National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center 

Fort Collins, Colorado 

San Francisco Bay Area Network Vital Signs 

Monitoring Plan 

Natural Resource Report NPS/SFAN/NRR—2006/017 
ON THE COVER 

Susan O'Neil (Natural Resource Specialist with the SFAN Inventory and Monitoring Program) collects plants at John Muir 

National Historic Site. NPS photo. 
i 

San Francisco Bay Area Network Vital Signs 

Monitoring Plan 

Natural Resource Report NPS/SFAN/NRR—2006/017 

Dawn Adams, Sarah Allen, Jennifer Bjork, Mary Cooprider, Amy Fesnock, Marcus Koenen, 

Tom Leatherman, Susan O'Neil, David Press, David Schirokauer, Brad Welch, and Brian 

Witcher 

San Francisco Bay Area Network 

Golden Gate National Recreation Area 

Fort Cronkhite 

Sausalito, CA 94965 

October 2006 

U.S. Department of the Interior 

National Park Service 

Natural Resource Program Center 

Fort Collins, Colorado
The Natural Resource Publication series addresses natural resource topics that are of interest and 

applicability to a broad readership in the National Park Service and to others in the management 

of natural resources, including the scientific community, the public, and the NPS conservation 

and environmental constituencies. Manuscripts are peer-reviewed to ensure that the information 

is scientifically credible, technically accurate, appropriately written for the intended audience, 

and is designed and published in a professional manner. 

Natural Resource Reports are the designated medium for disseminating high priority, current 

natural resource management information with managerial application. The series targets a 

general, diverse audience, and may contain NPS policy considerations or address sensitive issues 

of management applicability. Examples of the diverse array of reports published in this series 

include vital signs monitoring plans; "how to" resource management papers; proceedings of 

resource management workshops or conferences; annual reports of resource programs or 

divisions of the Natural Resource Program Center; resource action plans; fact sheets; and 

regularly-published newsletters. 

Views and conclusions in this report are those of the authors and do not necessarily reflect 

policies of the National Park Service. Mention of trade names or commercial products does not 

constitute endorsement or recommendation for use by the National Park Service. 

Printed copies of reports in these series may be produced in a limited quantity and they are only 

available as long as the supply lasts. This report is also available from the Natural Resource 

Publications Management website (http://www.nature.nps.gov/im/units/SFAN) on the Internet or 

by sending a request to the address on the back cover. 

Please cite this publication as: 

Adams, D., S. Allen, J. Bjork, M. Cooprider, A. Fesnock, M. Koenen, T. Leatherman, S. O'Neil, 

D. Press, D. Schirokauer, B. Welch, and B. Witcher. 2006. San Francisco Bay Area Network 

Vital Signs Monitoring Plan. NPS/SFAN/NRR 2006/017. National Park Service, Fort Collins, 

Colorado. 

NPS D-40, October 2006 
iii 

Contents 

Page 

Contents .........................................................................................................................................iii 

Figures........................................................................................................................................... vii 

Tables...........................................................................................................................................viii 

Appendixes ..................................................................................................................................... x 

Approval Signatures....................................................................................................................... xi 

Acknowledgments......................................................................................................................... xii 

Executive Summary.....................................................................................................................xiii 

Note to the reader:....................................................................................................................... xvii 

Chapter 1 Introduction and Background......................................................................................... 1

1.1 Purpose .................................................................................................................................. 1 

1.2 Monitoring Goals and Strategies ........................................................................................... 4

1.3 Overview of Network Parks and Selected Natural Resources ............................................ 13 

1.4 Status of Monitoring Programs in and Adjacent to the SFAN Parks .................................. 27 

Chapter 2 Conceptual Models....................................................................................................... 33 

2.1 Ecological Conceptual Models............................................................................................ 33 

2.2 Organizational Structure of SFAN Conceptual Models...................................................... 33 

2.3 Description of Drivers ......................................................................................................... 34 

2.4 Descriptions of Stressors ..................................................................................................... 38 

2.5 Generalized Conceptual Model ........................................................................................... 43 

2.6 Driver, Stressor, and Vital Signs Matrix ............................................................................. 45 

2.7 Ecosystem Models............................................................................................................... 45 

2.8 Specific Vital Sign Example................................................................................................ 51 

2.9 Implications for Vital Signs Selection................................................................................. 51 
iv 

Chapter 3 Vital Signs.................................................................................................................... 57 

3.1 Overview of the Vital Signs Selection Process ................................................................... 57 

3.2 SFAN Vital Signs Selection Process................................................................................... 57 

3.3 Selected Vital Signs............................................................................................................. 63 

3.4 Connectivity Between Selected Vital Signs and the SFAN Conceptual Model.................. 68 

Chapter 4 Sampling Design .......................................................................................................... 73 

4.1 Overview of Sampling Design ............................................................................................ 73 

4.2 Sampling Concepts and Definitions .................................................................................... 73 

4.3 Sampling Approaches.......................................................................................................... 75 

4.4 Grid-based Sampling ........................................................................................................... 77 

4.5 List-based Sampling ............................................................................................................ 79 

4.6 Index Sites ........................................................................................................................... 81 

4.7 Multi-Pronged Approaches.................................................................................................. 82 

Chapter 5 Sampling Protocols ...................................................................................................... 85 

5.1 Overview of High Priority Vital signs................................................................................. 85 

Chapter 6 Data Management ........................................................................................................ 95 

6.1 Overview of Data Management........................................................................................... 95 

6.2 Data Management Roles and Responsibilities .................................................................... 97 

6.3 Data Management Infrastructure......................................................................................... 99 

6.4 Data Management Standards............................................................................................. 101 

6.5 Data Acquisition and Processing....................................................................................... 101 

6.6 Quality Assurance/Quality Control ................................................................................... 102 

6.7 Data Documentation.......................................................................................................... 103 

6.8 Data and Information Dissemination................................................................................. 105 

6.9 Data Maintenance, Storage, and Archiving....................................................................... 106 
v 

6.10 Water Quality Data.......................................................................................................... 107 

Chapter 7 Data Analysis and Reporting...................................................................................... 109 

7.1 Overview of Data Analysis and Reporting........................................................................ 109 

7.2 Data Analysis..................................................................................................................... 109 

7.3 Reporting ........................................................................................................................... 110 

7.4 Interpretation and Outreach............................................................................................... 116 

Chapter 8 Administration/Implementation of the Monitoring Program..................................... 119 

8.1 Board of Directors ............................................................................................................. 119 

8.2 Technical Steering Committee .......................................................................................... 119 

8.3 Other Committees.............................................................................................................. 120 

8.4 Network Staff .................................................................................................................... 120 

8.5 Shared Positions ................................................................................................................ 122 

8.6 The PWR Inventory and Monitoring Coordinator ............................................................ 123 

8.7 Integration with Other Divisions ....................................................................................... 123 

8.8 Existing and Potential Monitoring Partnerships................................................................ 123 

8.9 Program Integration........................................................................................................... 125 

8.10 Program Reviews............................................................................................................. 126 

Chapter 9 Schedule ..................................................................................................................... 127 

9.1 Timing and Frequency....................................................................................................... 127 

9.2 Water Quality Schedule..................................................................................................... 130 

Chapter 10 Budget ...................................................................................................................... 131 

10.1 Annual Funding Sources ................................................................................................. 131

10.2 Annual Program Budget .................................................................................................. 131

10.3 Annual Vital Signs Allocation......................................................................................... 131 

10.4 Protocol Development and Implementation Costs .......................................................... 132 
vi 

10.5 Projected Costs ................................................................................................................ 134 

Chapter 11 Literature Cited ........................................................................................................ 135 

Glossary ...................................................................................................................................... 143 
vii 

Figures 

Page 

Figure 1.1. Relationships between monitoring, inventories, research, and natural resource 

management activities in national parks (modified from Jenkins et al. 2002).............. 5 

Figure 1.2. Basic approach to identifying and selecting vital signs for integrated monitoring of 

park resources (source: K. Jenkins, USGS Olympic Field Station). ............................. 7 

Figure 1.3. Conceptual approach for selecting vital signs.............................................................. 9 

Figure 1.4. Location of the SFAN parks....................................................................................... 14

Figure 2.1. Nested spatial scale example relevant to the conceptual model, as depicted for PINN.

..................................................................................................................................... 34 

Figure 2.2. Generalized conceptual model for the SFAN............................................................. 44 

Figure 2.3. Marine ecosystems conceptual model of how drivers and stressors act through 

different marine ecosystem forms to produce changes in components of different 

resource realms within the SFAN................................................................................ 52 

Figure 2.4. Aquatic/Wetland ecosystem conceptual model of how drivers and stressors act 

through different aquatic ecosystem forms to produce changes in components of 

different resource realms within the SFAN................................................................. 53 

Figure 2.5. Terrestrial ecosystem conceptual model of how drivers and stressors act through 

different terrestrial ecosystem forms to produce changes in components of different 

resource realms within the SFAN................................................................................ 54 

Figure 2.6 Example of a conceptual model for a specific vital sign (raptors and condors) and a 

measurable parameter (prairie falcon nest success). ................................................... 55 

Figure 6.1 Core project data stewardship duties of project leaders and data managers. .............. 99 

Figure 6.2 Model of the national-level application architecture................................................. 100 

Figure 6.3 Schematic representing the layout and connectivity of SFAN computer resources. 101 

Figure 6.4 Diagram of the typical project data life cycle. .......................................................... 104 

Figure 6.5 Data flow diagram for water quality data.................................................................. 108 
viii 

Tables 

Page 

Table 1.1 GPRA goals for each park that pertain to information generated by the Inventory and 

Monitoring program of the SFAN............................................................................... 11 

Table 1.2. Timeline for the SFAN to complete the 3-phase planning and design process for 

developing a monitoring program. .............................................................................. 12 

Table 1.3. Management objectives for SFAN parks..................................................................... 23 

Table 1.4. Monitoring questions and potential vital signs related to management issues for the 

SFAN parks. ................................................................................................................ 25 

Table 1.5. Summary of current and historical monitoring programs within the SFAN parks as of 

2004. Numbers in the columns for each park represent the number of years monitoring 

has been conducted in that park for the .orresponding program. Participating agencies 

and partners are listed for each program. .................................................................... 28 

Table 1.6. Water resources monitoring summary......................................................................... 30 

Table 2.1 Significant relationships between general atmospheric vital signs and drivers and 

stressors in the SFAN parks......................................................................................... 46 

Table 2.2 Significant relationships between general biotic (faunal) vital signs and drivers and 

stressors in the SFAN parks......................................................................................... 47 

Table 2.3 Significant relationships between general biotic (vegetation) vital signs and drivers and 

stressors in the SFAN parks......................................................................................... 48 

Table 2.4 Significant relationships between general hydrospheric vital signs and drivers and 

stressors in the SFAN parks......................................................................................... 49 

Table 2.5 Significant relationships between general lithospheric vital signs and drivers and 

stressors in the SFAN parks......................................................................................... 50 

Table 3.1 Important activities and dates in the SFAN vital signs selection process. ................... 58 

Table 3.2 Criteria used to prioritize SFAN vital signs.................................................................. 59 

Table 3.3 Vital signs selected by the SFAN within the NPS Ecological Monitoring Framework. 

Vital signs selected by SFAN are assigned to the national framework Level 3 category 

that most closely pertains to that vital sign. Bolded vital signs ranked in the top 18 of 

the list of 63 vital signs and will be implemented first................................................ 64 

Table 3.4 Revised vital sign names for water resources vital signs from scoping workshops..... 67
ix 

Tables (continued) 

Page 

Table 3.5 List of specific vital signs linked to conceptual models. Rank number is the priority. 68 

Table 4.1 Notational representation of five revisit designs. An ‘X’ in a cell indicates that all 

members of the panel are visited that occasion. .......................................................... 76 

Table 4.2 The overall sample design approach, methods for spatially allocating samples, and the 

revisit plan for vital signs monitoring.......................................................................... 78 

Table 5.1 Key information from Protocol Development Summaries (PDS) for each of the top 18 

vital signs (see Appendix 4). ....................................................................................... 86 

Table 6.1 Categories of data products and project deliverables. .................................................. 97 

Table 6.2 Summary or programmatic roles and responsibilities for data stewardship................. 98 

Table 6.3 Repositories for SFAN products................................................................................. 106 

Table 7.1 Data analysis and reporting schedule for SFAN vital signs monitoring program. ..... 112 

Table 9.1 Schedule of vital signs protocol development. ........................................................... 127 

Table 9.2 Annual schedule of vital signs data collection............................................................ 129 

Table 9.3 Water quality monitoring schedule. Note that the table displays on monitoring cycle; 

therefore FY10 will mirror FY06. ............................................................................. 130 

Table 10.1 Annual funding sources. ........................................................................................... 131 

Table 10.2 Annual monitoring budget........................................................................................ 132 

Table 10.3 Estimated annual vital signs project costs for FY05-FY09. ..................................... 133 

 

 
x 

Appendixes 

 

Appendix A. Brief Descriptions of Parks in the San Francisco Bay Area Network 

 

Appendix B. SFAN Species of Special Interest 

Appendix C. Current and Historic Monitoring Programs within the SFAN 

Appendix D. Protocol Development Summaries 
xi 

Approval Signatures 

[original signatures on file] 

___________________________________________________ ______9/30/05____ 

Steve Fancy, Monitoring Program Leader Date 
xii 

Acknowledgments 

The SFAN Monitoring Plan was prepared by Dawn Adams, Dr. Sarah Allen, Jennifer Bjork, 

Mary Cooprider, Amy Fesnock, Marcus Koenen, Tom Leatherman, Susan O’Neil, Dave Press, 

Dave Schirokauer, Dr. Brad Welch and Brian Witcher. 

Valuable reviews and additional contributions were made by Marie Denn, Sharon Franklet, Dr. 

Paul Geissler, Daphne Hatch, Jason Herynk, Brannon Ketcham, Dr. William Merkle, Chad 

Moore, Jane Rodgers, Lorraine Parsons, and Dr. Andrea Woodward. 

We would like to thank the SFAN Board of Directors, Mai-Liis Bartling, Glenn Fuller, Tom 

Leatherman, Martha Lee, Cicely Muldoon, and Don Neubacher, for their support and 

participation in the processes leading to this Monitoring Plan. Thanks to representatives from all 

the SFAN parks who contributed their time and expertise to the process of identifying, ranking 

and prioritizing the Vital signs. 

Reviews, perspectives and insights were gratefully appreciated from the researchers and 

managers of U. S. Geological Service-Biological Resource Division, University of California 

and California State University systems, PRBO Conservation Science, NPS Pacific West 

Regional Office and parks, and other agencies that participated in the Vital signs Scoping 

Workshops, Vital Signs Ranking Process and Vital Signs Prioritization Meetings. The process 

was uncharted and the patience of everyone involved is much appreciated. 

In particular, we would like to thank the reviewers of the Phase II and III versions of this 

document which include Dr. Penny Latham, Pacific West Regional I&M Coordinator, Dr. John 

Gross of the National I&M Program Office, Dr. Debbie Elliott-Fisk of University of California at 

Davis, Dr. Reginald Barrett of University of California at Berkeley, Dr. Steve Schwarzbach, 

Deputy Center Director of USGS Western Ecological ResearchCenter, and seven anonymous 

reviewers. 

We are especially grateful to Dr. Steve Fancy and the staff at the NPS National Inventory and 

Monitoring Program Office and the NPS Water Resource Division for their guidance on the vital 

signs selection and prioritization process and the preparation of this Monitoring Plan. 
xiii 

Executive Summary 

In 2000, the National Park Service (NPS) created 32 networks of NPS units across the United 

States that were formed and funded to “improve the ability of the NPS to provide state-of-the-art 

management, protection, and interpretation of and research on the resources on the NPS ... and 

to assure the full and proper utilization of the results of scientific studies for park management 

decisions” (National Parks Omnibus Management Act of 1998). The San Francisco Bay Area 

Network (SFAN) is one of eight of these networks in the Pacific West Region of the NPS. The 

SFAN is composed of eight park units and includes Point Reyes National Seashore, Pinnacles 

National Monument, John Muir National Historic Site, Eugene O’Neill National Historic Site, 

and Golden Gate National Recreation Area including Muir Woods National Monument, Fort 

Point National Historic Site, and Presidio of San Francisco. The network fosters collaboration 

and creates efficiencies of scale in designing and implementing a natural resource focused 

Inventory and Monitoring (I&M) program. 

The SFAN parks are within the Central California Coast Ranges and share many ecological 

systems and associated anthropogenic influences which include invasions of non-native species, 

altered fire regimes, degraded air and water quality, heavy recreational pressure, adjacent habitat 

loss, and climate change with associated sea level rise. The parks are extremely diverse in natural 

resources and have a unique set of complex management challenges within a densely populated 

setting. Most of the SFAN units are part of the Central California International Biosphere 

Reserve (Myers et al 2000), and are part of the California Floristic Province, an area recognized 

by Conservation International as a hotspot of biodiversity. 

The first step in developing a monitoring plan, which began in 2000, was to complete species 

inventories for vascular plants and vertebrate animals. These inventories are currently being 

certified and natural resource bibliographic and metadata information systems are being updated. 

In 2003, the SFAN implemented a conceptual model-based strategy to create a natural resources 

monitoring program. This document describes the strategy, the process, some of the background 

information used and articulates the resulting monitoring plan. 

The broad goals of NPS and SFAN Vital Signs Monitoring program are to: 

1) determine status and trends in selected indicators of the condition of park ecosystems 

to allow managers to make better-informed decisions; 

2) provide early warning of abnormal conditions and impairment of selected resources to 

help develop effective mitigation measures and reduce costs of management; 

3) provide data to better understand the dynamic nature and condition of park ecosystems 

and to provide reference points for comparisons with other, altered environments; 

4) provide data to meet certain legal and Congressional mandates related to natural 

resource protection and visitor enjoyment; and, 

5) provide a means of measuring progress towards performance goals. 
xiv 

Subject matter experts and park natural resource managers convened to create a series of 

conceptual models that identified the natural drivers and anthropogenic stressors (agents of 

change) that are linked to key resources and natural processes of interest. The conceptual model, 

described in chapter 2, displays these elements and linkages at three hierarchical levels. Over 60 

potential vital signs (chapter 3) were identified based on these relationships. “Vital Signs” are a 

subset of physical, chemical, and biological elements and processes of ecosystems, selected to 

represent the condition of natural resources, effects of stressors, or elements that have important 

management values. A group of 55 subject matter experts and natural resource managers 

prioritized the list of 63 vital signs using 4 ranking criteria - ecological significance, management 

significance, cost and feasibility, and legal mandate. The existence of active long-term 

monitoring datasets in the parks and region were also considered as a factor in the ranking. From 

the prioritized list of 63 vital signs, the SFAN I&M Technical Steering Committee identified 18 

vital signs for which detailed protocol development would commence (Table I). Six of the 

selected vital signs (stream fish assemblages, pinnipeds, northern spotted owl, raptors and 

condors, landbird population dynamics, and western snowy plover) had monitoring programs in 

place and were incorporated into the larger SFAN I&M program. 

Table I. Vital signs selected for protocol development and their rank. 

 

SFAN Vital Signs Rank SFAN Vital Signs Rank 

Weather and Climate 1,2 1 Pinnipeds 1,2 10 

Invasive Plant Species (early detection) 2 2 Plant Community Change 11 

Freshwater Quality 1,2 3 Landscape Dynamics 12 

Air Quality 1

 4 Threatened and Endangered (T&E) Butterflies 

1 13 

Stream Fish Assemblages 1,2 5 Freshwater Dynamics 1,2 14 

Rare Plant Species 1,2 6 Wetlands 15 

Northern Spotted Owl 1,2 7 Riparian Habitat 16 

Amphibians and Reptiles 8 Landbird Population Dynamics 1,2 17 

Western Snowy Plover 1,2 9 Raptors and Condors 1,2 18 

1

Previous monitoring data exists 

2

Scheduled to receive funding in FY2006 

Sampling design (chapter 4) is generally tied to the specific trend or phenomena (e.g., detecting 

population change in a focal species) a vital sign is designed to detect. Many of these 18 vital 

signs measure trends or phenomena in different resources realms, such as hydrosphere and 

atmosphere, and at different spatial scales and thus do not lend themselves to co-design of 

sampling regimes. However, potentially close linkages exist between some vital signs, especially 

1) freshwater dynamics and stream fish assemblages, 2) invasive species, threatened and 

endangered (T&E) butterflies, and rare plants, and 3) wetlands and riparian habitat with plant 

communities. A grid-based sampling design for plant community change is described. A A list-
xv 

based sampling design is described for water quality, freshwater dynamics, raptors and condors, 

pinnipeds, and Western Snowy Plovers. Index sites will be used for weather and climate, air 

quality, landbirds, and Northern Spotted Owls. 

