error increases greatly when recruitment is continuous or 
Final Study Report – Murray et al. 

192

occurs over several months, or where environmental factors make age classes difficult to 

distinguish. The absence of a particular recruitment class also can make size frequencydetermined parameters difficult to interpret. 

Fig. 8-8. Size-Frequency plots for the owl limpet Lottia gigantea at eight southern California 

study sites. The indicated number of animals (n) at each site were sorted by 5-mm size classes. 

Size-frequency distributions differed significantly among sites based on the χ

2

 test. Largest 

individuals were found at sites receiving the least human visitation and collecting pressure 

(Source: Kido 2000). 

Cerrato (1980), Grant et al. (1987), and Ebert (1999) provide excellent discussions of the various 

approaches for analyzing size-frequency data to make estimates of growth rates and other 

demographic parameters. Grant et al. (1987) recommend the use of an optimization method such 

as that described by Macdonald and Pilcher (1979), and describe the Peterson method as the 

simplest means for separating age classes. In this method, each of the modes in the size- 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 193

frequency histogram is interpreted as representing a single age class and all age classes are 

assumed to occur in the sample. Other analytical methods for breaking down size-frequency 

distributions also are available, but these usually assume that the profiles of individuals in each 

age class approximate a normal distribution. Graphical methods of analysis (see Cerrato 1980) 

may not always be reproducible and should not be used except under conditions where 

distributional modes are distinct and sample sizes are large (Grant et al. 1987). 

Reproductive Condition and Output 

With the exception of certain invertebrates that are either simultaneous (e.g., barnacles and 

opisthobranchs) or sequential (e.g., certain patellid limpets) hermaphrodites, most common 

intertidal invertebrates are characterized by separate sexes and are dioecious or gonochoristic. 

Interestingly, sexes may not be equally represented in dioecious species, particularly in molluscs 

where females tend to be more numerous than males with this disparity increasing with 

population age (Fretter and Graham 1964). Because sexual dimorphism is not obvious in most 

dioecious species, gender is difficult if not impossible to determine without killing animals and 

observing internal sexual structures. Animals are dissected to find male or female sex organs or 

to observe male and female gonads, which usually differ in shape and color. Because animals 

usually must be sacrificed, determining the gender composition of a population or establishing 

relationships between gender and parameters such as size or age is time consuming and for most 

species is probably best and most efficiently done in conjunction with a destructive sampling 

program. 

In a few kinds of invertebrates, sex can be determined without sacrificing individuals. For 

example, crabs and many other crustaceans have external features that can be used to indicate 

sex, and in some dioecious gastropod mollusks, such as abalone, distinctive gonadal material can 

be observed protruding from the pallial cavity when an animal is very ripe. In some other 

gastropods, subtle differences between males and females occur in shell characteristics and these 

differences can be used by trained observers to sex specimens (Fretter and Graham 1964). 

Occasionally, sex can be differentiated in very ripe sea urchins by sharply shaking animals to 

discharge eggs and sperm (Lambert, personal communication). 

Gender determination by biopsy can be an attractive and potentially nondestructive alternative 

for certain dioecious invertebrates, but this procedure requires time-consuming handling of 

animals. Individuals also will likely be lost to injury from biopsy procedures, with smaller 

animals probably more vulnerable than larger ones. Also, biopsy sampling is particularly 

difficult to perform non-destructively in molluscs because they seal punctures to their tissues so 

poorly. Biopsy sampling can be performed in sea stars and limpets by removing a tiny plug from 

the gonad and then inspecting the tissue for color or the presence of eggs and sperm. For 

patellacean limpets, Wright and Lindberg (1979) and Lindberg and Wright (1989) have 
Final Study Report – Murray et al. 

194

pioneered a non-fatal technique for gender determination. This involves carefully removing a 

small amount of gonadal material by inserting a fine syringe needle through the body wall at a 

prescribed angle. Another approach, used by Frank (1965) to sex turban snails, is to drill a small 

hole through the shell to reveal the gonad. By following snails whose shells had been drilled and 

then sealed for two years, Frank determined that growth was not significantly affected by this 

procedure. 

Besides sampling intertidal invertebrate populations to determine gender composition or to 

compare size structures or growth rates of males and females, inspection of gonadal material can 

be used to determine reproductive (spawning) periodicity and spatial variations in the degree of 

gonadal production among populations. Seasonal or spatial differences in reproductive condition 

can be determined by collecting specimens and returning them to the laboratory where they are 

dissected and their gonads inspected and weighed. If analyses cannot be done immediately, 

animals can be frozen or preserved with the latter approach generally yielding better visual 

discrimination while also providing the ability to obtain quantitative data on gonadal mass and 

egg production. Reproductive condition can be categorized by subjectively grading the state of 

gonadal development (Seapy 1966). Alternatively, the mass or volumetric ratio of gonadal to 

non-reproductive (somatic) body tissue can be determined separately for each sex to provide 

quantitative information describing seasonal or spatial variation in reproductive condition or age 

or size related patterns of fecundity. If required, the fecundity or the quantity of egg production 

in the population can be determined by inspecting the ovaries of females microscopically. When 

using this procedure, eggs can be further categorized in terms of the stage of maturity or 

development. 

Subjective grading of the state of gonadal development is usually based on shape, color, and the 

quantity of observed gonadal material. These data can be used to determine the frequency of 

spawning or differences in spawning periodicity among populations. Individuals sampled from 

the population are dissected to expose gonadal material which is then graded according to a predetermined qualitative scale. Care must be taken to ensure that the appearance (size, color, 

shape) of gonadal material is not altered by maintenance (e.g., holding animals in aquariums) or 

preservation procedures (e.g., fixation, freezing). However, in patellid limpets and 

archaeogastropods, simple qualitative observations of the shape and color of the ovary alone may 

not be good indicators of reproductive cycles (Creese 1980). 

Quantitative determination of gonadal size can be used to estimate the reproductive output of the 

population. Working on the assumption that the quantity of gamete production is strongly related 

to gonadal size, determinations of gonadal mass or volume can be used to estimate fecundity. 

However, because fertile intertidal invertebrates generally show a strong correlation between 

body size and gonadal size, gonadal mass or volume should be determined together with the 

mass of non-reproductive body tissues (Fig. 8-9). These determinations can be facilitated in 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 195

molluscs by preserving and storing specimens in 10% formalin-seawater which will cause the 

gonads and other tissues to harden and simplify extraction and weight determination. To ensure 

best preservation in snails with effective opercula, animals should first be relaxed in magnesium 

chloride solution so body tissues are evenly exposed to the fixative. Creese (1980) reports that 

the wet body weight of limpets decreases by about 2% following preservation so weight changes 

due to preservation should be determined. For molluscs and many other invertebrates, the soft 

body parts of animals must first be removed from their shells or tests. For gastropods, shells can 

be cracked or cut open or animals can be boiled, a procedure that often detaches the retractor 

muscles holding the body to the shell. Alternatively, the calcium carbonate component of 

molluscan shells can be dissolved by holding animals for a few days in an acidified formalin 

solution [(15 mL concentrated glacial acetic acid, 15 mL diluted acetic acid (= commercial 

vinegar), and 10 mL 10% formalin-seawater)]. The de-calcified shells will then consist only of 

an organic matrix that can easily be cut open to remove the organic contents. 

Following dissection and separation, the wet or dry weights of gonads and somatic body tissues 

should be determined as described in Chapter 7. Obtaining dry weights will produce better 

precision by reducing weighing errors due to tissue retention of external water or fixative. 

However, gonads should not be dried if ovaries are to be examined microscopically and eggs 

counted. Qualitative assessments of reproductive condition can be performed by smearing small 

amounts of ovarian tissue onto a microscope slide and, upon microscopic examination, grading 

the sample based on whether it contains mature, immature, or spent oocytes. Alternatively, 

quantitative determinations of fecundity can be made by microscopically inspecting a known 

mass of female gonadal material sliced from the ovary and counting and classifying eggs 

according to their state of development. If the counts obtained for this subsample of ovarian 

tissue are expressed per mg of ovarian tissue and are representative of the ovary as a whole, the 

fecundity of each examined female can be calculated based on its total ovary weight. Together 

with size-frequency data, this information can be used to calculate the total number of eggs 

potentially produced by female members of the sampled population. For example, based on size 

data and quantitative analyses of gonadal tissues, Creese (1980) determined that, the average 

female of the Australian limpets Notoacmaea petteridi and Patelloida alticostata could produce 

from 400 to 29,700 eggs and large animals could release 30,000 to 45,000 eggs per year. 
Final Study Report – Murray et al. 

196

Fig. 8-9. Relationships between body size and gonadal mass for a southern California 

population of the speckled turban snail Tegula gallina Plotted are gonadal dry mass versus 

maximum shell width for males and females. Note the great increase in gonadal mass when 

snails reached shell widths > 20 mm (Source: Sato and Murray, unpublished data). 