One of the most significant and enduring products of the I&M program are the detailed 

individual monitoring protocols and associated Standard Operating Procedures (SOPs; 

summarized in chapter 5). These dynamic documents are designed to communicate data 

collection, analysis, and reporting methods to peers and managers and to allow these long-term 

monitoring programs to continue in the face of inevitable staff change. Protocols for six on-going 

vital signs have been developed and are currently in various stages of the peer review and 

revision process. Protocols for the remaining 12 vital signs will be developed over the next 

several years based on their priority, funding availability, and protocol development activity at 

the regional and national levels. SFAN and park-based staff are currently working on the rare 

plant, invasive non-native plant species-early detection, water quality, weather/climate, and 

freshwater dynamics protocols. Air quality, weather, water quality and invasive species early 

detection protocol development are also receiving significant attention at the regional and 

national levels within the I&M program. 

The amount of data and information this monitoring program generates will steadily increase 

over the next several years as network and park staff complete additional protocols and 

monitoring begins on new vital signs. Careful data collection and management, and 

dissemination of data and information products are essential if the results are to be used in 

resource management decisions. Considerable human and technological resources are required to 

adequately manage the large quantities of highly complex data generated for each vital sign. The 

data management plan (summarized in chapter 6), describes data and information management 

and dissemination, and outlines the duties of the networks’ three data managers. More specific 

procedures for information management and reporting are contained in the specific protocols. 

Reporting trends in park vital signs in annual reports, synthesis reports, program reviews, and 

peer reviewed literature are all goals of the SFAN I&M program outlined in chapter 7. 

In order to ensure for a successful monitoring program, chapters 8, 9, and 10 present an 

operation strategy which includes the administrative plan, implementation schedule, and budget 

for the first few years. The administrative plan includes: a staffing plan, network integration with 

other park operations, key partnerships, and how in-house field work will be carried out. The 

network relies strongly on existing park personnel as principal investigators for some vital signs. 

Key partnerships include the Bureau of Land Management, California Native Plant Society, 

California Department of Fish and Game, California State Parks, NOAA Fisheries and NOAA 

Marine Sanctuaries, PRBO Conservation Science, USGS- Biological Resources Division, and 

Ventana Wilderness Society. Annual funding for the SFAN is $747,200 with an additional 

$69,000 coming from the National Park Service Water Resources Division for water quality 

monitoring. During the first year of full implementation of the monitoring plan (FY 2006), 

approximately 76% of the budget will be spent on personnel (permanent, term, seasonal) and 

17% on cooperative agreements and contracts. Only three percent of the budget goes to 

administration and seven percent goes to operations and equipment. It should be noted that at 

least 30% of the budget goes to information/data management. 
xvi 

The SFAN I&M program is embarking on a long-term vital signs monitoring program, the full 

value of which will continue to increase for many years.. Many drivers and stressors of 

ecosystem process impose their effects at multiple time scales. The level of detail in this and the 

specific vital signs protocol documents is an acknowledgment of the long-term nature of this 

program’s goals. It is likely that data collection and analysis for most of these protocols 

implemented by the SFAN within the next five years will span the careers of several program 

managers. The long-term nature of this program also dictates that stressors and resources of 

concern may change along with the technology and analysis methods available to the vital signs 

program. The periodic programmatic reviews will insure that import changes are considered and 

incorporated into subsequent updates of this document. 
xvii 

Note to the reader: 

Throughout the report, references are made to supporting sections, external documents, and web 

sites. For those references that appear as blue underlined text when the document is viewed in its 

electronic format, a hyperlink will connect the reader to the supporting information. Depress the 

“Ctrl” button and click the left mouse button simultaneously to follow the link. The web address 

is supplied for web-based documents. 

For updates and supporting documentation: 

http://www1.nature.nps.gov/im/units/sfan/index.htm 

For more information about the NPS Inventory and Monitoring Program: 

http://science.nature.nps.gov/im/monitor/index.htm 
xviii 
1

Chapter 1 Introduction and Background 

1.1 Purpose 

1.1.1 Justification for Integrated Natural Resource Monitoring 

Knowing the condition of natural resources in national parks is fundamental to the National Park 

Service's ability to manage park resources “unimpaired for the enjoyment of future generations 

(National Park Service Organic Act 1916).” National Park managers across the country are 

confronted with increasingly complex and challenging issues that require a broad-based 

understanding of the status and trends of park resources as a basis for making decisions and 

working with other agencies and the public to preserve and protect these resources. For years, 

managers and scientists have sought a way to characterize and determine trends in the condition 

of parks and other protected areas to assess the efficacy of management practices and restoration 

efforts and to provide early warning of impending threats. 

The challenge of protecting and managing a park’s natural resources requires a multi-agency, 

ecosystem approach because most parks are open systems, with threats such as air and water 

pollution, invasive species, exotic diseases, water withdrawals, resources extraction and habitat 

fragmentation originating from outside of the park’s boundaries. An ecosystem approach is 

needed because no single spatial scale is appropriate for all system components and processes; 

the appropriate scale for understanding and effectively managing a resource might be at the 

home range, habitat patch, or landscape level, and in some cases may require a regional, national 

or international effort to understand and manage the resource. Variations in ecological 

phenomena also occur at different temporal scales; for example, plant community succession 

occurs over decades while insect pollinator populations often vary from one year or season to the 

next. Furthermore, biological diversity is organized in a hierarchical manner (genetic, 

population, species, community, ecosystem, and landscape) and ecosystem stressors can act on 

any level in this hierarchy. For example, several species in SFAN parks have gone through 

population bottlenecks resulting in a loss of genetic diversity. Other species have been extirpated 

with consequences cascading to other ecosystem components. National parks are part of larger 

ecosystems and natural resources and processes must be understood and managed in that context. 

Natural resource monitoring provides site-specific information needed to understand and identify 

change in complex, variable, and imperfectly understood natural systems. Monitoring is defined 

as the "collection and analysis of repeated observations or measurements to evaluate changes in 

condition and progress toward meeting a management objective” (Elzinga et al. 1998). 

Monitoring data help to define the recent limits of natural variation in park resources and provide 

a basis for understanding observed changes; monitoring results may also be used to determine 

what constitutes impairment and to identify the need for change in management practices. 

Understanding the dynamic nature of park ecosystems and the consequences of human activities 

is essential for management decision-making aimed to maintain, enhance, or restore the 

ecological integrity of park ecosystems and to avoid, minimize, or mitigate ecological threats to 

these systems (Davis 2005, Roman and Barrett 1999). 
2

The intent of the National Park Service (NPS) monitoring program is to track a subset of park 

resources and processes, known as “vital signs.”Vital signs are defined as “a subset of physical, 

chemical, and biological elements and processes of park ecosystems that are selected to represent 

the overall health or condition of park resources, known or hypothesized effects of stressors, or 

elements that have important human values” (Davis 2005). This subset of resources and 

processes is part of the total suite of natural resources that park managers are directed to preserve 

“unimpaired for future generations,” including water, air, geological resources, plants and 

animals, and the various ecological, biological, and physical processes that act on these 

resources. In situations where natural areas have been so highly altered that physical and 

biological processes no longer operate under natural conditions (e.g., control of fires and floods 

in developed areas), information obtained through monitoring can help managers understand 

how to develop the most effective approach to restoration or, in cases where restoration is not 

feasible, to apply ecologically sound management. The broad-based, scientifically sound 

information obtained through natural resource monitoring will have multiple applications for 

management decision-making, research, education, and promoting public understanding of park 

resources. 

1.1.2 Legislation, Policy, and Guidance 

National Park managers are directed by federal law and NPS policies and guidance to know the 

status and trends in the condition of natural resources under their stewardship to fulfill the NPS 

mission of conserving parks unimpaired (see Summary of Laws, Policies, and Guidance, 

http://science.nature.nps.gov/im/monitor/LawsPolicy.htm). The mission of the National Park 

Service is: 

"...to promote and regulate the use of the Federal areas known as national parks, 

monuments, and reservations hereinafter specified by such means and measures as 

conform to the fundamental purposes of the said parks, monuments, and reservations, 

which purpose is to conserve the scenery and the natural and historic objects and the 

wild life therein and to provide for the enjoyment of the same in such manner and by such 

means as will leave them unimpaired for the enjoyment of future generations (National 

Park Service Organic Act 1916)." 

As more natural and cultural resources were dedicated to National Park Service authority, 

Congress recognized that all parks are interrelated to preserve a single national heritage, require 

the same level of protection, and should operate under one set of guidelines. As a precursor to 

the concept of park networks, Congress affirmed: 

"...that the national park system, which began with establishment of Yellowstone National 

Park in 1872, has since grown to include superlative natural, historic, and recreation 

areas in every major region of the United States...; that these areas, though distinct in 

character, are united through their inter-related purposes and resources into one 

national park system as cumulative expressions of a single national heritage; that, 

individually and collectively, these areas derive increased national dignity and 

recognition of their superb environmental quality through their inclusion jointly with 

each other in one national park system preserved and managed for the benefit and 

inspiration of all the people of the United States (General Authorities Act 1970)." 
3

The Government Performance and Results Act (GPRA 1993) was established to ensure that daily 

actions and expenditures are guided by both long-term and short-term goals that are, in turn, 

consistent with Department of Interior agency missions. 

Specific, long-term goals must be quantifiable. As such, measurable outcomes provide the parks 

with tangible objectives and an effective means by which to measure progress toward their goals 

and objectives (see http://www.doi.gov/gpra/nps_sp_6.pdf for specific NPS long-term goals). A 

five-year strategic plan and an annual work plan outline the strategies for reaching these goals 

while an annual performance report evaluates the annual progress made toward GPRA goals 

(NPS 2000). 

Recognizing the need to understand the condition of natural resources within the park system, a 

servicewide inventory and monitoring (I&M) program was established (NPS 1995). The I&M 

program was given the responsibility to determine the nature and status of natural resources 

under NPS stewardship and to monitor changes in the condition of these resources over time. 

Information from inventory and monitoring efforts can then be incorporated into NPS planning, 

management, tracking performance, and decision-making. 

More recently, the National Parks Omnibus Management Act of 1998 established the framework 

for fully integrating natural resource monitoring and other science activities into the management 

processes of the National Park System. The Act charges the Secretary of the Interior to 

 “continually improve the ability of the National Park Service to provide state-of-the-art 

management, protection, and interpretation of and research on the resources of the National 

Park System,” and to “...assure the full and proper utilization of the results of scientific studies 

for park management decisions.” Section 5934 of the Act requires the Secretary of the Interior to 

develop a program of “inventory and monitoring of National Park System resources to establish 

baseline information and to provide information on the long-term trends in the condition of 

National Park System resources.” 

The Natural Resource Challenge (1999; http://www.nature.nps.gov/challengedoc/) action plan 

refined the goals delineated in the NPS Strategic Plan designed to address GPRA goals (NPS 

2000). The action plan presented the challenges confronting the Park Service and strategic 

approaches for addressing these challenges over a five-year period. Extension of the servicewide 

I&M program, the formation of collaborative park networks, and active recruitment and 

inclusion of scientists in complex park natural resource issues were among the strategies 

included in the action plan. 

Congress reinforced the message of the National Parks Omnibus Management Act of 1998 in its 

text of the FY 2000 Appropriations bill: 

The Committee applauds the Service for recognizing that the preservation of the diverse 

natural elements and the great scenic beauty of America's national parks and other units 

should be as high a priority in the Service as providing visitor services. A major part of 

protecting those resources is knowing what they are, where they are, how they interact 
4

with their environment and what condition they are in. This involves a serious 

commitment from the leadership of the National Park Service to insist that the 

superintendents carry out a systematic, consistent, professional inventory and monitoring 

program, along with other scientific activities, that is regularly updated to ensure that the 

Service makes sound resource decisions based on sound scientific data.

The 2001 NPS Management Policies updated previous policy and specifically directed the 

Service to inventory and monitor natural systems: 

Natural systems in the national park system, and the human influences upon them, will be 

monitored to detect change. The Service will use the results of monitoring and research to 

understand the detected change and to develop appropriate management actions. 

Further, "The Service will: 

♦ Identify, acquire, and interpret needed inventory, monitoring, and research, including 

applicable traditional knowledge, to obtain information and data that will help park 

managers accomplish park management objectives provided for in law and planning 

documents. 

♦ Define, assemble, and synthesize comprehensive baseline inventory data describing the 

natural resources under its stewardship, and identify the processes that influence those 

resources. 

♦ Use qualitative and quantitative techniques to monitor key aspects of resources and 

processes at regular intervals. 

♦ Analyze the resulting information to detect or predict changes, including interrelationships 

with visitor carrying capacities, that may require management intervention, and to provide 

reference points for comparison with other environments and time frames. 

♦ Use the resulting information to maintain-and, where necessary, restore-the integrity of 

natural systems (2001 NPS Management Policies)." 

Additional statutes provide legal direction for expending funds to determine the condition of 

natural resources in parks and specifically guide the natural resource management of network 

parks. Detailed information on these statues can be obtained from Bean and Rowland (1997). 

1.2 Monitoring Goals and Strategies 

1.2.1 Role of Inventory, Monitoring, and Research in Resource 

Management 

Monitoring is a central component of natural resource stewardship in the NPS, and in 

conjunction with natural resource inventories and research, provides the information needed for 

effective, science-based managerial decision-making and resource protection (Figure 1.1; see 

Monitoring is a central component of natural resource stewardship in the NPS, and in 

conjunction with natural resource inventories also Definitions of Natural Resource Inventories, 

Monitoring, and Research, 
5

http://www1.nrintra.nps.gov/im/monitor/cupn/IM_Definitions.doc). The NPS strategy to 

institutionalize inventory and monitoring throughout the agency consists of a framework (see 

Framework for National Park Service Inventory and Monitoring, 

http://www1.nrintra.nps.gov/im/monitor/cupn/IM_Framework.doc) with three major 

components: 

1. Completion of 12 basic resource inventories upon which monitoring efforts can be based; 

2. A network of 11 experimental or “prototype” long-term ecological monitoring (LTEM) 

programs begun in 1992 to evaluate alternative monitoring designs and strategies; and 

3. Implementation of operational monitoring of critical parameters (i.e., vital signs) in 

approximately 270 national parks with significant natural resources that have been 

grouped into 32 networks linked by geography and shared natural resource 

characteristics. 

Monitoring

Research

Resource

Management

Inventory

Objective

Achieved?

Intervention

Needed?

Cause

Understood?

Change

Detected?

Identifies trends 

and natural 

variation

Yes

Yes

Yes

No

No

No

Yes

No

Determines

Management 

Effectiveness

Intervention

Needed?

Yes

No

Figure 0.1. Relationships between monitoring, inventories, research, and natural resource 

management activities in national parks (modified from Jenkins et al. 2002). 

The network approach will facilitate collaboration, information sharing, and economies of scale 

in natural resource monitoring, and will provide parks with a minimum infrastructure for 

initiating natural resource monitoring that can be built upon in the future. Ten of the 32 networks 

include one or two prototype long-term ecological monitoring programs, which were established 

as experiments to learn how to design scientifically credible and cost-effective monitoring 

programs in ecological settings of major importance to a number of NPS units. Because of higher 
6

funding and staffing levels, as well as U.S. Geological Survey (USGS) involvement and funding 

in program design and protocol development, the prototypes serve as “centers of excellence” that 

are able to do more extensive and in-depth monitoring and continue research and development 

work to benefit other parks. 

In the Pacific West Region, there are eight networks. The San Francisco Bay Area Network 

(SFAN) consists of eight park units, including Eugene O’Neill National Historic Site (EUON), 

Fort Point National Historic Site (FOPO), Golden Gate National Recreation Area (GOGA), John 

Muir National Historic Site (JOMU), Muir Woods National Monument (MUWO), Pinnacles 

National Monument (PINN), Point Reyes National Seashore (PORE), and the Presidio of San 

Francisco (PRES). 

1.2.2 Goals for Vital Signs Monitoring 

The five servicewide goals for vital signs monitoring for the National Park Service are: 

1. Determine status and trends in selected indicators of the condition of park ecosystems to 

allow managers to make better-informed decisions and to work more effectively with 

other agencies and individuals for the benefit of park resources. 

2. Provide early warning of abnormal conditions and impairment of selected resources to 

help develop effective mitigation measures and reduce costs of management. 

3. Provide data to better understand the dynamic nature and condition of park ecosystems 

and to provide reference points for comparisons with other, altered environments. 

4. Provide data to meet certain legal and Congressional mandates related to natural resource 

protection and visitor enjoyment. 

5. Provide a means of measuring progress towards performance goals. 

The SFAN used the five servicewide goals as the backbone for developing and prioritizing the 

monitoring program being proposed. The Network parks’ management goals and servicewide 

monitoring goals were used to develop monitoring objectives and select vital signs for long-term 

monitoring. (See Table 1.1 and Appendix 1 for details on specific park management goals). 

1.2.3 Strategic Approaches to Monitoring 

1.2.3.1 Scope and Process for Developing an Integrated Monitoring Program: Each Network has 

a unique way of determining the best selection of vital signs to monitor. SFAN followed the five 

basic steps for developing a Network monitoring program as recommended by the NPS I & M 

Program, which are further discussed in the Recommended Approach for Developing a Network 

Monitoring Program (http://science.nature.nps.gov/im/monitor/index.htm): 

1. Define the purpose and scope of the monitoring program; 

2. Compile and summarize existing data and understanding of park ecosystems; 

3. Develop conceptual models of relevant ecosystem components; 

4. Select vital signs and specific monitoring objectives for each; and 

5. Determine the appropriate sampling design and sampling protocols. 
7

Parks need flexibility to develop an effective and cost-efficient monitoring program that 

addresses the most critical information needs of each park and that can be integrated with other 

park operations such as interpretation and maintenance activities. Additionally, this process 

needs to allow existing programs that have been carefully scrutinized, existing funding sources, 

and current staff to be combined with new funding and staffing available through the Natural 

Resource Challenge and the various divisions of the Natural Resource Program Center. 

Partnerships with federal and state agencies and adjacent landowners are necessary to effectively 

understand and manage resources and threats that extend beyond park boundaries, but these 

partnerships (and the appropriate vital signs and monitoring protocols involved) differ for parks 

throughout the national park system. 

Select Vital Signs

List Potential 

Vital Signs Establish 

Priorities

Predict Stress/Response 

Relationships 

Predict Linkages 

among Components 

and Processes

STRESSORS:

Identify key 

agents of change

FOCAL RESOURCES:

Identify key resources of 

interest 

SYSTEM HEALTH:

Identify key properties 

and processes

Scoping

Conceptual 

Modeling

Integration

Figure 0.2. Basic approach to identifying and selecting vital signs for integrated monitoring of 

park resources (source: K. Jenkins, USGS Olympic Field Station). 

The complicated task of developing a Network monitoring program requires an initial investment 

in planning and design to guarantee that monitoring meets the most critical information needs of 

each park, as well as the region and the nation. The program must produce scientifically credible 

results that are clearly understood and accepted by scientists, policy makers, and the public, and 

that are readily accessible to managers and researchers. These front-end investments also ensure 

that monitoring will build upon existing information and understanding of park ecosystems and 

make maximum use of leveraging and partnerships with other agencies, organizations, and 

academia. 

1.2.3.2 Strategies for Determining What to Monitor: Monitoring is an on-going effort to better 

understand how to sustain or restore ecosystems, and serves as an "early warning system" to 

detect declines in ecosystem integrity and species viability before irreversible loss has occurred. 

The goals of the vital signs monitoring program recognize the dynamic nature and condition of park 

ecosystems and the need to identify and separate “natural” variation from undesirable anthropogenic 

sources of change to park resources. 
8

One of the key initial decisions in designing a monitoring program is deciding how much relative 

weight should be given to tracking changes in focal resources and stressors that address current 

management issues versus measures that are thought to be important to the long-term understanding 

of park ecosystems. A vital sign is most useful when it can provide information to inform a 

management decision or to quantify the effects of past decisions. Vital signs must produce data 

that can be interpreted, clearly understood, and accepted by managers, scientists, policy makers, 

and the public. However, current understanding of ecological systems is imperfect, and 

consequently, predictions of how park resources might respond to changes in various system 

drivers and stressors is limited. A monitoring program that focuses only on current 

threat/response relationships and current issues may not provide the long-term data and 

understanding needed to address high-priority issues that will arise in the future. 