A Gonadal-Somatic Index (GSI) also can be calculated from gonadal and somatic weights to 

describe the reproductive condition of animals in the population. This index can be expressed as 

either the ratio of gonadal mass to somatic body mass or, alternatively (see Creese 1980), as the 

value of the slope of the linear regression of gonadal mass on somatic mass. Usually, the GSI is 

expressed as a percentage when calculated as the ratio of gonadal to somatic weight. GSI values 

can be determined separately for each sampled individual and mean values calculated for the 

population as a whole or, if informative, for each defined size or age class. Mean GSI values 

calculated for different periods also can be used to determine temporal variation in reproductive 

development and to document spawning periodicity in the population. If gonads are graded 

according to oocyte status, gamete output can be calculated by establishing regression equations 

that describe the relationship between somatic body mass and gonad mass under conditions when 

the ovaries are both laden with mature oocytes and also after spawning when only immature 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 197

oocytes are present. The difference between these two gonadal-somatic mass relationships will 

provide an estimate of gonadal output. Together with size or age structure data, GSIs also can be 

used to estimate changes in the reproductive output of the population resulting from changes in 

size or age structure. For example, Branch (1975) determined that gonadal output for the South 

African limpet Patella concolor was reduced by approximately 90% at a site where humans had 

removed the larger animals from the population for consumption. Hence, GSI data can be used to 

compare the reproductive conditions of populations at different sites to assess, for example, the 

impact of an oil spill or the effects of human collecting. 

Summary 

Abundance data usually provide the foundation for most monitoring and impact studies, yet these 

data generally have a high “noise to signal” ratio and do not adequately describe the status (or 

the ecological services and functions) of rocky intertidal populations. Data describing primary 

population parameters, such as recruitment and mortality rates, or secondary parameters, such as 

size and age class distribution, sex ratios, and gonadal production, provide stronger descriptions 

of population status and dynamics. Moreover, these data provide more accurate information 

about population recovery following major impacts such as an oil spill. For example, abundance 

data might show that cover of an upper shore fucoid or densities of a limpet have returned to the 

values expected if a spill had not occurred. However, the size or age structures and reproductive 

outputs of these populations may not yet resemble the structures or outputs of control 

populations representing their status in the absence of the spill. In this case, species abundances 

indicate recovery, but the population structures, and very likely the ecological services and 

functions provided by the impacted fucoid and limpet populations, have yet to be fully restored. 

Unfortunately, data on primary and secondary population parameters are more time consuming 

and costly to collect compared with abundance data, and for these reasons usually are targeted on 

only one or a few key species and rarely incorporated into monitoring programs. Nevertheless, in 

monitoring and other long-term sampling programs designed to determine spatial and temporal 

changes in rocky intertidal ecosystems, efforts should be made to incorporate data collection for 

at least a few key species on two population parameters: recruitment and size structure. 

Recruitment of most rocky intertidal species is known to be highly variable in both space and 

time, and to be closely linked with prevailing oceanographic conditions. A series of poor 

recruitment years resulting, for example from warmer sea temperatures, can lead to changes in 

population structure and decreases in species abundances even in the absence of major 

disturbances. Knowledge of spatial and temporal variations in the size structures of targeted 

populations can indirectly provide information on recruitment and other biological responses to 

major disturbances or changing environmental conditions. 
Final Study Report – Murray et al. 

198

Valuable information can be collected on population status by taking size measurements of 

organisms when carrying out rocky intertidal sampling programs because the ecological 

functions performed by intertidal seaweeds and invertebrates are probably best correlated with 

their size. Careful consideration must be given to the species selected, how they are sampled, and 

to the parameters (e.g., seaweed axis length or limpet shell length) selected for measurement 

during program design. Size structure data can be used to follow temporal patterns in the influx 

of tiny benthic recruits, to gain insight into population age structure, estimate its reproductive 

output, and to otherwise compare the status of populations across sites, over time, or before and 

after a catastrophic event. Approaches also are available to estimate growth rates and various 

other population parameters from size structure data. 

The growth rates of rocky intertidal seaweeds and invertebrates vary over both spatial and 

temporal scales and can lead to significant differences in population structures. Except for a few 

species (e.g., kelps), growth rates of most seaweeds are difficult to measure in the field because 

of morphological plasticity and variable growth axes. Growth in most benthic invertebrates, 

however, is predictably distributed along identifiable axes and can be measured in the field by 

following marked individuals. 

The vast majority of seaweeds and invertebrates are virtually impossible to age using anatomical 

features. Hence, age must be determined by following marked individuals over time or by 

estimating age from growth rate data. Marking methods must be carefully considered and 

customized to the species being studied because tags can cause injury to seaweeds and most softbodied intertidal invertebrates and in even hard shelled gastropods and bivalves can easily be 

lost. Growth rate data can be used to estimate the age of invertebrates using various 

mathematical functions such as the von Bertalanffy Growth Equation. However, this approach 

requires several assumptions and provides poorer estimates for slow growing older animals that 

have neared the theoretical asymptotic size for the population. Improved understanding of the 

growth rates and age structures of most rocky intertidal seaweed and invertebrate populations is 

needed to determine the effectiveness of natural recruitment cycles and to predict recovery times 

for returning the ecosystem functions of perturbated species populations following catastrophic 

events. 

Successful reproduction is critical to sustaining a rocky intertidal population over long time 

scales. Most seaweeds have complex life histories, that include both gametophyte and 

sporophyte phases, and many can perennate or regrow new upright axes from persistent basal 

systems (= perennation). Seaweeds recruit new individuals into their populations by releasing 

spores, zygotes, or other propagules that disperse various distances, and also by regrowing from 

detached vegetative fragments. Although few quantitative data are available, it is generally 

assumed that larger sized seaweeds produce greater numbers of reproductive propagules. Most 

common rocky intertidal invertebrates inhabiting temperate shores, including most limpets, 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 199

trochid snails, chitons, littorines, mussels, barnacles, urchins, and sea stars, recruit from 

planktonic larvae carried variable distances by oceanographic currents. Most also are broadcast 

spawners that release their gametes into the water column where fertilization occurs. 

Consequently, fertilization success increases with increasing densities of reproductively mature 

individuals, and because the amount of gonadal mass increases greatly with body size, larger, 

more fecund individuals tend to dominate the reproductive outputs of most populations. Hence, 

populations with large numbers of big individuals produce and export more larvae, and are good 

sources of larvae for other intertidal sites. 

Collecting by humans and other disturbances that kill bigger animals can change the size 

structure and reduce the reproductive output of an intertidal population. Therefore, data on 

spatial and temporal variations in the sex ratios, production of gonadal mass, and gamete output 

can be used together with density and size structure data to evaluate the reproductive status of an 

intertidal invertebrate population and to determine whether it may serve as an important regional 

or local source of larvae. Moreover, these data can be used to determine whether the 

reproductive functions of a population have fully recovered following a catastrophic event such 

as an oil spill. Unfortunately reproductive data on intertidal populations are time consuming and 

costly to obtain, and large gaps exist in our understanding of the reproductive and recruitment 

cycles and reproductive outputs of most rocky intertidal seaweeds and invertebrates. Although 

difficult to build in to long-term monitoring programs, studies designed to determine the 

reproductive status of impacted populations should be considered, where possible, when 

evaluating the effects of oil spills or other major environmental disturbances. 

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Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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Subject Index 

abalone 32, 34, 106, 110, 113, 118, 130, 185, 193 

abundance data 49, 51, 99, 124, 128, 129, 148, 156, 197 

aerial photographs 31 

age 

structure 176-178 

determination in macrophytes 174-175 

determination in macroinvertebrates 182, 187-189 

angled order distance sampling (see distance-based sampling) 

anemones 32, 53, 54, 159, 163, 183 

annelids 51, 57, 58 

annelid pollution index 61 

ANOSIM 65, 66 

band transects 102, 104, 105, 118 

bar code readers 103 

barnacles 32, 53, 54, 55, 57, 64, 85, 108, 110, 124, 127, 130, 133, 134, 135, 137, 141, 143, 159, 

164, 183, 190, 193 

baseline studies 12, 13 

basic distance sampling (see distance-based sampling) 

biological units 49-60 

biomass 156-167 

ash-free dry biomass 165-167 

dry biomass 164-165 

wet biomass 163-164 

harvesting procedures 159-163 

biomass determination in shelled Molluscs 186-187 

biopsy methods for sex determination in Molluscs 193 

blue-green algae (Cyanobacteria) 34, 60 

boulderfields 33, 35, 115-118 

brachiopods 186 

Braun-Blanquet 125, 126 

broadcast spawners 199 

bryozoans 124, 132, 186 

calcein 185-186 

chitons 130, 161, 185, 187, 188, 190 

cockles 186 

colonial invertebrates 130, 132, 156 

community-level sampling 60, 108, 156 

computer simulated sampling 85, 107 

control sites 15-16 

coralline algae 

 articulated 32, 60, 64, 108, 110, 133, 157, 164, 174 

 crustose 54, 60, 64, 127, 141, 148, 175, 181 
Final Study Report – Murray et al. 

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cost considerations (see study costs) 

counts (see data type: density) 

cover (see data type) 