The best way to meet the challenges of monitoring in national parks and other protected areas is to 

achieve a balance among different monitoring approaches, while recognizing that the program will 

not succeed without also considering political issues. NPS, therefore, has adopted a multi-faceted 

approach for monitoring park resources, based on both integrated and threat-specific monitoring 

approaches and that builds upon concepts presented originally for the Canadian National Parks 

(Figure 1.3; Woodley 1993). 

Specifically, it is recommended that vital signs be chosen from each of the following broad 

categories: 

1. Ecosystem drivers and processes that fundamentally affect park ecosystems, 

2. Stressors and their ecological effects, 

3. Focal resources of parks, and 

4. Key properties and processes of ecosystem integrity. 

Collectively, these basic strategies for choosing vital signs achieve the diverse monitoring goals of 

the National Park Service. 

1.2.3.3 Integration: Ecological, Spatial, Temporal, and Programmatic: One of the most difficult 

aspects of designing a comprehensive monitoring program is integration of monitoring projects 

so that the interpretation of the whole monitoring program yields information more useful than 

that of individual parts. Integration involves ecological, spatial, temporal, and programmatic 

aspects. An ideal ecosystem monitoring strategy will employ a suite of individual measurements 

that collectively monitor the integrity of the entire ecosystem. One approach for effective 

ecological integration is to select vital signs at various 
9

Figure 0.3. Conceptual approach for selecting vital signs. 

In certain cases where good understanding exists between potential effects and responses by park 

resources (Known Effects), monitoring of system drivers, stressors, and effected park resources 

is conducted. A set of focal resources (including ecological processes) will be monitored to 

address both known and unknown effects of system drivers and stressors on park resources. Key 

properties and processes of ecosystem status and integrity will be monitored to detect changes 

and potentially warn managers of undesirable changes in park resources. 

hierarchical levels of ecological organization (e.g., landscape, community, population, genetic; 

see Noss 1990). Similarly, spatial integration requires understanding of the scale at which 

variation in the phenomenon under investigation is best detected and how this variation presents 

at other scales. Subsequently, coordinated location of comparably scaled vital signs, and design 

of statistical sampling frameworks that permit the extrapolation and interpolation of data to 

scales other than the scale at which the data was collected can be considered. Temporal 

integration requires the development of a meaningful timeline for sampling different vital signs 

while considering characteristics of temporal variation in these vital signs. Programmatic 

integration requires coordinated monitoring planning and design by the Natural Resources 

Program Center (NRPC) divisions (Air Resources, Biological Resource Management, Geologic 

Resources, Natural Resource Information, and Water Resources) to provide guidance, technical 

support and funding to the networks. Furthermore, park-based, outside researcher, and project 

specific monitoring programs should be integrated whenever new efficiencies can be generated. 

Planning for vital signs monitoring also must be coordinated and results communicated within and 

among parks and with other agencies and institutions. Coordinated monitoring planning, design, and 

implementation efforts encourage cooperative resource use, promote sharing of data among 

neighboring land management agencies, provide context for interpreting data, and encourage 

additional research. 

 
10

1.2.3.4 Limitations of the Monitoring Program: All monitoring programs have limitations that 

are a result of the inherent complexity and variability of park ecosystems, coupled with limited 

time, funding, and staffing available for monitoring. Ecosystems are loosely defined assemblages 

that exhibit characteristic patterns on a range of scales of time, space, and organization 

complexity (De Leo and Levin 1997). Natural systems as well as human activities change over 

time, and it is extremely challenging to distinguish natural variability and desirable changes from 

undesirable anthropogenic sources of change to park resources. 

The monitoring program simply cannot address all resource management interests because of 

limitations of funding, staffing, and logistical constraints. Rather, the intent of vital signs 

monitoring is to monitor a select sub-set of ecosystem components and processes that reflect the 

condition of the park ecosystem and is relevant to management issues. Cause and effect 

relationships usually cannot be demonstrated with monitoring data, but monitoring data might 

suggest a cause and effect relationship that can then be investigated with a research study. There 

are also inherent limitations in data due to imperfect understanding of ecosystem function and 

component interactions. The monitoring plan, therefore, should be viewed as a working 

document, subject to periodic review and adjustments over time as our understanding improves 

and new issues and technological advances arise. 

1.2.3.5 SFAN Monitoring Plan and GPRA Goals: The SFAN Monitoring Plan is a significant 

and specific step towards fulfilling GPRA Goal Category I (Preserve Park Resources) for the 

network. The servicewide goal pertaining to Natural Resource Inventories specifically identifies 

the strategic objective of inventorying the resources of the parks as an initial step in protecting 

and preserving park resources (GPRA Goal Ib1). This goal tracks the basic natural resources 

information that is available to parks; performance is measured by what datasets are obtained. 

The servicewide long-term goal is to “acquire or develop 87% of the outstanding datasets 

identified in 1999 of basic natural resource inventories for all parks” based on the I&M 

Program’s 12 basic datasets (Section 1.2.1). The SFAN Inventory Study Plan (NPS 2000) 

delineated what information exists for the network, its format and condition, and what 

information is missing. 

The Monitoring Plan will identify the vital signs of the SFAN network and develop a strategy for 

long-term monitoring to detect trends in resource condition (GPRA Goal Ib3; see Table 1.1). The 

2002 Annual Performance Report identifies what steps have been accomplished to date and the 

number of personnel involved. The network goal is to identify vital signs in a Monitoring 

Plan to be completed by September 30, 2005. GPRA goals specific to SFAN parks and relevant 

to the Monitoring Plan are listed in Table 1.1. 

1.2.3.6 San Francisco Bay Area Network Strategic Approach to Monitoring: The SFAN has 

followed the basic process depicted in Figure 1.2 to select a subset of park resources and 

processes for monitoring. The schedule for completing the 3-phase planning and design process 

is shown in Table 1.2 (http://science.nature.nps.gov/im/monitor/schedule.htm). 
11

Table 0.1 GPRA goals for each park that pertain to information generated by the Inventory and 

Monitoring program of the SFAN. 

GPRA Goal Goal #* Parks with this goal 

Resources maintained Ia EUON, FOPO, JOMU, GOGA, MUWO, PINN, 

PORE, PRES 

Disturbed lands restored Ia01A 

Ia01B 

Ia1A 

Ib01A 

PORE 

PORE 

GOGA, PRES 

JOMU 

Exotic vegetation contained Ia1B EUON, FOPO, JOMU, GOGA, MUWO, PINN, 

PORE, PRES 

Natural resource inventories acquired or developed Ib01 EUON, FOPO, JOMU, GOGA, MUWO, PINN, 

PORE, PRES 

Stable populations of federal T&E species or species 

of concern have improved status 

Ia2B 

Ib02d 

GOGA, MUWO, PORE 

Federal T&E species or species of concern 

populations have improved status 

Ia2D PORE 

Improving federal T&E species or species of concern 

populations have improved status 

Ia2A PINN, PORE, GOGA, MUWO, PRES 

Species of concern populations have improved status Ia2X GOGA, PRES, PORE 

Vital signs for natural resource monitoring identified Ib3a EUON, FOPO, JOMU, GOGA, MUWO, PINN, 

PORE, PRES 

Vital signs for natural resource monitoring 

implemented 

Ib3b EUON, FOPO, JOMU, GOGA, MUWO, PINN, 

PORE, PRES 

Water quality improvement Ia04 FOPO, JOMU, GOGA, MUWO, PINN, PORE, 

PRES 

* for GPRA Goal numbers refer to the National Park Service Strategic Plan (NPS 2000) 

The SFAN held several Vital Signs Monitoring Workshops to identify significant resources in 

the parks, identify key processes and stressors affecting the parks, potential monitoring 

questions, and recommend vital signs that could address the monitoring questions. An initial 

prioritization of vital signs and development of a conceptual model also were addressed during 

some of the workshops. Participants included park service managers and staff, external natural 

resource managers, and scientists. 

PINN held a workshop in September 2001 (a summary is available at: 

http://www1.nature.nps.gov/im/units/sfan/reports/appendixpinn.pdf). EUON and JOMU jointly 

held workshops in January and August 2002 since both parks are in close proximity, have similar 

natural resources and issues, and are administered jointly (summaries available at: 

http://www1.nature.nps.gov/im/units/sfan/meeting/euonjomu2ndsummary.pdf). Because of their 

previous collaborative efforts and the overlap in resources and management issues, PORE and 

the parks administered by GOGA jointly held a workshop in 1997 and held another workshop in 

July 2002 to revisit changes in national guidelines 
12

Table 0.2. Timeline for the SFAN to complete the 3-phase planning and design process for 

developing a monitoring program. 

(http://www1.nature.nps.gov/im/units/sfan/meeting/POGO_VSsummary.pdf). Subsequently, the 

SFAN Steering Committee integrated findings and recommendations from the separate 

workshops into a conceptual model for the network of parks that includes significant natural 

resources, key processes and stressors, and monitoring questions with suggested vital signs (see 

Chapter 2). The SFAN Vital Signs Workshop held March 19-20, 2003, was organized to review 

the SFAN integrated model and its related components and to identify network-wide vital signs. 

To help expedite the prioritization process and to prepare for future sampling design and protocol 

development, participants also were asked to complete a protocol questionnaire for each of the 

high priority vital signs identified by their workshop group. Monitoring protocols used by 

individual parks were integrated with those obtained from the workshop and from information 

generated by a geology working group that met in October 2002. Additionally, vegetation and 

faunal working groups convened after the Vital Signs Workshop to refine the vital signs protocol 

questionnaires by incorporating comments and suggestions from the workshop. A detailed 

description of the scoping workshop is included in the San Francisco Bay Area Network Vital 

Signs Workshop Summary March 2003 

(http://www1.nature.nps.gov/im/units/sfan/meeting/SFAN_VSsummaryV3.pdf). 

Information from the protocol questionnaires was entered into a web-based, network database 

that was used to prioritize vital signs and to develop monitoring protocols for the individual 

parks and for the SFAN. Over 100 specialists participated in the vital signs prioritization process 

(see Chapter 3: Vital Signs for more detail). 

Program 

Element 

FY01 

OctMar 

FY01 

AprSep 

FY02

OctMar 

FY02

AprSep 

FY03

OctMar 

FY03

AprSep 

FY04

OctMar 

FY04 

AprSep 

FY05 

OctMar 

FY05 

AprSep 

FY06 

OctMar 

Data gathering, 

internal scoping 

Inventories to 

Support 

Monitoring 

Scoping 

Workshops 

 

Conceptual 

Modeling 

 

Vital Signs 

Prioritization 

and Selection 

 

Protocol 

Development, 

Monitoring 

Design 

 

Monitoring Plan 

Due Dates 

Phase 1, 2, 3 

 Draft 

Phase 

I 

Oct 

‘02 

Draft 

Phase 

II 

Oct 

‘03 

Draft 

Phase 

III 

Dec 

‘04 

Final 

Plan 

Sep. 

‘05 
13

1.2.3.6.1 Water Quality Planning (Scoping) Meetings: While the SFAN Vital Signs Workshop 

provided a forum for discussing and selecting water resources vital signs, additional water 

quality-specific information was needed from the parks. Therefore, additional planning meetings 

were held for JOMU and EUON, GOGA and MUWO, PINN, PORE, and PRES. The desired 

outcome of the meetings was to gather park information related to water quality, identify and 

prioritize water quality issues, and identify the resources available to monitor. The meetings also 

provided an opportunity to introduce the I&M Water Quality Monitoring Program and plan 

development process to those unfamiliar with it. Park staff, local agencies, watershed groups, 

and university staff were invited to participate. Results of these meetings plus a summary of 

water quality data is included in the SFAN Preliminary Water Quality Status Report (Cooprider 

2004). 

1.3 Overview of Network Parks and Selected Natural Resources 

The SFAN is one of eight networks formed in October 2000 in the Pacific West Region (PWR) 

of the National Park Service. The network is composed of eight park units including Eugene 

O’Neill National Historic Site (EUON), Fort Point National Historic Site (FOPO), Golden Gate 

National Recreation Area (GOGA), John Muir National Historic Site (JOMU), Muir Woods 

National Monument (MUWO), Pinnacles National Monument (PINN), Point Reyes National 

Seashore (PORE), and the Presidio of San Francisco (PRES). PRES and EUON were not 

originally selected by the NPS Washington Support Office (WASO; now known as the Natural 

Resource Program Center - NRPC) as part of the 270 parks nationwide with significant natural 

resources; however, the SFAN Steering Committee and Board of Directors decided that natural 

resource issues within these parks were sufficient to be included in the network. The SFAN was 

selected as one of the first three networks in the region to obtain monitoring funds because of 

need, capacity, and existing monitoring effort. The San Francisco Bay Area, and the parks 

therein, are extremely diverse in natural resources and represent a unique set of management 

challenges within a very populated setting 

SFAN represents one of the 6 most significant areas in the nation for biodiversity (Grossman 

1998). Nationally, the parks are significant to the National Park System for: 1) supporting many 

endemic species and communities despite close proximity to the large urban zone of the San 

Francisco Bay region, 2) preserving biologically and geologically diverse habitats and their 

associated species, and thereby 3) providing opportunities for recreation, education and aesthetic 

enjoyment to a large urban population. Internationally, the SFBAN of parks falls within the 8th 

most significant “hot spot” in the world for biodiversity and at great risk due to rapid human 

population growth. With a current population of 6.9 million and large metropolitan centers, the 

San Francisco Bay Area is forecast to have a population of 8 million by 2020 (Association of 

Bay Area Governments 2000). Recognizing the extraordinary significance and exposure to 

threats in the region, the UNESCO Man in the Biosphere program designated the Central 

California International Biosphere Reserve in 1995. (See appendix 1 for descriptions of 

individual park units and their natural resources). 
14

Figure 0.4. Location of the SFAN parks. 
15

1.3.1 Ecological Context: Park Resources and Issues 

The following sections briefly describe the range of environmental conditions and anthropogenic 

influences prevalent in the San Francisco Bay Area. The natural resources resulting from the 

interactions of these forces and existing raw materials also are considered. 

1.3.1.1 Setting and Boundary: The parks of the SFAN are within the central California coast 

range and share many ecosystems, ecosystem components, and associated threats. The elements 

that define the limits of a boundary include leadership (as within a community), authority (as 

dictated by legal action), and zone of influence. The legislative boundaries of the coastal parks of 

central California extend from Tomales Point, Marin County in the north, south to Milagra 

Ridge, San Mateo County, and reach their eastern and southern extremes inland in the Gabilan 

Mountains of San Benito County (Figure 1.4). The SFAN parks’ administrative boundaries 

include nearly 170,242 acres, of which about 30 mi2

 are surface waters (including streams, 

tributaries, lagoons, lakes, ponds, and reservoirs), and nearly 120 linear miles of shoreline. 

In the vicinity of SFAN parks are three National Marine Sanctuaries (Gulf of the Farallones, 

Monterey Bay, and Cordell Bank), Bureau of Land Management (BLM) lands including the 

Clear Creek Management Area and the California Coastal National Monument, two National 

Wildlife Refuges, several state Areas of Special Biological Significance, and numerous state and 

regional parks such as Mt. Tamalpais State Park, Las Trampas Regional Wilderness Park (part of 

East Bay Regional Parks District), and Fremont Peak State Park. The California Coastal 

National Monument was designated by Presidential Proclamation in 2000, and includes all BLM 

administered islands, rocks, exposed reefs and pinnacles off the California coast above the high 

water mark. GOGA and PORE are part of an International Biosphere Reserve and function as a 

part of a community of internationally significant reserves. The network includes two 

internationally significant RAMSAR wetland sites (Bolinas Lagoon and Tomales Bay), 

designated under UNESCO. 

The vital signs monitoring plan designates two spatially nested network boundaries. The core 

area is composed of the NPS boundaries, including state parks, and adjacent watersheds. The 

broader area is delineated by the boundary of the Golden Gate Biosphere Reserve, the three 

National Marine Sanctuaries, BLM lands, and the mouth and center of San Francisco Bay. The 

core limit takes into account the need to monitor upper and lower reaches of watersheds that 

extend beyond the legislative boundaries of the parks. The broader area takes into account that 

marine species range widely in the region, and that shared monitoring activities with other 

partners is encouraged. 

1.3.1.2 Air quality: Parks within the SFAN are influenced by the close proximity of urban and 

suburban populations in a variety of ways, including air quality. Also, air quality can have 

biological effects on health and productivity of plants and animals. The NPS Air Resources 

Division (ARD) focuses on three main areas for monitoring air quality: 

(1) Atmospheric deposition 

(2) Ozone pollution 

(3) Visibility 
16

The two Class I air quality parks in SFAN are PINN and PORE. Both parks are experiencing an 

increase in development along their borders, as well as influences from major population centers 

in the bay area. The San Francisco Bay Area has extensive industrial facilities including 

petroleum refineries and energy production plants, as well as a very congested freeway system. 

Depending on the season, wind and temperature, the air quality at SFAN parks can be impacted 

by these factors. 

At PINN, the NPS Air Quality Office and the Environmental Protection Agency (EPA) 

established a monitoring station near the east entrance in 1987. An air clarity study (using a 

transmissometer) has been completed, but particulate and ozone monitoring continues. Despite 

the occasional hazy days, the air quality at PINN is a defining feature of the Monument and an 

important resource. PORE has monitored air quality for over 20 years. The Interagency 

Monitoring of Protected Visual Environments (IMPROVE) program has been in operation since 

1988 at the PORE North District Ranger Station and includes the measurement of the 

composition and concentration of fine particles. There is also a web-cam installed at the PORE 

lighthouse for visibility monitoring. The Bay Area Air Quality Management District 

(BAAQMD) operates an air quality station at GOGA, to monitor dioxin at Fort Cronkite. 

1.3.1.3 Climate: Hot, dry summers and rainy, mild winters are typical of a moderate 

Mediterranean climate, that characterize the SFAN. Temperatures average 50 to 65°F in the 

Coast Range, but in the inland valleys and at PINN, temperatures can exceed 90°F regularly in 

the summer. Precipitation, which ranges from 15 to 40 inches per year, extends from fall through 

spring, and increases with elevation. Precipitation typically occurs as rainfall. Snowfall is rare in 

the region. Frost and short periods of freezing weather occur occasionally in winter and mostly in 

inland valleys. The growing season lasts 120 to 270 days (National Weather Service 2003). 

Coastal areas have a more moderate climate than the interior and can receive significant moisture 

from fog in summer. Consequently, inland areas receive about half the rainfall as areas along the 

coastal range. With this variability, many microclimates occur. For example at PORE, Point 

Reyes Headland in the summer can be 55°F with fog and wind, in contrast to Olema Valley, just 

15 miles distant, with temperatures above 80°F and no wind (National Weather Service 2003). 

Global climate change resulting from greenhouse gas accumulation in the atmosphere is 

expected to increase weather variability in unpredictable ways including droughts or increased 

precipitation. The SFAN is predicted to have increased rainfall, and more intense and more 

frequent El Niño-Southern Oscillation (ENSO) events. Sea level already has risen 4-8 inches in 

the past century, and models predict that this rise will accelerate, potentially rising from 5 to 37 

inches over the next 100 years (NAST 2001). Climate change may impact shoreline erosion, 

saltwater intrusion in groundwater supplies, and altering the water regimes of wetlands and 

estuaries. These are vital resource management concerns along the 120 miles of the SFAN 

shoreline. Increased and more intense precipitation would also increase erosion and flood events 

at all of the parks, where erodible soils occur. Sea temperature is also predicted to continue to 

rise. Central California waters have already increased in temperature over the past 30 years, with 

changes in the distribution of many marine species of invertebrates and fishes (Croll et al. 2000). 

1.3.1.4 Geology: Geologic history has shaped the topography of the region creating large bays, 

coastal ridges paralleling the coastline, and unusual features. Coastal ridges that parallel the coast 
17

vary in elevation between 500 to 3,500 feet. They include the Inverness and Bolinas Ridges in 

the north, Diablo Mountains inland of San Francisco Bay, and the Gabilan Mountains to the 

south. Special features include the Pinnacles rock formations and Point Reyes Headland. The 

area, located in the Coast Ranges geomorphic province, consists of parallel ranges, and folded, 

faulted, and metamorphosed strata; the rounded crests are of sub-equal height. 

In geologic time, central California has been exposed to extraordinary forces that have shaped 

the region. The San Andreas Fault links all of the park units. The fault starts at Pinnacles as a 

block in the middle of Miocene volcanics and extends northward to Point Reyes where the fault 

ruptures the surface and forms Bolinas Lagoon and Tomales Bay. Movement of the Pacific plate 

northward along the San Andreas faultline continues to create the distinctive topography of the 

region. 