crabs 128, 130, 159, 183, 187, 190, 193 

crevices 28, 33, 81, 106, 112, 114, 116 

crustose algae 54, 60, 64, 127, 141, 148, 175, 181 

cryptic species (see also “difficult to see” species) 113, 119 

data type 

biomass 156-159, 163-167 

cover 100, 124, 128, 132-148, 149, 156 

density 105, 113, 128, 130-132, 149, 156, 159 

frequency 125 

presence-absence 125, 137 

qualitative scales 124-127 

size-frequency 176-178, 189-193 

Decimal Coated Wire Tags (DCWTs) 184 

demographic attributes of populations 173, 176 

Desmarestiales (brown algal order) 178-179 

developmental stage (seaweeds and plants) 176 

Dictyotales (brown algal Order) 60, 178-179 

“difficult to see” taxa (see also cryptic species) 141, 144, 145, 146, 147, 149 

distance-based sampling 111-114 

angled ordered 111-112 

basic distance method 111-112 

Kendall-Moran 111-112 

ordered distance 111-112 

variable area transect 111-112 

distributions: species 55 

diversity 54, 58, 62, 157 

indexes 17, 61, 62, 103, 130 

phyletic 10 

richness 54, 58, 61, 62, 86, 91, 108, 113, 136, 140 

ecological significance 78 

edge effects 106, 109, 131, 141, 159-160 

effect species groups 58 

effect size 17, 51, 77, 78, 91, 141, 157, 171 

Environmental Monitoring and Assessment Program (EMAP) 19, 36 

Environmental Sensitivity Maps 31 

Exxon Valdez 15, 38, 53, 57 

filamentous algae 58, 60 

fixed plots 55, 106 

foliose algae 60 

Ford- Walford plots 188 

freeze-drying 165 

freeze event 55 

Fucales (brown algal order) 32, 52, 53, 54, 60, 64, 110, 174, 175, 176, 177, 178-182, 197 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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fucoids (see Fucales) 

functional groups 58-59, 67 

genets 124, 174 

Geographical Information Systems (GIS) 33, 88 

geophysical features 24-30 

Global Positioning System (GPS) 81, 88, 175 

Gompertz growth function 188 

gonadal production in invertebrates 55, 194-196 

grading 194-195, 196 

mass 194-196 

preservation 194 

Gonadal-Somatic Index (GSI) 196 

growth annuli or rings 187-188 

Growth Functions 188-189 

Gompertz 188 

logistic 188 

Von Bertalanffy 188-189 

growth rates 55, 56, 173 

in macrophytes and seaweeds 173 

in macroinvertebrates 182-189 

from size frequency profiles 191-193 

guilds 58-59 

habitat structuring biota 36, 52 

habitat types 33-36 

boulderfields 33, 35, 115-118 

crevices 28, 33, 81, 106, 112, 114, 116 

hummocks 28, 114 

tidepools 28, 33, 35, 79, 81 

haphazard sampling 12, 81 

headland 28 

helicopter overflights 31, 32 

heterotrichous growth 174 

human disturbance 24, 30, 34, 52 

trampling 30, 59, 62, 177 

collecting 30, 197, 199 

hummocks 28, 114 

ice 24 

image-analysis software 135, 140, 148, 173 

impact sites 15-16 

impact studies (see study types) 

impact Study Designs 10-19 

Asymmetrical Before-After-Control-impact (BACI) design 16, 39 

Before-After Impact design 15 

Before-After-Control-Impact (BACI) design 16, 39, 51, 65, 97 

Before-After-Control-Impact Paired Series (BACIPS) design 16, 97 

Control-impact design 15, 39, 40, 94 
Final Study Report – Murray et al. 

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Gradient Impact designs 15, 39, 40, 94 

Index of Biological Integrity (IBI) 17, 61 

indexes 

annelid pollution index 61 

diversity (see diversity) 

Index of Biological Integrity (IBI) 17, 61 

Morisita’s index of similarity 92 

nematode to copepod ratio 61 

similarity 130 

individual-based parameters 49, 55-56, 66, 171 

intermediate disturbance 62 

kelps 32, 59, 60, 64, 105, 119, 132, 134, 173, 174, 175, 176, 178-181 

Laminariales (brown algal order) (see kelps) 

layering 134, 135, 141, 144, 146, 149, 159 

lichens 127 

limpets 106, 108, 110, 127, 130, 159, 161, 185, 188-189, 190, 192, 193, 194-195, 197 

line of sight methods 112 

line transects 99, 100-103, 107, 118, 148 

line intercepts 85, 100-103, 129 

point contacts 85, 100-103, 129 

lipofuscin 187 

littorines 32, 53, 110, 127, 130, 190 

lobsters 128, 183, 184 

maps 31-33 

environmental sensitivity maps 31 

helicopter overflights 31, 32 

photographs 55, 88 

mark-recapture methods 128 

marking plots (see reference points and markers) 

MDS (see Statistical Analyses: Multivariate Analyses) 

metal detector 88 

microalgae 58, 60 

mobile invertebrates (see also abalone, sea stars, limpets, snails, chitons) 104, 107, 124, 132, 

157, 159, 160, 183, 184, 191 

monitoring studies (see study types) 

multiple response permutation procedures 65 

mussels 32, 34, 36, 51, 52, 53, 55, 59, 88, 108, 110, 124, 127, 133, 135, 141, 143, 159 

natural variability (see also spatial and temporal variation) 9, 13, 17, 18, 43, 50, 61, 66, 94 

nematode to copepod ratio 61 

noise to signal ratio (see also statistical variance) 10, 36, 51, 78, 87, 171, 197 

octopus 113 

oil and oil spills 12, 15, 28, 29, 31, 34, 35, 37, 38, 39, 51, 53, 55, 94, 171, 189, 197, 199 

one-time or “one-off” studies/surveys (see study types) 

oysters 185, 187 

parallax 115, 131, 138, 141, 159 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

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patchiness 50, 53, 85, 86, 89, 109, 113, 124 

patterns and processes studies (see study types) 

Personal Data Assistants (PDAs) 103 

Peterson method for separating age classes 192 

PCA (See Statistical Analyses: Multivariate Analyses) 

photographic sampling 136, 140-148, 150, 158 

35 mm and digital cameras 140, 141-144, 145, 146 

video cameras 145-148 

camera stands 144 

quadrats 107, 142, 143 

reference points (from) 55, 88 

resolution 142, 145 

planimetry 135, 140, 148, 173 

plotless sampling methods 110-114, 128-129, 148 

plots 

as sample units 99-110, 130-148, 158 

borders 131, 132, 160 

dimensions 99, 104, 108-110, 131, 138 

fixed 55, 106 

gridded or sectioned 136-137 

shape 106, 146 

point-based sampling methods 85, 100-103, 107, 126, 128, 129, 135, 137-140, 146, 148, 149 

population parameters 171-172, 198 

population structure 55, 174-178, 198 

age structure in seaweeds 174-178, 198 

age structure in macroinvertebrates 198 

size structure in seaweeds 176-178 

size structure in macroinvertebrates 189-193, 197, 198 

presence-absence data 63 

primary productivity 58, 156 

PRIMER software 65 

pseudoreplication 75, 85 

quadrats (see plots) 

random sampling 12, 75, 81, 88, 102, 190 

random site selection 36-38 

random walk 80 

randomly located plots 79-81, 89 

rapid surveys 63, 107, 124-129, 148 

recruitment 55, 171, 189, 197, 198 

red algae 32, 54, 60, 64, 88, 110, 174, 175, 177, 179 

reference points and marks 55, 88, 175, 183 

regional approaches 15, 18, 37, 97 

repeated sampling 17, 79, 86, 118, 157, 167 

reproduction in seaweeds 178-182 

reproduction in macroinvertebrates 193-196 

reproductive output/allocation in seaweeds 179-182 
Final Study Report – Murray et al. 

212

reproductive output/allocation in macroinvertebrates 193-196 

resorcinol 179 

response species groups 58 

retrospective goals 37 

retrospective risk assessment 13 

risk assessment 13 

rockweeds (see fucoids) 

rocky intertidal habitats: characteristics 9-10 

salinity 

factor 24, 30 

measurement 30 

sample storage and preservation 161, 162-164 

sample unit dimensions 108-110 

sample number or sample size 78, 84, 89-93, 109 

sample units 99-110 

sampling accuracy 81, 85-86, 107, 136, 139 

sampling bias 81-82, 101, 131 

sampling effort 79, 109 

sampling error 136, 137, 138, 159 

sampling precision or repeatability 82, 84, 90, 137, 149 

sampling design 77-86 

aggregated design 77 

isolative segregation design 77 

proportional stratified sampling 82, 83 

randomized sampling 77, 79-81 

stratification of sampling units 82 

stratified sampling with optimum allocation 83, 84 

stratified simple random sampling 82, 83, 87 

matic sampling 77, 80-82 

targeted sampling 80, 82, 87, 89 

sampling time (see sampling effort) 

sampling units: placement ( see sampling designs) 

sand influence 

factor 24, 29-30 

measurement 30, 133 

satellite photography 31 

sea grasses (see surfgrasses) 

sea stars 53, 105, 106, 108, 110, 112, 113, 118, 130, 159, 183, 184, 190, 193 

seaweeds 

age 173, 174-175 

lifespan 174 

axis length 176-177, 198 

growth rates 173 

morphology and morphological variation 173, 176-177, 198 

life history phases 178-179 

reproduction 178-182 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 213

reproductive output/allocation 179-182 

size determination and categorization 176-178 

sessile invertebrates (see also barnacles, anemones, mussels, colonial invertebrates, sponges, 

bryozoans) 107, 124, 131, 133, 135, 159, 183 

sewage 12, 16, 40, 51, 52, 65 

sex ratios 193 

sexual dimorphism 193 

shell allometry 188, 190 

shell decalcification 195 

shore aspect and slope 28 

shoreline classification 24-33 

Shoreline Classification and Landscape Extrapolation (SCALE) 26, 33-34 

similarity index 92, 130 

SIMPER 65 

sites 

geographic proximity 40 

physically matching 40, 41 

replication 41 

types 

control 15-16 

impact 15-16 

reference 38 

sentinel 36, 38, 42 

site selection 

bias 39 

methods 36-40 

impact studies 39-40 

monitoring studies 36-39 

design-based inference 36-39 

model-based inference 36-39 

size classes 190 

size structure (see population structure) 

snails 52, 108, 110, 127, 130, 159, 161, 164, 184, 185, 187, 188, 190, 193, 194, 196 

sociability 125-126 

Southern California Bight Pilot Project 37 

Spatial Autocorrelation 85, 102, 107 

spatial variation (see also natural variation) 9-10, 12, 15, 16, 31, 36, 41, 56, 78, 82, 86, 89, 141, 