Coastal processes accrete and erode shorelines seasonally and annually along GOGA and PORE, 

particularly at Ocean Beach and Drakes Beach. During intense winter storm years such as ENSO 

events, erosion can be severe causing nearshore flooding and undermining structures such as 

roadways. USGS mapped the coastline of PORE with LIDAR in 1997 and 1998, and will update 

coastal mapping in the future for both GOGA and PORE. The NPS Geologic Resources Division 

(GRD) and USGS-Coastal and Marine Division developed a coastal vulnerability index in 2004, 

mapping areas at PORE and GOGA that would be vulnerable to sea level rise 

(http://woodshole.er.usgs.gov/project-pages/nps-cvi/). 

1.3.1.5 Water Resources: The SFAN has many unique aquatic resources that are significant in 

an ecological and economic context. Aquatic resources in the SFAN include streams, bays, 

estuaries, high energy coast, lagoons, lakes, reservoirs, freshwater and estuarine marshes, 

nearshore oceanic waters, and seeps. The combination of marine and freshwater aquatic systems 

within the network supports a variety of threatened and endangered species. 

Several NPS efforts to improve the condition of water resources within SFAN are underway. The 

Redwood Creek watershed and MUWO are currently the focus of a variety of activities including 

watershed planning, transportation planning, water quality and water rights investigations, 

sensitive species monitoring, aquatic system and riparian restoration, invasive non-native plant 

removal and habitat restoration, and GIS mapping of all watershed features. Several stream 

restoration projects are on-going at PORE including bank stabilization and dam removal 

projects. Restoration efforts for Chalone Creek (PINN) and its floodplain have also been 

initiated. Streambank restoration (including removal of invasive species, erosion control, and 

bank stabilization) is also proposed along Alhambra Creek and its tributaries (JOMU). Tidal 

wetland restoration efforts are on-going at PORE, GOGA, and PRES. 

Many of the watersheds within SFAN parks receive substantial attention from the surrounding 

communities and jurisdiction over water resources is shared by other agencies including the State 

Water Quality Control Board and water utility districts. A variety of stake-holder based 

watershed groups have been established in the last 10 years to address problems related to water 

quality and watershed health. Examples of these organizations include the Tomales Bay 

Watershed Council (TBWC), the Tomales Bay Shellfish Technical Advisory Committee 

(TBSTAC), the Tomales Bay Agricultural Group (TBAG), the Bolinas Lagoon Technical 
18

Advisory Committee (BLTAC), the Friends of Alhambra Creek and other groups. NPS staff are 

involved to varying degrees with these community groups, often providing technical expertise in 

a variety of resource management fields. 

1.3.1.5.1 Watershed Characteristics and Water Quantity: The hydrologic systems have high 

runoff in the wet winter, occasional flash floods, and very low to intermittent flow dominating 

summer conditions. In response to these hydrologic conditions and the highly active geologic 

processes associated with the San Andreas Fault, stream channels are typically dynamic. Outside 

of the SFAN parks many of these systems are highly confined, with natural processes engineered 

out of the stream system. Within the Marin and San Mateo County portions of GOGA, as well as 

PORE, watersheds remain fairly stable and functional, supporting threatened species such as 

coho salmon and steelhead trout. Stream systems in these areas have been impacted by historic 

or current agricultural activities, as well as more dispersed development. 

The size of watersheds ranges throughout the SFAN: from the relatively small 1 mi2

 Franklin 

Creek watershed (JOMU) and 9 mi2

 Redwood Creek watershed (MUWO) to the approximately 

88 mi2 Lagunitas Creek watershed (PORE andGOGA). The drainage area of Chalone Creek 

(PINN) just downstream of the park is roughly 70 mi2

. There are 130 linear miles of streams 

within the legislative boundaries of the SFAN. 

Stream discharge in network streams has been monitored by NPS for several years. Lagunitas 

Creek has been monitored by the USGS since 1974. The extremes for Lagunitas Creek for the 

period of record range from 22,100 cubic feet per second (cfs) in the floods of January 1982, to 

0.01 cfs during the drought of 1977. Flows in Redwood Creek, Olema Creek, and Pine Gulch 

Creek range from intermittent to 3,000-4,000 cfs. The portion of Chalone Creek within PINN is 

ephemeral to intermittent in the summer. In winter, the highest recorded discharge of 2,850 cfs 

was recorded in 1998, an ENSO year. 

The SFAN is located within two subregions of USGS Water Resource Region 18. These include 

Subregion 1805 – San Francisco Bay and Subregion 1806-Central California Coastal. PORE, 

GOGA, PRES, MUWO, FOPO, JOMU, and EUON fall within Subregion 1805 and PINN falls 

within Subregion 1806. JOMU is within the 644 mi2 Suisan Bay hydrologic unit code (HUC). 

Parts of GOGA and EUON are within the 1200 mi2 San Francisco Bay HUC. PORE and portions 

of GOGA are within the 339 mi2

 Tomales-Drakes Bay HUC. Portions of GOGA are within the 

San Francisco Coastal South HUC (256 mi2). 

1.3.1.5.2 Water Quality Criteria: The San Francisco Bay Regional Water Quality Control Board 

(RWQCB, part of the State Water Resources Control Board), regulates all of the park units 

except PINN. PINN is within the Central California Coast RWQCB. These Regional Boards 

establish management criteria for water bodies within the state of California. Through their Basin 

Plans the Regional Boards have set numerical and narrative objectives for surface waters 

(Cooprider 2004). Several parameters (e.g., nitrates, phosphates) that are considered of 

importance to existing SFAN park water quality monitoring programs do not have criteria 

established by the Regional Board. Basin Plans outline the beneficial uses assigned to each 

stream that is a significant surface water feature. The specific water quality criteria to be met will 

depend on the beneficial uses of each water body. The beneficial uses of the streams within the 
19

network range from wildlife habitat to municipal and agricultural supply. A separate document, 

the California Ocean Plan, was produced by the State Board to regulate ocean waters (California 

EPA 2001). 

1.3.1.5.3 Significant Waters: The State Water Resources Control Board (part of the California 

Environmental Protection Agency) established five Areas of Special Biological Significance 

(ASBS) within the legislative boundaries of the SFAN parks in the 1970s. These include Point 

Reyes Headlands, Bird Rock, Double Point, and Duxbury Reef. The Point Reyes Headlands, 

Bird Rock, and Double Point are managed by PORE. Duxbury Reef is partly included within the 

PORE legislative boundary and extending into a Marin County park. These areas were chosen 

through a nomination process based primarily on habitat quality and are limited to coastal areas; 

inland areas have not yet been assessed. The procedure for this nomination process is in the 

California Ocean Plan (CEPA 2001) developed by the State Water Resources Control Board. No 

other “significant waters” (e.g., Outstanding Natural Resource Waters, or ONRW) exist in the 

SFAN or its extended watersheds. 

1.3.1.5.4 Impaired Waters: In 2000, the San Francisco Bay RWQCB identified both Lagunitas 

Creek and Tomales Bay (PORE/GOGA) as impaired by fecal coliform, sediment, and nutrients 

(Cooprider 2004). In the same year, Marin County announced a fish consumption advisory for 

Tomales Bay due to mercury bioaccumulation associated with an abandoned mercury mine in 

the Walker Creek watershed. The RWQCB has established a timeline for development of Total 

Maximum Daily Loads (TMDLs) associated with these impairment listings. Required 

monitoring (by NPS and others) for the TMDL program will include monthly monitoring plus 

five consecutive weeks of monitoring in the winter. The preliminary water quality status report 

also includes a complete list of all impaired waterbodies within the SFAN and a review of past 

and proposed water quality monitoring (Cooprider 2004). 

1.3.1.6 Biome: Biomes are large geographical areas characterized by major ecological 

communities of plants and animals that display distinctive adaptations to that particular 

environment (Botkin and Keller 1995). Climate and geology are the dominant environmental 

variables influencing organisms in a given area and are, therefore, the key determinants of biome 

types in a region. Biomes are classified according to their predominant vegetation, but associated 

seral communities and persistent, sub-dominant communities also are considered in most 

classification schemes. 

The Mediterranean Division of eco-regions of California is situated on the Pacific coast between 

latitudes 30° and 45° N and is distinguished by alternate wet and dry seasons (Bailey 1995). Both 

the SFAN and the Mediterranean Network are within this division. The area is distinguished as a 

transition zone between the dry west coastal desert and the wet west coast. Mediterranean-type 

ecosystems host a disproportionate share of plant species worldwide in both the number of 

species and the number of rare or locally endemic species (Dallman 1998). The major biomes of 

the parks include forests, grasslands, savannahs, shrublands, wetlands and several types of 

aquatic environments. 

The vegetation is typically dominated by hard-leaved evergreen trees and shrubs (sclerophyll 

forests) that can withstand severe drought and evaporation in the summer (Bailey 1995). The 
20

pattern of plant community distribution consistently has forest on north facing slopes and on 

wetter sites, chaparral/scrub on south facing slopes and drier sites, and riparian corridors between 

ridges and along valleys. Additionally, the plant communities vary with distance from the marine 

influence, and elevation. The SFAN parks span this Mediterranean transition zone and fall within 

three terrestrial provinces: the California Coastal Chaparral Forest and Shrub, the California Dry 

Steppe, and the California Coastal Steppe, Mixed Forest and Redwood Forest (Bailey 1995). 

1.3.1.7 Marine Communities: Just as climate and geology determine the terrestrial biomes, so 

too are the marine biotic communities of central California. The California Pacific oceanic 

waters are in a transition zone between the Californian and Oregonian provinces (Valentine 

1966). Generally, warm-temperate water species are associated with the southern, Californian 

province and cold-temperate species with the Oregonian province. The marine zones are 

generally divided into pelagic, subtidal, and intertidal zones based on water masses, distance 

from shore, bathymetry, and tidal exposure. The biota of these zones have distinctive 

communities. For example, in the pelagic zone, phytoplankton that bloom in summer and fall are 

the dominant vegetation type. In the subtidal zone, though, various species of kelp are dominant, 

and in the intertidal zone numerous algae adapted to daily desiccation are dominant. The simple 

classification by zonation, though, belies the complexity and dynamic nature of these 

ecosystems. Some habitats such as upwelling areas around islands and headlands are semipermanent. However, nearshore currents driven by winds and tides form micro-habitats in the 

water column with jets, squirts and eddies are where organisms such as zooplankton are 

entrained. Predators are then attracted to these semi-permanent and ephemeral features. 

Convergence of oceanic currents rising from the abyssal plain over a steep submarine cliff also 

makes the marine and coastal shoreline habitats complex and diverse. The California coast is 

only one of five areas of eastern boundary coastal upwelling, oceanic currents worldwide and the 

only one in North America (Thurman 1988). In addition, a plume of warmer, freshwater exiting 

the San Francisco Bay extends out into the Gulf of the Farallones. These nutrient rich waters 

support abundant and diverse fauna. This upwelling-driven productivity cycle is vulnerable, 

though, to changes in sea temperature along the equator resulting in changes in wind persistence 

and intensity (i.e., the Pacific Decadal Oscillation, the El Niño-Southern Oscillation, or La Niña 

events). 

More than one-third of the world’s cetacean species occur in these waters. Significant haul-out 

areas for five species of pinnipeds are used year round and represent one of only eleven mainland 

breeding areas for northern elephant seals in the world and 20% of the mainland breeding 

population of harbor seals in California. Eleven species of seabirds breed within the parks and 

over 80 waterbird and shorebirds species were identified in the parks during the 1997-99 

inventories (Kelly and Etienne 1999). 

Recognizing the extraordinary significance of the marine region, the California Department of 

Fish and Game designated Point Reyes Headlands as a Marine Reserve and Limantour Estero as 

a an Ecological Reserve. 

1.3.1.8 Natural and Anthropogenic Disturbances: Both abiotic and biotic processes comprise the 

natural disturbance regime responsible for shaping and reshaping ecosystems within the SFAN. 
21

The dominant geological force—plate movement along the San Andreas Fault—has created 

unusual habitats from Pinnacles to Point Reyes for a variety of species including endemics and 

edge-of-range species. Seismic activity continues to alter the geologic landscape and soils, 

impacting the associated biota. The El Niño-Southern Oscillation and the Pacific Decadal 

Oscillation, natural change processes influenced by a combination of weather, climatic events, 

and oceanographic processes affect precipitation patterns and drought conditions, thereby 

enhancing fire potential, all of which affect community composition, structure, and function. 

They also dramatically change coastal and oceanographic processes, resulting in significant 

disruption of the trophic food webs of the marine ecosystems. 

Fire is a significant source of ecological change that has historically shaped terrestrial 

ecosystems in the San Francisco area and continues to impact them (Moratto 1984). Sources of 

fire predominantly have been anthropogenic in nature, but non-anthropogenic wildfire has had a 

significant impact on SFAN ecosystems. Indigenous Americans frequently used fire in the Bay 

Area (Blackburn and Anderson 1993). Many managers and fire ecologists now consider preEuropean indigenous burning to be part of the natural fire regime. The National Fire Plan 

(www.fireplan.gov) includes pre-European indigenous fire regimes in Fire Regime Condition 

Class analysis and in specifying desired conditions for landscape conditions. Several endemic 

plant species are fire adapted and require this natural disturbance for regeneration. Years of fire 

suppression and adjacent land management practices have altered the habitat. Poor fire timing 

and incorrect intensity of prescribed burns have converted entire vegetation communities, 

especially chaparral in PINN, to grassland (T. Leatherman, Chief of Natural Resources, 

Pinnacles National Monument, personal communication, 19 September 2001). Additionally, 

post-fire bare ground often encourages the growth of non-native plants. Human safety concerns 

continue to require wildland fire suppression, especially where vegetation communities are in 

close proximity to human structures. Air quality concerns in the Bay Area also limit park 

managers’ ability to use prescribed fire. 

Coastal ecosystems are created and recreated by erosional and accretive forces that change 

coastal habitats subtly over time or rapidly and dramatically as in the case of major storm events. 

Erosion and deposition are a part of hydrologic disturbance regimes in freshwater ecosystems, 

too. Flooding events shape stream morphology, deposit and flush materials from riparian 

wetlands, and transport materials and organisms to downstream ecosystems. Hydrologic 

disturbance may open small patches for colonization or restructure entire stream channels over 

both the long term and the short term. 

With a current population of 7 million, the metropolitan centers of San Francisco, Oakland, and 

San Jose are forecast to have a population of 8 million by 2020 (Association of Bay Area 

Governments 2000). As a result, anthropogenic disturbances pose a significant threat to the 

integrity, connectivity and sustainability of the SFAN park ecosystems. The degree of threat to 

these resources is a result of the parks’ juxtaposition within the urban landscape and the 

extensive urban/ wildland interface within the parks. 

The PWR identified several of the most important anthropogenic issues to parks of the region in 

2002 that included habitat fragmentation, fire management, rare and endangered species, 
22

invasive species, global climate change, and water quality/quantity (PWR Science Meeting, July 

2002). These conservation issues are also the primary threats to the SFAN parks. 

Recreational and development pressures on parks are intense in the SF Bay Area and will 

increase with the growing human population. GOGA, located in and around San Francisco has 

one of the largest visitation rates in NPS (19.7 million) and PORE has a visitation rate of around 

2.5 million. PINN, though, is not as accessible and has a lower visitation rate of 160,000. Many 

activities have the potential to disrupt park resources, such as rock climbing and nesting falcons. 

These activities have the potential to exacerbate fragmentation by development by creating 

barriers to movement or isolating species. Recreational activities also have the potential to create 

pathways facilitating the spread of invasive non-native species. 

Invasive species, plant and animal, terrestrial and aquatic, are one of the most significant threats 

to the long-term sustainability of the parks’ native ecosystems. One third of the approximately 

1200 plant species of GOGA, MUWO, and PORE are non-native. European beach grass has 

caused a type change in the coastal dune plant community. Feral pigs pose a major threat to 

native plants, displace native animals from traditional home ranges, degrade water quality, and 

threaten riparian habitats and species at PINN. Non-native deer and turkeys at PORE pose a 

serious threat to native plant and animal species. 

Disease, herbivory, fire, flooding, mowing, mechanical fuel treatments, road and trail 

maintenance, and (human and equine) trampling are among the sources of biotic disturbance in 

the SFAN. Outbreaks of pine bark beetles, which can lead to pine pitch canker (Fusarium 

subglutinans ssp. pini) infestations destroy individual trees or entire stands, opening gaps in the 

forest canopy to colonization by the same or other tree species (Adams 1989). Likewise, periodic 

surges in ungulate populations can lead to over browsing of herbaceous vegetation, altering 

competitive interactions among plants and changing species composition of plants and, 

indirectly, animals. Sudden Oak Death (SOD) caused by an introduced pathogen (Phytophthora 

ramorum) first emerged nationally in the San Francisco Bay Area centered in Marin County in 

the mid-1990s. There is still a lot of research underway to determine the cause, extent and effects 

of this pathogen which has several native host species, and primarily kills oaks. Animal diseases 

have been documented in the area including Johne’s disease, a paratuberculosis bacterium found 

in dairy cattle. This disease can infect native elk and deer populations. Human and domestic 

feline diseases were documented in native wildlife, including feline transmitted toxoplasmosis in 

California sea otters. 

1.3.1.9 Species of Special Concern: The SFAN’s unique ecological setting and close proximity 

to urban development have combined to produce an environment that is home to a variety of 

species of special concern. These species include endemic, sensitive, rare, threatened, or 

endangered species recognized by federal, state, regional, and park authorities (Appendix 2). 

GOGA and PORE combined have some of the highest numbers of listed species for any parks. 

Indeed, the Nature Conservancy identified central California as one of the 6th most biodiverse 

and at risk areas in the United States (Grossman 1998). Simultaneously, environmental 

conditions and anthropogenic activities have created suitable pathways for invasion by exotic 

species, exacerbating the stress on unique and at-risk species. Non-native species of concern also 

are listed in Appendix 2. 
23

1.3.2 Management Objectives, Issues, and Monitoring Questions for 

Network Parks 

1.3.2.1 Management Objectives: Each park was established to protect and preserve unique 

natural and cultural resources contained within its boundaries while providing for public 

enjoyment of these resources. Park-enabling legislation and other relevant documents such as 

Resource Management Plans direct park managers to identify management goals necessary to 

fulfill the park’s founding purposes (Appendix 1). Management goals necessitate more specific 

management objectives. Management objectives and matching park resources need to be 

considered together for a monitoring plan to be successful and for the park to meet the overall 

goal of conservation. Table 1.3 lists the management objectives identified for the SFAN parks. 

These management objectives are compatible with a multi-faceted approach to monitoring 

natural resources that address specific management issues, focal species, and key properties and 

processes of ecosystem integrity. Collectively, individual park management objectives form the basis 

of the SFAN’s management issues and monitoring questions. 

1.3.2.2 Management Issues, Monitoring Questions, and Potential Vital Signs: The PWR has 

identified habitat fragmentation, water quality / quantity degradation, global climate change, 

endangered or sensitive species protection, non-native species invasions, fire management, and 

lack of scientific knowledge as the greatest issues facing ecosystem integrity in the region’s 

national parks (PWR Science Needs Workshop 2002). In 2005, the Science Council and the 

Natural Resources Advisory Committee of the PWR identified priority conservation issues in 

common which reinforced and added to the 2002 priority list. Relevant issues to the I&M 

program include habitat fragmentation, changing fire regimes, park visitor capacity, invasive 

species, global climate change, soundscapes, increasing demands for energy and increasing 

demands for water quality/quantity (minutes from NRAC 2005 meeting; 

http://inside.nps.gov/regions/region.cfm?rgn=64&lv=2). 

Table 0.3. Management objectives for SFAN parks. 

Park Management Objectives 

Eugene O’Neill 

NHS 

• Achieve an understanding of the natural ecosystem existing on the site prior to the 

O’Neill’s arrival, the remnants of that ecosystem today, and preserve, protect, and 

interpret the natural scene associated with the estate during O’Neill’s tenure. 

• Enhance conservation efforts of Las Trampas Regional Wilderness Area 

surrounding the site. 

• Contain or eliminate non-native invasive plants. 

• Evaluate the risk of and manage Sudden Oak Death. 

Golden Gate NRA* • Maintain the primitive and pastoral character of the parklands in northern Marin 

County. 

• Maintain and restore the character of natural environmental lands by maintaining 

the diversity of native park plant and animal life, identifying and protecting 

threatened and endangered species, marine mammals, and other sensitive natural 

resources, controlling exotic plants and checking erosion whenever feasible. 

• Locate development in areas previously disturbed by human activity whenever 

possible. 
24

Park Management Objectives 

John Muir NHS • Protect the natural scene associated with John Muir’s days at the ranch. 

• Identify, monitor and manage the flora and fauna of the Mt. Wanda area. 

• Protect sensitive species. 

• Manage human and animal impacts on park natural resources. 

• Contain or eliminate non-native invasive plants. 

Pinnacles NM • Maintain the primitive character of the wilderness. 

• Preserve natural ecologic and geologic processes (e.g. fire, flood, mass wasting). 

• Maximize native species, assemblages, communities and ecosystems across a 

variety of temporal and spatial scales. 

• Provide for the scientific study of natural processes and species. 

• Recognize and allow for the natural range of variability, while promoting 

ecosystem resilience, incorporating adaptive management strategies. 

• Control and eradicate, when practical, non-native species. 

Point Reyes NS • Identify, protect, and perpetuate the diversity of existing ecosystems, which are 

representative of the California seacoast. 

• Preserve and manage wilderness. 

• Protect marine mammals, threatened and endangered species, and other sensitive 

natural resources found within the seashore. 

• Retain research natural area status for the Estero de Limantour and the Point 

Reyes Headlands. 

• Manage seashore activities in the pastoral and estuarine areas in a manner 

compatible with resource carrying capacity. 

• Monitor grazing and improve range management practices in the pastoral zone in 

cooperation with the ranchers and the Natural Resource Conservation Service. 

• Enhance knowledge and expertise of ecosystem management through research 

and experimental programs that provide sound scientific information to guide 

management relating to wildlife, prescribed burning techniques, exotic plant and 

animal reduction, regulation and control of resource use, and pollution control. 

• Monitor mariculture operations, in particular, the oyster farm operation in Drakes 

Estero, in cooperation with the California Dept. of Fish and Game. 

* includes all parks administered by GOGA. 

The SFAN altered the list to reflect those natural resource issues that are most pertinent to the 

network. Input from Resource Management Plans, internal and external reviewers, and Vital 

Signs scoping workshops contributed to the list of management issues and monitoring questions 

in Table 1.4. Monitoring questions, in turn, have helped the SFAN identify potential vital signs 

that may suitably address the monitoring questions related to the various management issues. 

Monitoring questions in Table 1.4 are applicable to all parks of the network. The SFAN intends 

to maintain and expand existing monitoring partnerships, so that the network can efficiently and 

effectively tackle the management issues. 
25

Table 0.4. Monitoring questions and potential vital signs related to management issues for the 

SFAN parks. 

Management Issue Monitoring Questions Potential Vital Signs 

Climate Change Are climate and weather changing over time? 

What impact does this have on biotic and 

abiotic resources?

Weather/Climate 

Shoreline change 

Air Quality Degradation Is air quality degrading? Where, why and at 

what rate of change? What impact does this 

have on biotic and abiotic resources?

Air Quality 

Water Quality Degradation What are the existing levels of water quality 

parameters? What is our level of compliance 

with beneficial uses? What are the long-term 

trends and ranges of core parameters? What 

are the pollution sources within the 

watersheds? Are management actions 

reducing pollutant loads?

Water Quality—clarity, 

core parameters, nutrients, 

pathogenic bacteria 

Water Quantity Alteration Are water storage levels in existing aquifers 

decreasing? Are there groundwater impacts on 

riparian habitat and wildlife?

Groundwater Dynamics 

Human Population Increase Where is the natural dark night sky affected 

by light? Is this changing over time? What 

impact does this have on biotic resources? Are 

airplane overflights increasing over the park, 

affecting natural quiet?

Light Quality/Quantity 

Noise Levels 

Land Use 

Change/Development

What changes are occurring inside and outside 

park borders that may alter terrestrial and 

marine habitats?

Plant Community Change 

& Landscape Dynamics

Resource Extraction How are commercial and recreational fisheries 

affecting marine resources? 

Estuarine and Marine Fish 

Bycatch rates for nontarget species 

Soil Alteration What effects do engineered structures and 

other anthropogenic stresses have on soil 

structure, texture and chemistry? 

Soil Structure, Texture 

and Chemistry 

Nutrient Enrichment Are the effects of ranching degrading 

surrounding ecosystems? What are the effects 

of farming on surrounding ecosystems? 

Riparian Habitat 

Water Quality 

Algal blooms 

Park Development and 

Operations

Are deposition patterns changing on park 

beaches? Is erosion increasing in development 

zones?

Riparian Habitat 

Coastal processes 

Recreational Use Are recreational activities affecting birds 

including raptors, snowy plovers and spotted 

owls? Are recreational activities affecting 

breeding harbor seals? 

Raptors—breeding 

Snowy plovers - breeding 

Harbor seals–breeding 

Fire Management How is the distribution and occurrence 

frequency, intensity or magnitude of wildland 

fires changing over time? What impact does 

this have on biotic and abiotic resources?

Catastrophic Events 

Documentation—

Wildland Fire 

Non-native Invasive 

Species/ Disease

What non-native taxa are present and how are 

they affecting distribution and abundance of 

other species in ecosystems such as rocky 

intertidal communities?

Rocky Intertidal 

Community; Non-native 

plant and animal species 
26

Management Issue Monitoring Questions Potential Vital Signs 

Native Species Decline and 

Extirpation

What are the trends in native species 

populations? What are the changes in cover of 

invasive species and native species? Are new 

rare plant populations becoming established 

within park boundaries? 

Rare Plant Species 

Changes in biodiversity, 

abundance and dominance

Descriptions of the predominant drivers and stressors associated with these issues are included in 

Chapter 2: Conceptual Models. Specific research to address these overarching management 

issues are presented in the Pacific Coast Learning Center Science Needs web site for the SFAN 

(http://www.nps.gov/pore/science.htm). Science needs fall into fifteen categories including the 

definition of desired conditions, development of non-native species controls, and paleoecology. 

1.3.2.3 Water Resources Monitoring Efforts and Questions, and Potential Vital Signs: Water 

Quality Planning meetings were conducted for each park or group of parks (GOGA/MUWO, 

PRES, PINN, JOMU, EUON, and PORE). A list of discussion questions was addressed at each 

meeting to determine park priorities, issues, and data needs (Cooprider 2004). 

Information gathered from the Water Quality Planning Meetings (and from the SFAN Vital 

Signs Workshop in March 2003) was used to develop water resources and water quality 

monitoring questions and contribute to the list of potential water resources vital signs. Vital 

Signs Workshop participants recommended a suite of potential vital signs for monitoring water 

resources from harmful algal blooms to water clarity (a full list is included in the SFAN 

Preliminary Water Quality Status Report (Cooprider 2004)). The desired future condition is for 

water parameters to vary within natural ranges. The three key objectives are: 

Objective1: Maintain waters that vary within their natural chemical and biological ranges and 

meet applicable federal and state water quality criteria (and/or parks’ desired ranges) 

Objective 2: Improve water quality of impaired waters (CWA Section 303d listed and other 

waters known to have poor water quality)? 

Objective 3: Maintain high water quality where it exists. 

This refers specifically to Areas of Special Biological Significance as designated by the state or 

other water bodies known (through past monitoring) to be of high quality (i.e., sites sometimes 

referred to as “reference”, “control”, or “wilderness” sites). 

 

Based on these objectives, there are five monitoring questions: 

1) What are the existing levels of water quality parameters (i.e., what is the baseline 

condition)? 

2) What percentage of samples within a site and within a water body meet/exceed the criteria 

for aquatic health and public health (threshold values) and how does this vary seasonally (for 

core parameters, nutrients, and bacteria)? 
27

3) What are the long-term trends and ranges in pH, D.O. temperature, specific conductance, 

and flow? (this aids in determining natural variability) 

4) What are the pollution sources within the watershed? 

5) Are management actions reducing pollutant loads? 

1.4 Status of Monitoring Programs in and Adjacent to the SFAN Parks 

1.4.1 Summary of Historical, Current, and Potential Monitoring 

Programs 

Monitoring programs currently exist for some of the parks under previously developed vital 

signs models that include marine, freshwater, and terrestrial plant and vertebrate components as 

well as abiotic components. Several threatened or endangered (T&E) species, plant communities, 

water quality, air quality, geologic processes, and non-native invasive plants and animals are 

currently monitored (Table 1.5). The existence of these long-term data sets was considered as 

part of the vital signs selection and prioritization process. Many of the existing monitoring 

protocols for these vital signs require review and will need to be integrated into a larger, longterm monitoring program. Historic monitoring programs are described further in Appendix 3; 

however, it is not the intent of this document to provide an exhaustive account of other 

monitoring programs. Participating agencies and existing and potential monitoring partnerships 

are further described in Chapter 8. Much of the potential for monitoring partnerships exists 

because other agencies and institutions are planning or conducting their own monitoring 

programs on lands adjacent to the parks. 

1.4.2 Summary and Analysis of Water Quality Monitoring Data 

Key water quality issues in the network include impacts from agricultural operations on water 

quality and aquatic habitat, marine and estuarine protection and restoration, and restoration of 

aquatic and riparian habitat. Many of the park units in the SFAN have completed some level of 

land use assessment and water quality monitoring. The context of monitoring has been both 

regulatory and status/trends related. Through outside agency involvement and park initiative, 

recreational monitoring programs are in place for beaches at PORE and GOGA. NPS Director's 

Order # 83 is followed for beach water quality monitoring. Regional Water Quality Control 
28

Table 0.5. Summary of current and historical monitoring programs within the SFAN parks as of 

2004. Numbers in the columns for each park represent the number of years monitoring has been 

conducted in that park for the .orresponding program. Participating agencies and partners are 

listed for each program. 

Monitoring Program 

EUON FOPO GOGA JOMU MUWO PORE PINN PRES 

Participating Agencies 

and Partners**

ABIOTIC 

Air quality 20+ 14 NPS, State 

Air quality--visibility H* NPS 

Cave conditions 6 NPS 

Erosion monitoring 5 4 NPS 

Fire history 30 24 NPS 

Hydrologic monitoring 7-50 7 NPS, USGS 

Night sky monitoring 1 3 NPS 

Prescribed burn plots 14 14 NPS 

Restoration site geomorphology 6 NPS 

Scour chains (vertical) H NPS 

Seismic activity 35 35 35 35 35 35 35 35 USGS 

Shoreline change (LIDAR) 4 7 USGS 

Stream geomorphology 2 7 6 NPS 

Visitor trail use 5 NPS 

Water quality 4 2 4 4 6 NPS, State 

Watershed assessment 5 2 5 5 NPS, USGS 

Weather 2 2 38 67 NPS, NOAA 

BIOTIC 

Acorn production H NPS 

Amphibians 10 10 4 USGS/NPS 

Bank Swallows 9 NPS 

Beached bird surveys 9 30 NPS, 

Benthic invertebrates/intertidal zone 8 8 NOAA PRBO NPS 

Butterflies (listed species) 10 10 NPS, Stanford 

Cattle grazing (RDMs) 15 15 NPS 

Coho salmon and steelhead trout 10 7 NPS 

Cooper’s Hawk H NPS 

Eel grass beds 10 10 NPS, CDFG 
29

Monitoring Program 

EUON FOPO GOGA JOMU MUWO PORE PINN PRES 

Participating Agencies 

and Partners**

Harbor seals 26 27 PRBO/NPS 

Herons, egrets 10 7 NPS, Audubon 

Juvenile rockfish 20 20 NMFS 

Landbirds 9 1 39 NPS, PRBO 

Mountain beaver 7 7 USGS 

Nearshore productivity (CODAR) 3 UCD 

Non-native plants (selected species) 10+ 2 8 6 NPS 

Northern elephant seals 22 PRBO/NPS 

Northern Spotted Owls 9 9 9 NPS, PRBO 

Oak mortality/reproduction 1 4 NPS 

Pacific herring 25 25 CDFG 

Prairie Falcon 16 NPS 

Raptors 15 GGRO 

Rare plants 10+ 10+ CNPS, NPS 

Red-legged frog 10 4 NPS, USGS 

Seabirds (several species) 10 20 FWS, PRBO, NPS 

Shorebirds/water birds 16 16 NPS, Audubon, 

Small bird distribution/abundance 20 PRBO NPS 

Small mammals 5 20 NPS, USGS 

Steller and California sea lions 10 NPS 

Stranded marine mammals 10+ 20+ NMFS,MMC,MVZ 

Terrestrial vertebrates 5 5 NPS, USGS 

Townsend’s big-eared bats 10+ 6 NPS, USGS 

Turkeys/Peafowl 4 NPS 

Ungulates—elk 24 NPS, CDFG 

Ungulates—native & exotic deer 3 3 NPS, CDFG 

Western Snowy Plover 8 30 PRBO, NPS 

Wildlife diseases (several) 5 NPS, UCD 

*H=historical monitoring projects. 

**Audubon=National Audubon Society; CNPS=California Native Plant Society; CDFG=California Department of 

Fish and Game; FWS=U.S. Fish and Wildlife Service; GGRO=Golden Gate Raptor Observatory; MMC=Marine 

Mammal Center; MVZ=Museum of Vertebrate Zoology; NMFS=US National Marine Fisheries Service; 

NOAA=US National Oceanographic and Atmospheric Administration; NPS=National Park Service; PRBO=Point 

Reyes Bird Observatory; Stanford=Stanford University; State=California state agencies; UCD=University of 

California at Davis; USGS=US Geological Survey. 
30

Board requirements and American Public Health Association (1998) Standard Methods protocols 

are followed for all water quality monitoring. The USGS protocol is followed for all aspects of a 

pilot project to determine sediment load using the Turbidity Threshold Sampling Technique. 

Table 0.6. Water resources monitoring summary. 

 Vital Sign Monitoring Purpose Parks Monitoring* 

Water Quality Status & trends / Regulatory GOGA, PINN, PORE 

Water Clarity Status & trends / Regulatory GOGA, PORE, PINN 

Nutrients Status & trends / Regulatory GOGA, PORE, PINN 

Metals Status GOGA, PINN 

Pathogenic Bacteria Status & trends / Regulatory GOGA, PORE, PINN 

Benthic Macroinvertebrates Status GOGA, PINN, PORE,JOMU 

Oil/Hydrocarbons Status & trends 

HAB Status & trends 

Surface Water Dynamics Status & trends GOGA, PINN, PORE, JOMU 

Groundwater Dynamics Status & trends PINN, PORE, GOGA 

Oceanographic Physical 

Parameters 

Status & trends 

Flooding Status & trends 

Waves Status & trends 

Drought Status & trends 

* Includes past or present monitoring 

Although data quality assurance indices have not been formerly developed for the water quality 

data, standard operating procedures were followed and metadata are available. Much of the data 

has been entered into established databases, but a significant amount of data also exists in 

spreadsheet or raw form. Portions of the existing water quality monitoring data for PORE and 

GOGA have been analyzed and synthesized into reports (Cooprider 2004). Data from PINN, 

GOGA, and PORE was analyzed through a contract with UC Berkeley. Parameters monitored 

include flow, temperature, pH, dissolved oxygen, salinity, specific conductance, nitrates, nitrites, 

ammonia, orthophosphates, indicator bacteria (fecal/total coliform, E. coli, and enterococci), 

metals, and total suspended solids. Not all of these parameters have been monitored at all parks 

or all stations within each park. 

Monitoring efforts within GOGA (including PRES and MUWO) have been on going (though not 

continuous) since the late 1980’s. Sites have been located in several different watersheds and 

monitoring has focused primarily on evaluating impacts associated with stable operations. PINN 

has conducted baseline water quality monitoring in Chalone Creek (at sites throughout the park) 

since 1997. PORE monitoring (since 1999) has focused on evaluating the impacts of agricultural 

operations (dairy cattle, beef cattle, and equestrian operations). Water quality monitoring of 

Tomales Bay and Drakes Estero has been ongoing since the early 1990s in conjunction with 

State Department of Health Services shellfish production requirements. In addition, the USGS 

has recently completed the last of a three-year National Water Quality Assessment Program 

(NAQWA) level water quality monitoring of four watersheds (within GOGA and PORE) 

supporting coho salmon and steelhead trout. 
31

Pathogenic bacteria are a primary threat to water quality in SFAN. Indicator bacteria have 

consistently exceeded water quality criteria at many inland surface water monitoring sites at 

PORE and GOGA. This pollutant is also suspected to be a threat at JOMU and possibly PINN. 

Seasonal variability in bacteria concentrations has been detected and correlates with rainfall and 

runoff conditions. Efforts to improve water quality are on-going. A consultant for PORE has 

performed "Dairy Waste Management System Evaluations" for all of the ranches in the park. 

Best Management Practices have been implemented and research by local universities is 

proposed for the Tomales Bay watershed. For a more detailed summary of water quality data, see 

the SFAN Preliminary Water Quality Status Report (Cooprider 2004). 
32
33

Chapter 2 Conceptual Models 

2.1 Ecological Conceptual Models 

An ecological conceptual model is a visual or narrative summary that describes the important 

components of an ecosystem and the interactions among them. Development of a conceptual 

model helps in understanding how the physical, chemical, and biological elements of a 

monitoring program interact, and promotes integration and communication among scientists and 

managers from different disciplines. Increased understanding and communication gained 

throughout this process may lead to the identification of potential vital signs (Roman and Barrett 

1999). Ecological conceptual models also aid in defining relevant spatial and temporal scales to 

provide an appropriate context for the ecosystem components and processes being considered. 

Conceptual models are expressed in many different forms, including tables, matrices, box and 

arrow diagrams, graphics, descriptive text, and combinations of these forms (Jenkins et al. 2002). 

Typically, audiences are most receptive to visual models, but the specific model form used will 

depend on the modeler’s objectives (Noss 1990). Diagrams depict simplified relationships and 

system components, whereas text and tables provide details that may be lost in the simplified 

pictorial representations. 

Unfortunately, no single model form describes an entire system adequately. Model generality is 

needed to characterize broad-scale influences and relationships among park resources, while 

model specificity is required to identify detailed relationships and components in the system that 

can be effectively monitored and subsequently managed. Consequently, both broad-scale models 

and specific models are needed to adequately represent ecological systems contained within large 

areas the size of national parks. Because of this need to integrate both broad- and fine-scale 

components and processes into an ecological conceptual model, the SFAN developed a 

hierarchical model with successive layers representing increasing model specificity. 

Conceptual model development is an iterative and interactive process. Models are expected to 

change as a network’s monitoring program develops and as ecological linkages are better 

understood. Details will be added to SFAN models, especially for vital sign specific models, as 

monitoring programs are implemented and assessed for the network. 

2.2 Organizational Structure of SFAN Conceptual Models 

The SFAN model is hierarchical, with each layer of the model becoming increasingly more 

specific. Layers of the SFAN model include: 

1. A generalized conceptual model; 

2. A matrix representing the relationship between drivers and stressors and general vital 

signs categories that group similar ecosystem components and processes; and 

3. Three ecosystem models representing the dominant ecosystem types in the network - 

marine, aquatic/wetland, and terrestrial ecosystems. 
34

Figure 0.1. Nested spatial scale 

example relevant to the conceptual 

model, as depicted for PINN. 

Coarse vital signs categories, that were more 

comparable for ranking purposes, were used in 

the matrix at the second level. The third level, 

ecosystem models, represent dominant drivers 

and stressors, the types of effects that can be 

measured, and specific indicators that were 

identified as potential vital signs for each 

ecosystem. Based on the third, fine-scale layer of 

the model, specific indicators were ranked to 

produce a list of high-priority vital signs. As the 

SFAN Vital Signs Monitoring Program develops, 

more refined diagrams will be created depicting 

understood and hypothesized relationships 

between drivers/stressors and specific, highpriority vital signs. 

Nested spatial scales (Figure 2.1) ranging from 

20-m2

 habitat patches to 100 km2 coastal zones 

for marine ecosystems emphasize the importance 

of selecting vital signs that may be used to 

evaluate ecosystem integrity at various levels of 

ecological organization. 

 

2.3 Description of Drivers 

Ecosystem drivers are major external driving forces such as climate, biological processes, 

hydrologic cycles, and natural disturbance events (e.g., earthquakes, fire, droughts, floods) that 

have large scale influences on natural systems. Ecosystem drivers listed below are the product of 

network vital signs scoping workshops and represent the dominant external forces for the SFAN. 

Natural disturbance regimes are considered as part of each driver category. The strength, 

duration, and effects of these drivers will vary with the temporal scales at which they are 

measured. Furthermore, different species, communities and ecosystem will respond at different 

rates to these drivers. For example, the current species composition of some forest communities 

is the result of ecosystem drivers that were present several hundred years ago. 