167, 186, 197 

species-level sampling 49 

species richness (see diversity, richness) 

species types 

charismatic 52, 66 

disturbance resistant species 29, 40, 49 

indicator species 17, 27, 51, 53, 61, 66, 94 

key or keystone species 17, 51, 52, 53, 66 

long-lived 49, 52 
Final Study Report – Murray et al. 

214

millstone 52, 66 

morphospecies 58 

opportunistic species 29, 30, 59, 157, 174 

psammophytic species 30 

rare or scarce 53-54, 76, 86, 113, 131, 139, 140, 149 

surrogate 58 

sponges 124, 130, 132, 156, 159 

statistical considerations 75-79, 157 

statistical power 54, 56, 61, 77-79, 87, 89, 91, 93, 109, 141, 171 

statistical tests 

analysis of variance (ANOVA) 15, 16, 40, 65 

analysis of covariance (ANCOVA) 15 

chi square 191 

Kolmogorov-Smirnov 191 

multivariate analyses 15, 53, 54, 63-65, 67, 157 

cluster 63, 64 

discriminant analysis 63 

non-metric multidimensional scaling (MDS) 63, 65, 66 

principal component analysis (PCA) 63, 65 

regression analysis 15, 40, 159, 187, 188, 196 

statistical variance 12, 53, 54, 61, 77, 78, 84, 86, 87, 89, 91, 108, 109, 141, 171 

stressors 13, 34, 36, 37, 38, 39, 51, 52, 57, 62 

study cost issues 12, 13, 18-19, 37, 40, 54, 56, 57, 75, 81, 109, 117, 139, 143, 144, 150, 157, 158, 

167, 184, 193, 197 

study goals 10 

study types 12 

baseline or one-time/“one-off’ studies 12, 13, 79, 86 

field studies 12 

impact studies (see also impact study designs) 12, 13-16, 86, 93, 171 

monitoring studies 12, 17-19, 61, 86, 87, 113, 149, 157, 167, 171, 197 

patterns and processes studies 12 

substratum 

aspect 24, 28 

roughness 24 

slope 24, 28 

topographical heterogeneity 28-29, 134 

type 24, 28 

supra-species level sampling 56 

surf similarity index 26 

surfgrasses and sea grasses 32, 34, 36, 52, 64, 101-102, 174, 178 

surveys (see rapid surveys) 

tags and tagging organisms 175, 183-185, 188 

targeted plots 89 

taxonomic expertise 10, 54, 56, 57, 58, 62, 63, 113 

taxonomic sufficiency 57 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 215

temporal variation (see also natural variation) 10, 12, 15, 18, 26, 31, 36, 39, 51, 78, 86, 87, 88, 

89, 150, 167, 197 

tetracycline 185 

tidepools 28, 33, 35, 79, 81 

tidal height or elevation 25, 84 

timed search 113-114 

topographical heterogeneity 28-29 

index 28-29 

measurement 29 

transects (see line transects) 

tube dwelling organisms 32, 36, 64, 124, 127, 133 

type I error 77-78 

type II error 77-78 

urchins 32, 127, 159, 183, 186, 190, 193 

value-based decisions 34 

variable area transect distance sampling (see distance-based sampling) 

video sampling 126-145, 148 

visual estimates or visual scanning 135, 140 

von Bertalanffy growth function 188-189 

wave energy 

factor 24, 25-27 

measurement 25-26 

wave fetch 24, 27 

zero-rich data 53, 63 

zonation 9 
Final Study Report – Murray et al. 

216

Taxonomic Index 

Abietinaria spp. 

Anthopleura spp. 

Anthopleura elegantissima 

Ascophyllum nodosum 

Astraea undosa (see Lithopoma undosum) 

Babylonia japonica 

Balanus spp. 

Bangia spp. 

Bossiella spp. 

Brachidontes rodriguezi 

Callinectes sapidus 

Capitella capitata 

Cellana radiata 

Chiton tuberculatus 

Chondracanthus spp. 

Chondracanthus canaliculatus 

Chondrus spp. 

Chthamalus spp. 

Cladophora spp. 

Constantinea simplex 

Corallina spp. 

Crassostrea virginica 

Cystoseira spp. 