2.3.1 Solar/Lunar Cycles 

Solar and lunar cycles include the rotation of Earth on its axis causing daily periodicity (i.e. night 

and day), the revolution of the moon around Earth creating variation in tides and lunar phases 

(lunar cycles), and the revolution of Earth around the sun causing seasonal changes. Over the 

course of time, plants, animals, and entire communities have evolved reproductive, growth, and 

behavioral characteristics in response to these cycles. For example, kangaroo rats avoid the heat 

of the desert sun through nocturnal habits, which are synchronized with lunar phases. Moonlight 

has been shown to affect many species including habitat use by small rodents. On full moon 

nights, some rodents are less likely to use open habitats for foraging (Jensen and Honess 1995). 

Moonlight also affects the nocturnal activities of seabirds during the nesting season (Hyrenbach 

and Dotson 2001). Organisms living in intertidal communities have adapted various physiologic 
35

traits and behavioral responses to contend with tidal fluctuations. Deciduous plants lose their 

leaves to reduce transpiration rates during winter months. Both solar and lunar cycles influence 

ecosystem dynamics at various spatial and temporal scales. 

2.3.2 Climate/Weather 

Climate is associated with the broad-scale, long-term patterns of weather which drive the 

distribution and abundance of biota in a given region or biome. For the SFAN, the temperature 

and precipitation patterns governing the flora and fauna are characterized by a moderate 

Mediterranean climate which offers long growing seasons and supports diverse plant and animal 

communities (Bailey 1995). On a geologic time scale, climate changes along with the organisms 

that are representative of a given biome. In contrast, weather is so variable from year to year that 

detection of significant change is difficult and requires long-term monitoring. Changes in the 

frequency and duration of weather events cause changes in the onset and duration of the growing 

season, phenology and other aspects of natural disturbance regimes, and may alter natural 

communities and facilitate general change in species/habitat distributions (Spellerberg 1991). 

Regime shifts are also considered by some to be a natural driver for changes in ecosystems, 

especially marine systems. Regime shifts occur when previously steady patterns in population 

indices such as recruitment patterns and abundance or community indices, like species 

composition or trophic relationships, change concurrently with physical changes in climate 

systems (McKinnell et al.2001). Regime shifts are usually visible in multiple indices, such the 

Aleutian Low Pressure Index and Pacific Decadal Oscillation (Mantua et al.1997, Beamish and 

Bouillon 1993). For instance, recurring Pacific Decadal Oscillation or El Niño-Southern 

Oscillation events affect temperature and precipitation patterns and produce significant changes 

in abiotic and biotic ecosystem components (Thurman 1988). These changes are within the 

natural range of variation; although, human activities may be altering the frequency and intensity 

of these events (NAST 2001). Potential impacts to sensitive ecosystems, endemic species, and 

threatened or endangered species are of particular concern. A long-term meteorological 

monitoring program is essential to evaluate how meteorological change influences the 

functioning of ecosystems. 

2.3.3 Geologic Processes 

Geologic processes include tectonic, volcanic, surficial, and geomorphic processes. Volcanic 

activity, the force partly responsible for the Pinnacles formations, brings minerals and rock to the 

Earth’s surface from its interior. Earthquakes, which can play a part in the physical breakdown 

and burial of rock surfaces, can expose new rock surfaces and minerals through uplift and rock 

shearing. Tectonic activity along the San Andreas Fault is a significant force shaping SFAN 

ecosystems and is responsible for thrusting the volcanic material at Pinnacles upward and for the 

formation of Tomales Bay and Bolinas Lagoon of GOGA and PORE. Newly exposed features 

provide opportunities for colonization by both flora and fauna, sometimes on distinctive 

formations or minerals of regionally unique composition. Mass movement works to breakdown 

geologic materials on a range of spatial scales from erosion of stream bank material to large 

landslides. Mass movement of rock, debris and sediment may take place suddenly (i.e. debris 

avalanches, lahars, rock falls and slides, or debris flows) or more slowly (i.e. slumping, creep, or 

slip). Other natural forces such as wind, water, and fire can affect the rate and magnitude of mass 

movement. In concert, geologic processes create unique formations such as caves, spires, and 
36

abyssal trenches, expose minerals such as serpentinite that influence biological activity, and alter 

surficial and geomorphic features to create a heterogeneous landscape (i.e. topographic and 

bathymetric variation; Bloom 1998). These processes set and reset the stage for colonization and 

establishment by diverse biological communities. 

2.3.4 Nutrient Cycles 

Nutrient cycles link the biotic and abiotic components of an ecosystem through a constant 

change of materials. The carbon cycle, for example, is an essential ecosystem process, in which 

insects, vertebrates, saprophytes, bacteria, fungi, and fire all play important roles. Nutrient 

cycling is considered an integrating variable, because the cycles occur across scales and involve 

the atmosphere, biosphere, lithosphere, and hydrosphere. While nutrients may be transported 

great distances in water or air, the key transformations that make these limiting elements 

available to plants (and so to animals) are driven by soil microbes, as are the reactions that 

release the elements back to air or water, to repeat the cycle. Ecosystems on stable trajectories 

have biological interactions that tend to conserve key nutrients (Chapin et al. 2002). Significant 

loss or gain of elements is a good indicator of change in the system such as acidification or large 

accumulations or losses of biomass. Upwelling of nutrient rich seawater is a primary driver 

behind the region’s high level of productivity in the marine system. 

2.3.5 Physical Oceanography 

Oceanography is identified as the branch of science dealing with physical and biological aspects 

of the oceans. These physical and/biological aspects (including waves, oceanic circulation, tides, 

and the interactions with biotic elements) function together both as a driver and an indicator. 

Tsunamis, for example, inundate coastal areas causing changes in habitats, and species 

distribution and abundance. Daily, seasonal, and annual variation in tides and changes in ocean 

circulation (seasonal and annual) stress coastal areas. Examples of larger scale changes in ocean 

circulation include Pacific Decadal Oscillation, El Niño-Southern Oscillation, and North Pacific 

Oscillation and produce significant changes in abiotic and biotic components of the marine 

ecosystem (Thurman 1988). These physical and biological aspects of the oceans can also serve 

as excellent vital signs of ecosystem change. Examples of standard indicators measured by 

NOAA include sea surface temperature, sea surface salinity, seasonal and annual changes in sea 

level, the frequency of El Niño-Southern Oscillations, and the distribution of nearshore currents. 

2.3.6 Coastal Processes 

Erosion and accretion of shoreline deposits and relative shoreline position are important factors 

in determining the ecosystem health and appropriate land uses in coastal areas. Relative sea level 

variations may be natural responses to climate change, movements of the seafloor, isostatic 

adjustment, and other earth processes. Changes in relative sea level may alter the position and 

morphology of coastlines, causing coastal flooding, water-logging of soils, and a gain or loss of 

land (Carter 1988). Changes in the shoreline position may also create or destroy coastal wetlands 

and salt marshes, inundate coastal, and induce saltwater intrusion into aquifers, leading to 

groundwater salinization. Subtle changes in sediment supply and physical processes can shift the 

balance between shoreline stability and accretion or shoreline erosion (Carter and Woodroffe 

1994). These shoreline changes may have significant implications for coastal ecosystems, human 

settlements, and land uses. 
37

2.3.7 Hydrologic Processes 

The physical, hydraulic, and chemical properties of streams and rivers determine their suitability 

as habitat for aquatic plants and wildlife. Conditions appropriate for salmon spawning, for 

example, are defined by water depth, water velocity, size of substrate, and availability of cover 

provided by overhanging vegetation, undercut banks, submerged logs and rocks, among other 

stream characteristics (Regart 1991). Similarly, flow frequency and duration, water depth and 

velocity, seasonality, and stream morphology dictate the composition and abundance of aquatic 

organisms at any given time. Hydrologic disturbance, particularly in the form of seasonal 

fluctuations and flooding, plays a key role in aquatic ecosystems of the SFAN. Flooding events 

alter succession, shift species composition, flush nutrients and other compounds into and out of 

the system (influencing terrestrial ecosystems, too), and reshape channel morphology (Gordon et 

al. 1992). Changes in sediment yield reflect changes in basin conditions, including climate, soils, 

erosion rates, vegetation, and topography. Fluctuations in sediment discharge affect many 

ecosystem processes and components downstream due to nutrient transport and sedimentation. 

Consequently, water chemistry fluctuates naturally as and when environmental conditions 

change, thereby affecting aquatic communities downstream. 

2.3.8 Natural Fire Cycles 

Fire is a significant driver for many ecosystems especially those characteristic of Mediterranean 

climates. Chaparral communities and Bishop pine forests are considered fire adapted. Fire 

changes community composition by consuming much of the living vegetation, litter, and dead 

material, releasing and killing or reducing the density of some species (Barbour et al. 1980). Fire 

regimes drive the distribution and abundance of serial stages of terrestrial plant communities in 

Mediterranean climates worldwide. Because of its prevalence as a natural disturbance, some 

plant communities in the San Francisco Bay Area are adapted to fire. Some species such as 

Bishop pine are fire dependent, relying on fire to open and release seeds from resinous cones 

which benefit from improved growing conditions such as available sunlight, a seedbed of bare 

mineral soil, and released nutrients. Other species including coast live oaks are fire tolerant, 

surviving and regenerating vegetatively following fire disturbance. Lightning, the most 

significant source of natural fires, is rare in the SFAN, but sparks from falling rocks, and 

spontaneous combustion of plant materials and organic matter can also ignite fires (Barbour et al. 

1980). It is important to recognize that indigenous anthropogenic fire played an important role in 

shaping the plant communities and their distribution we see on the landscape today. The Fire 

Management Plans of SFAN parks and the NPS National Fire Plan acknowledge the ‘natural’ 

role of this historical fire regime. 

2.3.9 Biological Processes 

An ecosystem consists of plants, animals, and microorganisms interacting with each other (the 

community) and with their physical (e.g., soil conditions and disturbance regimes) and climatic 

environment in a given area. Communities change naturally over time in response to changes in 

environmental variables, disturbance regimes, and species interactions. Ecosystem integrity 

results from natural plant and animal interactions such as herbivory, facilitation, competition, 

biological invasions, predation, allelopathy, disease, and mutualism. These relationships allow 

for the flow of energy and the cycling of nutrients and other materials throughout the system 

(Chapin et al. 1997). Unnatural interactions between plants and animals may negatively affect 

ecosystem integrity (e.g., exotic deer browsing, invasive exotic plant species taking over 
38

dominance from native species, predation by non-native species or native species at unnatural 

population levels – predator pits). Natural genetic processes such as mutation, genetic drift, and 

natural selection are among the biological processes that occur on the wildlands managed by the 

NPS. The dynamic nature of interactions among species in an ecosystem may alter successional / 

evolutionary pathways, leading to changes in the structure, composition, and function of 

ecosystems (Chapin et al. 1997). For example, herbivory may lead to reductions in relative 

abundance or extirpation of one or more plant species, which may, in turn, reduce the abundance 

of certain habitat types for other organisms. These changes are part of natural fluctuations that 

ecosystems undergo and may lead to alternate developmental pathways for the ecosystem. 

2.4 Descriptions of Stressors 

Stressors are physical, chemical, or biological perturbations to a system that are either (a) foreign 

to that system or (b) natural to the system but applied at an excessive [or deficient] level (Barrett 

et al. 1976). Stressors cause changes in the patterns and processes of natural systems. 

2.4.1 Climate Change 

Long-term changes in weather produce The greenhouse effect, which warms the Earth’s 

atmosphere, results from the interaction of solar radiation with accumulated greenhouse gases 

(e.g., carbon dioxide, methane, hydroflorocarbons, nitrous oxide, sulfur hexane fluoride, 

perflorocarbons, and water vapor) in the atmosphere. This warming effect has been enhanced 

over the past century by increased contributions of these gases, particularly carbon dioxide, from 

anthropogenic sources (NAST 2001). Potential consequences of this enhancement are rising 

ambient temperatures, changes in the initiation and duration of the growing season, increased 

drought occurrences, increased storm/flooding severity and frequency, increased biological 

invasions, shifting species ranges, and decreased predictability of weather patterns, all of which 

directly affect ecosystems. 

These changes may also alter natural ecosystem disturbance regimes (including fire), and can 

facilitate nonnative species invasions. The San Francisco Bay Area is predicted to have increased 

rainfall, and more intense and more frequent El Niño-Southern Oscillation events (NAST 2001, 

Bakun 1990). Climate change models predict that sea levels may rise from 5-37 inches over the 

next 100 years (NAST 2001). Climate change may impact shoreline erosion, saltwater intrusion 

in groundwater supplies, and changes in wetland water regimes. These are vital resource 

management concerns along the 120 miles of the SFAN network shoreline. Increased and more 

intense precipitation would also increase erosion and flood events at all of the parks, which are 

characterized as erosible soils. Sea surface temperature is also predicted to continue to rise. 

Central California waters have already increased in temperature over the past 30 years, resulting 

in changes in the distribution of many marine species of invertebrates and fishes and the range 

extension of warmer water species (Croll et al. 2000). 

2.4.2 Air Quality Degradation 

Air quality degradation encompasses several different sources of stress including acid deposition, 

tropospheric ozone, an increase in the concentration and/or type of toxins and heavy metals, 

visibility/haze, and nitrification (EPA 1999). Any of these factors may interact with the others 

amplifying their effects on ecosystems. Of concern are impacts to plant communities, water 
39

quality, non-native species invasions, nutrient cycling, and unique habitats/species. For instance, 

acid deposition can result in the leaching of nitrogen and calcium from ecosystems thereby 

affecting productivity, soil chemistry, water quality, biodiversity, and resistance/tolerance of 

biota to other stresses (Adriano and Havas 1990). Increased deposition of heavy metals, 

especially mercury, may result in bioaccumulation and bioconcentration with potential toxic 

effects to primary, secondary, and higher consumers. Direct effects of elevated levels of carbon 

dioxide and tropospheric ozone on native and exotic biota include adverse changes in their 

competitive ability, distribution, and survival, reducing native biodiversity (Stiling et al 2002). 

Particulate matter reduces visibility, particularly with increased humidity, and can combine with 

tropospheric ozone to produce photochemical smog. Photochemical smog has been linked to 

respiratory ailments in fauna and reduced vigor in floral species (Chappelka et al. 1996, 1999). 

2.4.3 Water Quality Degradation 

Water resources are of national concern as water bodies are diverted, polluted, and used by 

conflicting interests. In the SFAN, water quality is a very high profile issue because of the 

network’s proximity to a large urban area. Water quality concerns include external sources of 

pollution, inappropriate visitor use, atmospheric deposition (stream acidification), water 

pollution effects on park ecosystems and water use, and loss of aquatic biota (Karr and Dudley 

1981). Industrial, agricultural and recreational pollution threatens the water resources of the 

parks. The Norwalk virus, for example, contaminated shellfish and sickened over 100 people in 

Tomales Bay in 1998 (Ketcham 2001). Where streams originate outside park boundaries, water 

quality changes, particularly nitrogen and phosphorus content, can be indicative of agricultural 

fertilizer use or signal a reduction in productivity and/or vegetative cover upstream (Fong and 

Canevaro 1998). Organic chemical content may indicate land use changes upstream, especially 

mining or industrial activity. These organics affect freshwater mussels and other aquatic 

organisms directly and are also indicative of overall watershed problems affecting riparian and 

terrestrial biota (Gordon et al. 1992). Inorganic chemicals such as pesticides and industrial waste 

also negatively affect aquatic biota. Increased acidity in aquatic systems can raise concentrations 

of dissolved aluminum, which is toxic to native aquatic and terrestrial biota (Adriano and Havas 

1990). 

2.4.4 Water Quantity Alteration 

Streams, lakes, wetlands, and groundwater resources can be altered by impoundments, water 

withdrawal, expansion of impermeable surfaces in watersheds, climate change, loss of riparian 

buffers, and changes in runoff characteristics due to changes in plant community composition. 

Water transport and diversion are also stressors affecting sediment deposition/erosion, 

accretive/avulsive meandering, flow regimes (bankfull/dominant discharge/peak flow), and longshore sediment transport (Brooks 2003). Impermeable surfaces and other products of 

urbanization can increase downstream flow extremes, causing habitat loss and fragmentation. 

Water level fluctuations in ponds, wetlands, and stream discharge are directly linked to 

groundwater levels and hydrology which influence vegetation dynamics. An understanding of 

water table levels is required for predicting the effects of natural and human-induced 

hydrological changes (e.g., sea level rise, drought conditions, municipal groundwater 

withdrawal) and the fate of contaminants (Fetter 2000). Groundwater may be the significant 

water source for certain riparian systems, wetlands, and municipal water supplies (sole-source 

aquifers). Altered water quantity can also affect water quality, flooding events, and water 
40

temperature profiles. Both terrestrial and aquatic ecosystems are affected by these alterations 

which, in turn, can lead to erosion or sedimentation, habitat degradation, non-native species 

invasions, riparian and wetland habitat loss, and decreased biodiversity (Gordon et al. 1992). 

2.4.5 Human Population Increase 

With a current population of 7 million people, the metropolitan centers of San Francisco, 

Oakland, and San Jose are forecast to have a population of 8 million by 2020 (Association of 

Bay Area Governments 2000). The preservation of biologically and geologically diverse habitats 

and their associated species, while providing opportunities for recreation, education and aesthetic 

enjoyment to a large urban population is a difficult balancing act. Population increase inevitably 

results in land use change. For the parks, this includes pressures from adjacent lands, as well as 

activities inside parks, such as trampling of sensitive plant communities, compaction of soils, 

creation of social trails, and excessive impact on caves, wetlands, and other sensitive ecosystems. 

Increasing human populations lead to sources of light and noise pollution, altering terrestrial and 

marine wildlife behavior and affecting feeding, migratory, and reproductive cycles (Avise and 

Crawford 1981, Bondello 1976, Brown 1990). Excessive noise levels also negatively affect 

visitor experiences. Human encroachment on park boundaries can also disrupt scenic overlooks 

that extend beyond park boundaries. Increasing numbers of people often increase the number of 

feral animals in the region, putting pressure on park wildlife and vegetation (Drost and Fellers 

1995). Increasing vehicle traffic volume in and around the parks also leads to increased road 

mortality and the introduction of non-native species. 

2.4.6 Land Use Change/Development 

Land use change and development pressures manifest themselves in different forms including 

industrial and residential development, coastal development, aquaculture, storm water 

management, intensive grazing and agriculture, hazardous material spills, increased habitat loss 

and fragmentation, and increased visitor pressure on park resources (NAS 2000). Habitat 

fragmentation is one of the most significant products of land use change and encompasses many 

of the other issues threatening park lands. Habitat fragmentation is a function of edge-to-area 

ratio and habitat connectivity. Habitat fragmentation has cascading effects on habitat quality, 

quantity and distribution, predator and prey densities and distribution, nutrient levels, pollutant 

loads, and disease and pathogen incidence and distribution (Wilcove et al. 1986). Changes in 

land use within and adjacent to parks can also create barriers preventing the normal distribution 

or dispersal of species, isolating them on islands of parklands and altering gene flow. Parks may 

become sources or sinks for populations, and consequently, increase complexity of species 

management. Development can include construction of roads, buildings, and parking lots, 

wetland conversion, or conversion of adjacent agricultural land from grazing to vineyards. 

Certain species require open space for all or part of their habitat requirements, while other 

species require vegetation cover for their survival. Changes in the ratio of open space to cover 

are good indications of shifts in habitat availability for the relevant species and communities 

(NAS 2000). Land use changes and development can have significant impacts on habitat 

availability. Both the type and quantity of different land uses should be identified and monitored 

in and around the park. 
41

2.4.7 Resource Extraction 

Resource extraction results from dredging, sand mining, timber harvesting, harvesting of animals 

and herbaceous plants, recreational and commercial fishing, aquaculture and withdrawal of 

limited water resources. Because of these activities, dredge soil disposal, contamination, erosion, 

siltation, species loss, alteration of habitat, reduced water quality and quantity, and impacts from 

construction and access become significant management issues. In the SFAN, these issues 

concern all ecosystems, marine, terrestrial, and freshwater. Mineral and soil extraction can 

increase sedimentation of downstream water bodies or increase pollutant concentrations 

associated with extractive by-products. Extracting water, river rock, sand and gravel can alter 

habitat by changing flow volume and patterns, reducing bank stability and changing sediment 

deposition patterns (Brooks 2003). Water table changes may also occur as a result of mining and 

well drilling, which can affect ground water-dependent habitats (Fetter 2000). Poaching is also a 

problem for park biota within and adjacent to parks. Oil spills and hazardous chemical spills are 

of concern as well, since San Francisco Bay is a major shipping port. Genetic process can also be 

altered by anthropogenic stressors. For example several species in SFAN parks, including tule 

elk and northern elephant seals, have gone through genetic bottlenecks across their range due to 

historic harvest levels that brought populations down to a few individuals. 

2.4.8 Soil Alteration 

Soils are important to ecosystem integrity because they provide the primary media and 

components for most nutrient cycles while, in some cases, dictating the structure and functions 

associated with ecosystems on a given soil type. Soils can be altered by development activities, 

atmospheric deposition, climate change, altered precipitation patterns, water quality and quantity 

alteration, resource extraction, and changes in disturbance regimes. Erosion or sedimentation, 

soil compaction, changes in soil carbon and organic matter content, loss of soil biotic diversity, 

and altered soil chemistry can result from soil stressors. Erosion and sedimentation are directly 

indicative of soil disturbance and provide a good indicator of the rate or extent of land use 

change (NAS 2000). Although sediments are a natural part of most aquatic ecosystems, human 

activities have dramatically increased sediment inputs to lakes, streams and wetlands (Brooks 

2003). Soil compaction can limit water infiltration, percolation, and storage, affect plant growth 

and alter nutrient cycling. Changes in soil carbon affect community productivity (Barbour et al. 

1980). Soil organisms, which are sensitive to changes in soil structure and chemistry, are 

essential to the formation and maintenance of soils as well as being key components in nutrient 

cycles (Crossley and Coleman 2003). Significant alterations in soil biota will inevitably affect 

nutrient cycling and ecosystem functions. 

2.4.9 Nutrient Enrichment 

Nutrient enrichment (excess nitrogen and phosphorus concentrations) can affect marine, 

terrestrial, and aquatic ecosystems. Typically, nutrient enrichment results from excessive erosion, 

atmospheric deposition, agricultural and commercial fertilizers, aquaculture loading from feces, 

and runoff. Elevated concentrations of nitrogen and phosphorus instigate dramatic shifts in 

vegetation and macroinvertebrate communities, paving the way for non-native species invasions 

and reduced biodiversity. As an example, nitrogen-loading in shallow estuarine embayments can 

lead to shifts in the dominant primary producers (e.g., macroalgae may replace eelgrass), which 

can lead to declines in dissolved oxygen, altered benthic community structure, altered fish and 

decapods communities, and higher trophic responses (Bricker 1999). 
42

2.4.10 Park Development and Operations 

Increasing population has increased visitation in SFAN parks. The rise in visitation puts greater 

demand on park resources and often requires changes in the amount of infrastructure and 

operations. Park roads may need resurfacing or be extended. Parking lots may need to be 

expanded. Visitor and interpretive centers, campgrounds, and other facilities may need to be 

built, upgraded or maintained more frequently. Interpretive media needs to be maintained and 

sometimes relocated. On a broader scale, management activities such as installation of coastal 

barriers, fire suppression, grazing, invasive species control, removal of vegetation, and 

reclamation of nearshore areas can alter ecosystem structure and function. All of these activities 

impact the parks’ natural resources and influence visitor use. 

2.4.11 Recreational Use 

Demographic changes can dramatically increase park visitation and recreational use, sometimes 

to unsustainable levels. This visitation pressure extends to trails, beaches and backcountry 

resources. The current broad variety of uses within the parks exacts a toll on the natural 

resources. Aircraft (hang gliders, ultralights, helicopters), surfing, dog walking, mountain bikes, 

horses, kayaking, environmental education groups and hikers combine to put continued strain on 

wildlife, vegetation, water resources, and soils. Also, the effects of recreational extraction (i.e. 

mushroom hunting, clam digging, fishing, seagrass harvesting) are poorly understood and has 

not been assessed for most activities. The millions of visitors that frequent the SFAN parks each 

year have adverse impacts to sensitive plants and wildlife. This high level of visitor use creates 

demands for continued park development, or upgrade of existing development, particularly of 

trails, which fragment wildlife habitat, bring people into sensitive areas, and contribute to offtrail use in these sensitive areas (NPS 1997). On the other hand, there is a direct correlation 

between visitor use and enjoyment, and public support for maintaining natural systems on NPS 

wildlands. 

2.4.12 Fire Management 

Fire can be a useful tool for managing fire adapted ecosystems in limiting invasive species, 

controlling fuel loads, and maintaining a mix of seral communities across the parks’ landscapes. 

Fire prevention, suppression, and prescription all affect the trajectories of natural resource 

changes. While fire management may be necessary to maintain native ecosystems, our 

understanding of the appropriate fire intensity, frequency and duration required to do so is 

limited (Debano et al. 1998). Often, prescribed fires do not replicate natural fire, and burnt areas 

become vectors of non-native plant invasions (Meyer and Shiffman 1999). Burnt areas also are 

susceptible to erosion. Conversely, infrequent burns can result in excessive fuel loads leading to 

intense fires that damage or destroy less-tolerant species, and to the persistence of diseases. 

2.4.13 Non-native Invasive Species/Disease 

Non-native invasive species can reduce or eliminate native populations of flora and fauna, alter 

natural disturbance regimes, and change ecosystem functions. The sources of non-native species 

are varied and increase with the proximity to urban centers. The sustainability of threatened and 

endangered species and the loss of more common species are of special concern. Non-native 

invasive plants, animals, and pathogens also affect the structure and quality of habitat, alter 

species genetics and pollination dynamics, impact soil structure, biota, and chemistry, and can 
43

significantly affect watershed hydrology including evapotranspiration rates, stream flow, and 

erosion and sedimentation dynamics (Mack et al. 2000). 

Disease is known to occur in all plant and wildlife populations and can significantly affect local 

demographics. However, the level of impact on a species population varies and is largely 

unknown. Bacteria, fungi, parasites, and viruses contribute to plant and wildlife diseases. Many 

disease agents and vectors are naturally found in the environment but their affect on species 

populations can be exacerbated by habitat fragmentation, overcrowding, genetic isolation, and 

climate change. Other diseases are introduced into populations by alien species and foreign 

sources and can have dramatic impacts on local populations. Sudden oak death syndrome is a 

major concern in the SFAN (Rizzo and Garbelotto 2003), and West Nile Virus is expanding in 

the region. 

2.4.14 Native Species Decline and Extirpation 

Significant change in native species diversity is a key early warning of ecosystem distress (NAS 

2000). But, significant decline or loss of native species populations can also be a stress to a 

community or ecosystem in its own right. Maintenance of viable populations of native species is 

a fundamental part of maintaining ecological integrity. Declining native populations, then, can 

lead to impaired ecosystem functions such as productivity, nutrient cycling, nutrient retention, 

energy transfer, habitat diversity and quality, terrestrial and aquatic linkages, and hydrologic 

function (Tilman 1999). In some cases, declining biodiversity may be linked to functional 

impairment. In other instances, a loss of functionality may be related to the decline or loss of a 

particular species. Loss of keystone species (e.g., starfish), umbrella species (e.g., Northern 

Spotted Owl), or ecosystem engineers (e.g., mountain beaver) may be indicative of a shift in 

ecosystem type, resulting in cascading effects on other species (Paine 1969, Lambeck 1997, 

Simberloff 1998). 

2.5 Generalized Conceptual Model 

A generalized conceptual model was created to introduce the organizational structure of the 

SFAN model subcomponents (Figure 2.2). For conceptual purposes, ecosystems were divided 

into dominant resource realms—air resources (atmosphere), biotic resources (biosphere), water 

resources (hydrosphere), and earth resources (lithosphere)—to assist in organizing similar ecosystem 

processes and components. Then, ecosystems within the SFAN were divided into three types—

marine, aquatic/wetland, and terrestrial—with each ecosystem type having associated subsystems or 

forms. Key drivers and stressors are also represented in this model acting on the different cosystems 

along pathways associated with each resource realm. Stressors can act on ecosystems through the 

different resource realms directly or they can affect drivers, which in turn, affect ecosystems via 

resource realm pathways. Note that socio-political forces influence anthropogenic stressors. 
44

Figure 0.2. Generalized conceptual model for the SFAN. 
45

2.6 Driver, Stressor, and Vital Signs Matrix 

Significant relationships between broad-scale (general) vital signs, and drivers and stressors are 

summarized in matrix format (Tables 2.3 a-e). The matrix is continued on subsequent pages 

starting with the atmospheric realm on the initial page and ending with the lithosphere realm on 

the final page of the matrix. General vital signs are organized again by resource realm along the 

vertical axis. Drivers and stressors are aligned along the horizontal axis. Represented in each 

model are the dominant ecosystem drivers and stressors identified by the SFAN and through vital 

signs scoping workshops. An “x” is placed in any box where a vital sign intersects with a driver 

or stressor with which there exists a suspected or known significant relationship. General vital 

signs rather than specific vital signs are used to limit the model’s complexity and to simplify the 

initial vital sign prioritization process for this layer of the model. 

Relationships represent our ecological understanding for one or more ecosystem types; therefore, 

not all relationships are applicable to all ecosystem types. Information collected from scoping 

workshops, inventory study plans, resource management plans, and from discussions with 

resource managers were used in the initial construction of the matrix. Relationships depicted in 

the final matrix are the result of expert input from network scoping workshops and may not 

represent all possible or “apparent” relationships. Rather, the matrix represents relationships 

between drivers/stressors and general vital signs identified by workshop participants as being 

scientifically justifiable and relevant to SFAN monitoring objectives. 

The matrix allows for the qualitative comparison of general vital signs by showing which vital 

signs are affected by multiple drivers and stressors as well as which stressors affect multiple vital 

signs. In some cases, it may be desirable to choose vital signs with relative specificity to a given 

stressor. In others, it may be desirable to choose a vital sign that can serve as an early warning 

for multiple stressors. Ideally, both types of vital signs are represented in a vital signs monitoring 

program, as well as vital signs that represent different resource realms. 

2.7 Ecosystem Models 

Individual conceptual models are presented for each ecosystem type: marine (Figure 2.4), 

aquatic/wetland (Figure 2.5), and terrestrial (Figure 2.6). Represented in each model are the 

dominant ecosystem drivers and stressors identified by the SFAN, which were also listed in 

Tables 2.3a-e. Natural and anthropogenic forces produce changes in ecosystem processes and 

components through their interactions with the forms associated with each ecosystem. Example 

effects resulting from these interactions are listed in the models. Vital signs selected by SFAN 

that may assist in monitoring the effects of ecosystem drivers and stressors on ecosystems are 

depicted in the models. In some cases, a stressor or driver is considered a vital sign. Depicted in 

each model in bold are vital signs, stressors and drivers considered by the network for long-term
46

Table 0.1 Significant relationships between general atmospheric vital signs and drivers and stressors in the SFAN 

DRIVERS STRESSORS 

RESOURCE REALM GENERAL VITAL SIGNS 

Solar/Lunar Cycles 

Climate/ Weather 

Geologic Processes 

Nutrient Cycles 

Oceanography 

Coastal Processes 

Hydrologic 

Processes 

Natural Fire Cycles 

Biological Processes 

Climate Change 

Air Quality 

Degradation 

Water Quality 

Degradation 

Water Quantity 

Alteration 

Human Population 

Increase 

Land Use Change/ 

Development 

Resource Extraction 

Soil Alteration 

Nutrient Enrichment 

AIR QUALITY Chemistry - contaminants x x Chemistry - nitrogen/ sulfur deposition 

 x x x 

Chemistry - ozone 

 x x 

Chemistry - carbon dioxide, methane 

 x x 

Physics - fine particles x x LIGHT and SOUND 

Lightscapes x x Ultraviolet light (B) Soundscapes x 

WEATHER and CLIMATE 

ATMOSPHERE 

Weather/ climate change x x x x x x x x 
47

Table 0.2 Significant relationships between general biotic (faunal) vital signs and drivers and stressors in the SFA

DRIVERS STRESSORS 

RESOURCE REALM GENERAL VITAL SIGNS 

Solar/Lunar Cycles 

Climate/ Weather 

Geologic Processes 

Nutrient Cycles 

Oceanography 

Coastal Processes 

Hydrologic 

Processes 

Natural Fire Cycles 

Biological Processes 

Climate Change 

Air Quality 

Degradation 

Water Quality 

Degradation 

Water Quantity 

Alteration 

Human Population 

Increase 

Land Use Change/ 

Development 

Resource Extraction 

Soil Alteration 

Nutrient Enrichment 

FAUNAL DYNAMICS Species distribution and abundance 

x x x x x x x x x x x x x x 

Native species of special interest x x x x x x x x x x Species at risk x x x x x x x x x x Non-native invasive species/disease 

 x x x x x x x x x x x 

Patch size and proximity x x x x x x x x x x x Community area and distribution x x x x x x x x x x x x Land use patterns x x x x x x x x 

BIOSPHERE 
48

Table 0.3 Significant relationships between general biotic (vegetation) vital signs and drivers and stressors in the 

DRIVERS STRESSORS 

RESOURCE REALM GENERAL VITAL SIGNS 

Solar/Lunar Cycles 

Climate/ Weather 

Geologic Processes 

Nutrient Cycles 

Oceanography 

Coastal Processes 

Hydrologic 

Processes 

Natural Fire Cycles 

Biological Processes 

Climate Change 

Air Quality 

Degradation 

Water Quality 

Degradation 

Water Quantity 

Alteration 

Human Population 

Increase 

Land Use Change/ 

Development 

Resource Extraction 

Soil Alteration 

Nutrient Enrichment 

VEGETATION DYNAMICS Species richness and diversity x x x x x x x x x Native species of special interest x x x x x x x x x x Species at risk x x x x x x x x x x 

Non-native invasive species/disease 

 x x x x x x x x x 

Vegetation composition and structure 

 x x x x x x x x x 

Community assemblages x x x x x x x x x x x Fragmentation and connectedness 

 x x x x x x x 

Land use patterns x x x x x Phenology x x x x x x x x x x x Biological processes 

x x x x x x x x x x x x x x 

BIOSPHERE 
49

Table 0.4 Significant relationships between general hydrospheric vital signs and drivers and stressors in the SFA

DRIVERS STRESSORS 

RESOURCE REALM GENERAL VITAL SIGNS 

Solar/Lunar Cycles 

Climate/ Weather 

Geologic Processes 

Nutrient Cycles 

Oceanography 

Coastal Processes 

Hydrologic 

Processes 

Natural Fire Cycles 

Biological Processes 

Climate Change 

Air Quality 

Degradation 

Water Quality 

Degradation 

Water Quantity 

Alteration 

Human Population 

Increase 

Land Use Change/ 

Development 

Resource Extraction 

Soil Alteration 

Nutrient Enrichment 

Water chemistry x x x x x x x x x x x x Water clarity x x x x x x x x x x x Water contaminants 

 x 

 x x x x x x x 

Pathogenic bacteria 

 x 

 x x x x x x x x x x 

Surface water dynamics 

 x 

x x x x x x x x 

Groundwater dynamics 

 x 

x x x x x x 

Physical oceanography 

 x 

 x x x x 

Flooding x x x x x x x Waves x x x x x Drought x x x x x x 

HYDROSPHERE 
50

Table 0.5 Significant relationships between general lithospheric vital signs and drivers and stressors in the SFAN 

DRIVERS STRESSORS 

RESOURCE REALM GENERAL VITAL SIGNS 

Solar/Lunar Cycles 

Climate/ Weather 

Geologic Processes 

Nutrient Cycles 

Oceanography 

Coastal Processes 

Hydrologic 

Processes 

Natural Fire Cycles 

Biological Processes 

Climate Change 

Air Quality 

Degradation 

Water Quality 

Degradation 

Water Quantity 

Alteration 

Human Population 

Increase 

Land Use Change/ 

Development 

Resource Extraction 

Soil Alteration 

Nutrient Enrichment 

Habitat patterns/surficial processes 

 x x x x x x x 

Soil biota x x Soil chemistry and contaminants x x x x x Soil structure and texture x x x x x x Soil erosion an deposition (paleoclimate) 

 x x x x x x x x 

Shoreline shifts x x x x x Earthquakes x x x x Mass wasting x x x x x 

LITHOSPHERE 
51

monitoring. Vital signs are organized by resource realm. Note that not all possible effects or all 

possible indicators are depicted in the diagrams because of spatial restrictions. Some vital signs, 

such as Air Quality, Water Quantity or Plant Communities, may appear in more than one 

ecosystem, because the changes in that indicator may reveal changes to more than one 

ecosystem. The bolded items that are circled indicate the high priority vital signs that have been 

chosen for long-term monitoring. The bolded effects will likely be monitored using the vital 

signs (see chapter 3 for details about the vital signs prioritization and selection process). 

2.8 Specific Vital Sign Example 

As the vital signs monitoring program proceeds, more detailed conceptual models will be 

designed focusing on chosen, high priority vital signs. Detailed models will allow the parks to 

evaluate and choose the most appropriate parameters to measure (Figure 2.6). 

2.9 Implications for Vital Signs Selection 

Ecosystems are, by definition, complex systems. Conceptual models assist in isolating ecosystem 

components, functions, and structures of known or potential importance to the integrity of the 

system. Each of these “vital” attributes can, therefore, serve as an indicator of ecosystem 

integrity. Still, the list of possible and credible vital signs is long, and there are often multiple 

metrics that can be measured for each vital sign. Spatial sampling design and sampling methods 

can be complex and may require expensive equipment or analyses. Park networks also have 

limited fiscal, temporal, and human resources. It is, therefore, necessary to prioritize the list of 

potential vital signs, to determine what vital signs are most important for individual parks and for 

the network. It is also necessary to select from the prioritized list of vital signs that integrate 

multiple attributes of ecosystem structure and function and that represent a variety of spatial and 

temporal scales (Holling 1986). Development of ecological conceptual models is the first step 

toward selecting appropriate vital signs. 
52

Figure 0.3. Marine ecosystems conceptual model of how drivers and stressors act through different marine ecosyproduce changes in components of different resource realms within the SFAN. 
53

Figure 0.4. Aquatic/Wetland ecosystem conceptual model of how drivers and stressors act through different aquato produce changes in components of different resource realms within the SFAN. 
54

Figure 0.5. Terrestrial ecosystem conceptual model of how drivers and stressors act through different terrestrial eproduce changes in components of different resource realms within the SFAN. 
55

Figure 0.6 Example of a conceptual model for a specific vital sign (raptors and condors) and a 

measurable parameter (prairie falcon nest success). 
56
57

Chapter 3 Vital Signs 

3.1 Overview of the Vital Signs Selection Process 

Vital signs are defined as “a subset of physical, chemical, and biological elements and processes 

of park ecosystems that are selected to represent the overall health or condition of park resources, 

known or hypothesized effects of stressors, or elements that have important human values” 

(Davis 2005). The elements and processes that are monitored are a subset of the total suite of 

natural resources that park managers are directed to preserve ‘unimpaired for future generations,’ 

including water, air, geological resources, plants and animals, and the various ecological, 

biological, and physical processes that act on those resources. Vital signs may occur at any level 

of organization including landscape, community, population, or genetic level, and may be 

compositional (referring to the variety of elements in the system), structural (referring to the 

organization or pattern of the system), or functional (referring to ecological processes).” 

The complex task of developing a network vital signs monitoring program requires a front-end 

investment in planning and design to ensure that monitoring will meet the most critical current 

and future information needs of each park and produce scientifically credible data that are 

accessible and meaningful to managers and researchers in a timely manner. The investment in 

planning and design also ensures that monitoring will build upon existing information and 

understanding of park ecosystems and make maximum use of partnerships with other agencies 

and academia. 

Vital signs selection is an iterative process; as our understanding of ecological processes, the 

nature of variation within and between vital signs and linkages grows, vital signs may change. 

Adjustments to the monitoring program also may occur as subsequent programmatic and 

individual protocol reviews provide feedback on the value of the selected vital signs toward the 

monitoring objectives. The following sections briefly explain the SFAN decision–making and 

prioritization process. A more detailed description of the process, methods, and products can be 

found in the SFAN Phase II Monitoring Plan (SFAN 2003). 

3.2 SFAN Vital Signs Selection Process 

The SFAN vital signs selection process began with a series of park scoping workshops and a 

network wide Vital Signs Workshop to create an initial broad list of potential vital signs. The list 

of potential vital signs was refined by technical expert focus groups and ranked by NPS staff and 

experts. SFAN and park staff reviewed the resulting, prioritized list to ensure that vital signs 

represented a range of resource realms. Table 3.1 highlights some of the important steps in the 

SFAN process and their action dates. 
58

Table 0.1 Important activities and dates in the SFAN vital signs selection process. 