Dictyota spp. 

Ecklonia radiata 

Egregia menziesii 

Eisenia arborea 

Endocladia muricata 

Fucus spp. 

Fucus gardneri 

Fucus serratus 

Fucus vesiculosus 

Gelidium pusillum 

Gelidium robustum 

Halidrys spp. and H. dioica 

Halimeda spp. 

Haliotis spp. 

Hesperophycus californicus 

Himanthalia elongata 

Laminaria spp. 

Laminaria digitata 

Laminaria hyperborea 

Laminaria saccharina 

Laurencia papillosa 

110 

32, 53 

54 

174, 175, 176, 177, 181 

188 

32, 85 

60 

32 

51 

187 

51 

188, 189 

188 

32, 60 

64 

60 

32, 64 

60 

175 

32, 60, 64 

187 

180 

60 

181 

32, 64 

64 

32, 54, 88, 110 

52, 60, 174, 180, 181 

54, 180 

181 

181 

64 

64 

32, 180 

60 

32 

32, 180 

181 

32, 60, 173, 175, 181 

179 

179 

174 

110 
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

217

Leathesia difformis 

Leptasterias spp. 

Lithophyllum incrustans 

Lithopoma undosum 

Lithothamnion spp. 

Littorina spp. 

Littorina scutulata 

Lottia gigantea 

Macclintockia scabra 

Macrocystis pyrifera 

Mastocarpus spp. 

Monostroma spp. 

Mytilus spp. 

Mytilus californianus 

Mytilus trossulus 

Notoacmaea petteridi 

Nucella spp. 

Nucella emarginata 

Patella concolor 

Patelloida alticostata 

Pelagophycus porra 

Pelvetia sp. (see also Silvetia) 

Pelvetia canaliculata 

Petrocelis middendorfii 

Peyssonnelia spp. 

Phragmatopoma californica 

Phyllospadix spp. 

Pollicipes polymerus 

Porphyra spp. 

Pseudolithoderma nigra 

Pseudolithophyllum spp. 

Pterocladia (see Pterocladiella) 

Pterocladiella capillacea 

Pterosiphonia complanata 

Pterygophora californica 

Ralfsia spp. 

Rhodymenia spp. 

Sargassum spp. 

Serpulorbis squamigerus 

Silvetia compressa 

Strongylocentrotus spp. 

Tegula funebralis 

Tegula gallina 

Turbo setosus 

Ulva spp. 

Ulva lactuca 

174 

110 

181 

188 

60 

32, 52, 110 

110 

110, 189, 192 

110 

64, 174, 181 

110, 175 

60 

32, 34 

59 

59 

195 

52 

184 

197 

195 

174 

174 

175 

60 

32 

32, 35, 64, 101 

32 

60, 177 

64 

64 

64, 174 

174 

175 

60 

177 

64 

64 

32, 53, 110, 174, 177, 181-182 

32 

110, 187 

196 

188 

60, 64 

181 
Final Study Report – Murray et al. 

218
Methods for Performing Monitoring, Impact, and Ecological Studies on Rocky Shores

 

The Department of the Interior Mission 

As the Nation's principal conservation agency, the Department of the Interior has responsibility for most 

of our nationally owned public lands and natural resources. This includes fostering sound use of our 

land and water resources; protecting our fish, wildlife, and biological diversity; preserving the 

environmental and cultural values of our national parks and historical places; and providing for the 

enjoyment of life through outdoor recreation. The Department assesses our energy and mineral 

resources and works to ensure that their development is in the best interests of all our people by 

encouraging stewardship and citizen participation in their care. The Department also has a major 

responsibility for American Indian reservation communities and for people who live in island territories 

under U.S. administration. 

The Minerals Management Service Mission 

As a bureau of the Department of the Interior, the Minerals Management Service's (MMS) primary 

responsibilities are to manage the mineral resources located on the Nation's Outer Continental Shelf 

(OCS), collect revenue from the Federal OCS and onshore Federal and Indian lands, and distribute 

those revenues. 

Moreover, in working to meet its responsibilities, the Offshore Minerals Management Program

administers the OCS competitive leasing program and oversees the safe and environmentally sound 

exploration and production of our Nation's offshore natural gas, oil and other mineral resources. The 

MMS Royalty Management Program meets its responsibilities by ensuring the efficient, timely and 

accurate collection and disbursement of revenue from mineral leasing and production due to Indian 

tribes and allottees, States and the U.S. Treasury. 

The MMS strives to fulfill its responsibilities through the general guiding principles of: (1) being 

responsive to the public's concerns and interests by maintaining a dialogue with all potentially affected 

parties and (2) carrying out its programs with an emphasis on working to enhance the quality of life for 

all Americans by lending MMS assistance and expertise to economic development and environmental 

protection.