Activity Date(s) 

GOGA and PORE workshop to identify joint vital signs July 1997 

Individual park workshops to identify vital signs 2001-2002 

SFAN Vital Signs Workshop March 19-20, 2003 

Ranking through online vital signs database June 20 – July 11, 2003 

Vital Signs Prioritization meeting with SFAN Park Staffs July 29-30, 2003 

Recommendations to Board of Directors August 25, 2003 

Submit draft Monitoring Plan (Phase II) to WASO September 26, 2003 

Submit draft Monitoring Plan (Phase III) to WASO December 15, 2004 

Submit final Monitoring Plan to NRPC September 30, 2005 

3.2.1 Scoping Workshops 

Vital signs scoping workshops at each SFAN park in 2001 provided the foundational materials 

and direction on which to build the SFAN vital signs selection process. In each of these 

workshops, participants identified significant resources in the parks, identified key processes and 

stressors affecting the parks, drafted potential monitoring questions, and recommended vital 

signs that could address the monitoring questions. An initial prioritization of vital signs and 

development of a conceptual model were also conducted at the park level. 

The March 2003 SFAN Vital Signs Workshop consolidated the park-specific information into a 

conceptual model, relevant monitoring questions, and potential vital signs that could be applied 

across the network. Information from the park workshops and the March scoping workshop was 

used to: 

• Revise conceptual model components; 

• Develop a vital signs list derived from completed protocol questionnaires; 

• Identify gaps in our understanding and organization of potential vital signs; 

• Select methodologies for prioritizing vital signs; and 

• Identify initial sampling designs and monitoring protocols related to the potential vital 

signs discussed in the workshops. 

A summary of the comments resulting from the workshops can be found in the SFAN Phase I 

Draft Report and the SFAN Phase II Draft Report (SFAN 2001b, SFAN 2003). 

3.2.2 Technical Expert Focus Groups 

Recommendations made during all of the workshops were further refined using technical expert 

focus groups, i.e. vegetation, wildlife, marine, geology, and water resources. Focus groups 

consolidated several of the potential vital signs so that comparisons could be made among larger 

groups of vital signs. Focus groups also developed the initial protocol development summaries, 

which provide in-depth information about vital sign justification, vital sign metrics, monitoring 

scale and methodologies, assumptions, constraints, potential thresholds for monitoring, and 

management actions if the thresholds are reached or exceeded. 
59

3.2.3 Ranking Criteria 

The four criteria utilized to rank vital signs reflect important qualities of an effective vital signs 

monitoring program and were modified from the Cumberland-Piedmont Network ranking 

criteria, Jackson et al. (2000), Tegler et al. (2001), and Andreasen et al. (2001) (Table 3.2). The 

four criteria are Ecological Significance, Management Significance, Legal Mandate and Cost and 

Feasibility. Sub-criteria describe the decisive factors associated with each primary criterion, and 

the prioritization scheme defines the rationale behind assigning a given value to each criterion. 

Only NPS staff ranked vital signs using the Legal Mandates criterion, because of the specific 

knowledge of NPS and federal policies used in the description of the prioritization scheme. Each 

criterion was weighted to reflect its relative contribution to the selection of SFAN vital signs. 

Table 0.2 Criteria used to prioritize SFAN vital signs. 

Primary 

Criteria 

Sub-criteria* Prioritization Scheme 

Ecological 

Significance 

o There is a strong, defensible linkage between 

the vital sign and the ecological function or 

critical resource it is intended to represent. 

o The vital sign represents a resource or 

function of high ecological importance based 

on the conceptual model of the system and 

the supporting ecological literature. 

o Data from the vital sign are needed by the 

parks to fill gaps in current ecological 

knowledge. 

o The vital sign provides early warning of 

undesirable changes to important resources. 

It can signify an impending change in the 

ecological system. 

o The vital sign has a high signal to noise ratio 

and does not exhibit large, naturally 

occurring variability. 

o The vital sign is sufficiently sensitive; small 

changes in the vital sign can be used to detect 

a significant change in the target resource or 

function. 

o Reference conditions exist within the region, 

and/or threshold values are specified in the 

available literature that can be used to 

measure deviance from a desired condition. 

o The vital sign complements vital signs at 

other scales and levels of biological 

organization.

Very High—I strongly agree with at 

least 7 of these statements. 

High—I strongly agree with at least 5 of 

these statements. 

 

Moderate—I strongly agree with at least 

4 of these statements. 

Low—I strongly agree with at least 1 of 

these statements. 

Very Low--This is an important vital sign 

to monitor, but I do not strongly agree

with any of these statements. 

No opinion--I do not know enough about 

this criterion for this vital sign to rank it. 
60

Primary 

Criteria 

Sub-criteria* Prioritization Scheme 

Management 

Significance 

o There is an obvious, direct application of the 

data to a key management decision, or for 

evaluating the effectiveness of past 

management decisions. 

o The vital sign will produce results that are 

clearly understood and accepted by park 

managers, other policy makers, research 

scientists, and the general public, all of whom 

should be able to recognize the implications 

of the vital sign’s results for protecting and 

managing the park’s natural resources. 

o Data are badly needed to give managers a 

better understanding of park resources so that 

they can make informed decisions. 

o Monitoring results are likely to provide early 

warning of resource impairment, and will 

save park resources and money if a problem 

is discovered early. 

o In addition to addressing a specific 

management decision, data provide 

information that strongly support other 

management decisions. 

o Data are of high interest to the public. 

o There is an obvious, direct application of the 

data to performance (GPRA) goals. 

Very high—I strongly agree with at least 

6 of these statements. 

 

High—I strongly agree with at least 5 of 

these statements. 

Moderate—I strongly agree with at least 

3 of these statements. 

Low—I strongly agree with at least 1 of 

these statements. 

Very Low— Some of the statements 

above apply to some degree, but I do not 

strongly agree with any of these 

statements. 

No opinion—I do not know enough about 

this criterion for this vital sign to rank it. 

Legal 

Mandate 

This criterion is part of ‘Management 

Significance’ but is purposely duplicated here to 

emphasize those vital signs and resources that are 

required to be monitored by some legal or policy 

mandate. The intent is to give additional priority 

to a vital sign if a park is directed to monitor 

specific resources because of some binding legal 

or Congressional mandate, such as specific 

legislation and executive orders, or park enabling 

legislation. The binding document may be with 

parties at the local, state, regional, or federal 

level. 

Very High—The park is required to 

monitor this specific resource/ vital sign 

by some specific, binding, legal mandate 

(e.g., Endangered Species Act for an 

endangered species, Clean Air Act for 

Class 1 airsheds), or park enabling 

legislation. 

High—The resource/vital sign is 

specifically covered by an Executive 

Order (e.g., invasive plants, wetlands) or 

a specific Memorandum of 

Understanding signed by the NPS (e.g., 

bird monitoring), as well as by the 

Organic Act, other general legislative or 

Congressional mandates, and NPS 

Management Policies. 

Moderate— There is a GPRA goal 

specifically mentioned for the 

resource/vital sign being monitored, or 

the need to monitor the resource is 

generally indicated by some type of 

federal or state law as well as by the 

Organic Act and other general legislative 

mandates and NPS Management Policies, 

but there is no specific legal mandate for 

this particular resource. 

 
61

Primary 

Criteria 

Sub-criteria* Prioritization Scheme 

Low— The resource/vital sign is listed as 

a sensitive resource or resource of 

concern by credible state, regional, or 

local conservation agencies or 

organizations, but it is not specifically 

identified in any legally-binding federal 

or state legislation. The resource/vital 

sign is also covered by the Organic Act 

and other general legislative or 

Congressional mandates such as the 

Omnibus Park Management Act and 

GPRA, and by NPS Management 

Policies. 

Very Low— The resource/vital sign is 

covered by the Organic Act and other 

general legislative or Congressional 

mandates such as the Omnibus Park 

Management Act and GPRA, and by NPS 

Management Policies, but there is no 

specific legal mandate for this particular 

resource. 

No opinion—I do not know enough about 

this criterion for this vital sign to rank it. 

Cost and 

Feasibility 

o Sampling and analysis techniques are costeffective. Cost-effective techniques may 

range from relatively simple methods applied 

frequently or more complex methods applied 

infrequently (e.g., data collection every five 

years results in low annual cost). 

o The vital sign has measureable results that are 

repeatable with different, qualified personnel. 

o Well-documented, scientifically sound 

monitoring protocols already exist for the 

vital sign. 

o Implementation of monitoring protocols is 

feasible given the constraints of site 

accessibility, sample size, equipment 

maintenance, etc. 

o Data will be comparable with data from other 

monitoring studies being conducted 

elsewhere in the region by other agencies, 

universities, or private organizations. 

o The opportunity for cost-sharing partnerships 

with other agencies, universities, or private 

organizations in the region exists. 

Very High—I strongly agree with all 6 

of these statements. 

High—I strongly agree with at least 4 of 

these statements. 

 

Moderate—I strongly agree with at least 

3 of these statements. 

Low—I strongly agree with at least 1 of 

these statements. 

 

Very Low—This is an important vital 

sign to monitor, but I do not strongly 

agree with any of these statements. 

No opinion—I do not know enough about 

this criterion for this vital sign to rank it. 
62

3.2.4 Initial Prioritization Process and Results 

NPS staff and experts ranked the initial vital sign list using an online vital sign database and vital 

sign ranking criteria. Participants from previous workshops, additional subject experts, regional 

NPS staff, and other selected agency officials completed the ranking process. Of the 156 people 

invited to rank the proposed SFAN vital signs, 55 people participated; 35 of the 55 participants 

were NPS employees. Participants were asked to rank each vital sign from very low to very high 

with respect to each criterion. Participants also had the option of choosing “no opinion” for each 

criterion if they had insufficient knowledge about the criterion or the vital sign to evaluate it. 

Participants were given two locations in which to provide feedback on the process or to provide 

additional information on the vital sign. Comments were taken into consideration as vital sign 

ranking results were reviewed and will be considered during protocol development. 

Weighted scores for the vital signs were calculated using three methodologies (i.e., weighted 

mean scores for each individual for each vital sign, weighted mean scores for each criterion for 

each vital sign, and mean weighted scores per individual without accounting for missing values). 

The resulting rank order of vital signs did not differ appreciably among methodologies 

suggesting that the results were relatively robust. In particular, the positions of the ten highest 

ranked vital signs and three lowest ranked vital signs changed very little. Most shifts in rank 

position from one calculation type to another occurred between adjacently ranked vital signs and 

were the result of slight differences in the second, third, or even fourth decimal place (accuracy 

beyond the limits of the data but useful for display purposes). 

The mean of weighted scores for each individual was calculated for each vital sign and analyzed 

using descriptive statistics (e.g., mean, mode, range, standard deviation). Analyses were 

performed on the complete data set as well as on subsets of the data. Vital sign rankings were 

sorted and compared based on management significance (only), ecological significance (only), 

NPS or non-NPS status, the participants’ areas of expertise, vital sign categories, and spatial 

scale. Although comparisons were also made with non-weighted mean scores, no comparisons 

were made with scores unadjusted for missing values since missing values could skew the data 

appreciably. Descriptive statistics were displayed for all data permutations. Detailed descriptions 

of the data calculations and the resulting data comparisons are presented in the Phase II Vital 

Signs Prioritization Meeting Summary 

(http://www1.nature.nps.gov/im/units/sfan/reports/phasereports.htm). 

3.2.5 Vital Signs Prioritization Meeting 

The purpose of the Vital Signs Prioritization Meeting was to have the Board of Directors and the 

Technical Steering Committee review the vital signs selection process and results, identify 

monitoring gaps in the prioritized list, adjust the order of the vital signs as necessary, and justify 

any changes made to the prioritized list. Alterations made to the initial prioritized list of vital 

sign were based on the need to cover, a variety of spatial scales, monitoring objectives, and vital 

sign types. 

Most changes to the vital sign list did not affect the outcome of the high priority list of vital signs 

on which the group is focused for the purposes of this monitoring plan. The most notable 

changes were 1) moving Weather and Climate to #1, because the data from this vital sign are 

essential to support most other vital signs, and 2) moving the Air Quality vital sign from #26 to 
63

#4, because of legal mandates (PORE and PINN both are Class I airsheds), ecological 

importance (air quality affects water and terrestrial resources), and significant contributions from 

partners. Wetlands were added as a vital sign. For the purposes of the vital sign, wetlands include 

not only plant communities, but also the hydrologic regime and the physical aspects of the land 

in both freshwater and marine wetland ecosystems. Wetlands were placed on the list next to 

related vital signs, such as riparian habitat and freshwater dynamics. 

3.3 Selected Vital Signs 

The SFAN presented the prioritized vital signs in rank order to emphasize the importance of each 

vital sign proposed during the selection and prioritization process. One contiguous list also 

emphasizes the partnership and monitoring potential that exists among many vital signs. The full 

vital sign list is placed in the three-level framework designed by the national I&M program 

(Table 3.3), which is a organizational tool for promoting communication, collaboration, and 

coordination among parks, networks, programs, and agencies involved in ecological monitoring. 

The network plans to develop monitoring protocols and databases consistent with national I&M 

standards for implementation of the highest ranked 18 (bolded in Table 3.3) vital signs first. 

Vital signs such as tule elk, rocky intertidal communities, non-native animals and Sudden Oak 

Death, which were ranked lower on the list, will continue to be monitored to some degree by 

SFAN parks and partners, because they are state species of special status, important 

communities, threats to native communities or emerging diseases (See Appendix 3 for additional 

monitoring programs). 

It is necessary to emphasize that many vital signs, especially those vital signs in the middle of the 

ranked list, had virtually identical mean weighted scores. As a result, there was very little 

distinction between many adjacently ranked vital signs. Adjustments to the monitoring program 

may occur as reviews provide feedback on the efficacy of the selected vital signs approximately 

every five years. Therefore, vital signs may be chosen for monitoring out of rank order if 

partnerships present themselves, management issues change, ecological information is updated, 

or linkages vital signs allow for efficient and effective monitoring. Modifications to wellestablished, long-term vital signs (e.g., weather data, freshwater dynamics) will be limited. 

3.3.1 Water Resources Vital Signs 

Water resources-related vital signs were discussed in Section 1.3.2.2: Water Resources 

Monitoring Efforts and Questions, and Potential Vital Signs. Modifications to that original list of 

vital signs/parameters resulted in broader vital signs (Table 3.4). For example, water clarity, 

water quality, nutrients, and pathogenic bacteria were combined into the “Freshwater Quality” 

vital sign. The Freshwater Quality Vital sign is the focus of the WRD Water Quality Monitoring 

Plan for the network. 
64

Table 0.3 Vital signs selected by the SFAN within the NPS Ecological Monitoring Framework. Vital signs select

assigned to the national framework Level 3 category that most closely pertains to that vital sign. Bolded vital sig18 of the list of 63 vital signs and will be implemented first. 

Level 1 

Category Level 2 Category Level 3 Category Vital Sign 

EUON 

FOPO 

GOGA 

JOMU 

Ozone Air Quality ◊ ◊ ◊ ◊ Wet and Dry Deposition Air Quality ◊ ◊ ◊ ◊ 

Air Quality 

Visibility and Particulate Matter 

Air Quality ◊ ◊ ● ◊ 

Air and Climate 

Weather and Climate Weather and Climate Weather and Climate + + + + 

Hillslope Features and Processes 

Mass Wasting (Landslide) ◊ ◊ ◊ ◊ 

Coastal / Oceanographic Features and Processes 

Coastal Dynamics 

- ● ● - 

Stream Channel and Watershed Characterization ◊ ◊ ● ◊ 

Geomorphology 

Stream / River Channel Characteristics 

Erosion and Deposition ◊ ◊ ● ● Soil Biota ◊ ◊ ◊ ◊ 

Geology and Soils 

Soil Quality Soil Function and Dynamics 

Soil Structure, Texture, and Chemistry ◊ ◊ ◊ ◊ 

Groundwater Dynamics Groundwater Dynamics ◊ ◊ ● ◊ Surface Water Dynamics Freshwater Dynamics - - + + 

Resilience Monitoring – Flood - - ◊ - 

Hydrology 

Marine Hydrology Physical Oceanography - ● ● - Water Chemistry Freshwater Quality - - + + Nutrient Dynamics Freshwater Quality - - + + 

Marine Water Quality - - ● - 

Microorganisms Freshwater Quality - - + + 

Water 

Water Quality 

Aquatic Macroinvertebrates and Algae 

Aquatic Invertebrates 

- - ● ● 

Invasive Species Invasive/Exotic Plants Invasive Plant Species + + + + 

Invasive/Exotic Animals Non-native Animals ◊ ◊ ◊ ◊ 

Infestations and Plant Diseases Sudden Oak Death ◊ - ● ◊ Disease Animal Diseases Wildlife Diseases ◊ ◊ ◊ ◊ 

Subtidal Monitoring - ◊ ◊ - 

Biological Integrity 

Focal Species or Communities 

Marine Communities 

Sandy Intertidal Community - ◊ ◊ - 
65

Level 1 

Category Level 2 Category Level 3 Category Vital Sign 

EUON 

FOPO 

GOGA 

JOMU 

Dune Vascular Plant Assemblages - ◊ ◊ - 

Intertidal Communities Rocky Intertidal Community - ● ● - Wetland Communities Wetlands - - + + Riparian Communities Riparian Habitat - - + + Grassland Vegetation /Herbaceous Communities 

Grassland Plant Communities 

- ◊ ◊ ◊ 

Forest/Woodland Communities 

Oak Woodlands 

- - ◊ ◊ 

Cave Communities Cave Communities - ◊ ◊ - Fishes Stream Fish Assemblages - - + + 

Marine and Estuarine Fish - ◊ ● - 

Amphibians and Reptiles Amphibians and Reptiles ◊ ◊ + + 

Landbird Population Dynamics ◊ ◊ + + Raptors and Condors - ◊ ● ◊ Shorebirds - ◊ ◊ - Seabirds - ◊ ● - Waterbirds - ◊ ● - Corvids ◊ ◊ ◊ ◊ 

Birds 

Pelagic Wildlife - - ● - Pinnipeds - - + - Tule Elk - - - - Medium to Large Carnivores - - ◊ ◊ Small Mammals and Herpetofauna ◊ ◊ ◊ ◊ Bat Guild ◊ ◊ ◊ ◊ Black-tailed Deer ◊ ◊ ◊ ◊ 

Mammals 

Cetaceans - - ● - Plant Community Change - + + + Ozone Sensitive Vegetation ◊ ◊ ◊ ◊ 

Vegetation Comples 

Plant Species (on edge of range) - - ◊ ◊ 

Terrestrial Complex Lichens ◊ ◊ ◊ ◊ 

Terrestrial Invertebrate Community ◊ ◊ ◊ ◊ Rare Plant Species - - + ● Northern Spotted Owl - - + - Western Snowy Plover - - + - T&E Butterflies - - + - 

At-risk Biota T&E Species and 

Communities 

Townsend’s Big-Eared Bats ◊ ◊ ◊ ◊ 
66

Level 1 

Category Level 2 Category Level 3 Category Vital Sign 

EUON 

FOPO 

GOGA 

JOMU 

Bank Swallow - - ● - 

Non-point Source Human Effects 

Non-point Source Human Effects 

Natural Lightscape ◊ ◊ ◊ ◊ 

Human use 

Cultural Landscapes Cultural Landscapes Viewshed ◊ ◊ ◊ ● Fire Fire and Fuel Dynamics Resilience Monitoring - Fire - - ● ◊ Landscape Dynamics Land Cover and Use Landscape Dynamics + + + + 

Landform Type ◊ ◊ ◊ ◊ 

Extreme Disturbance Events 

Extreme Disturbance Events Catastrophic Event Documentation ◊ ◊ ◊ ◊ 

Landscapes (Ecosystem Pattern and Processes) 

Soundscape Soundscape Natural Soundscapes - ◊ ● ● 

+ Vital signs for which the network will develop protocols and implement monitoring using funding from the vit

quality monitoring programs. 

● Vital signs that are monitored by a network park, another NPS program, or by another federal or state agency u

The network will collaborate with these monitoring efforts. 

◊ High priority vital signs for which monitoring will likely be done in the future, but which cannot currently be im

of limited staff and funding. 

- Vital sign does not apply to park, or for which there are no foreseeable plans to conduct monitoring. 
67

Table 0.4 Revised vital sign names for water resources vital signs from scoping workshops. 

Former Water Resources Vital Signs from Vital 

Signs Scoping Workshop New Vital Sign for Ranking 

Water Quality Freshwater Quality 

Water Clarity Freshwater Quality 

Nutrients Freshwater Quality 

Metals Freshwater Quality 

Pathogenic Bacteria Freshwater Quality 

Benthic Macroinvertebrates Aquatic Invertebrates 

Oil/Hydrocarbons Marine Water Quality 

HAB (Harmful Algal Blooms) Marine Water Quality 

Surface Water Dynamics Freshwater Dynamics 

Groundwater Dynamics Groundwater Dynamics 

Oceanographic Physical Parameters Physical Oceanography 

Flooding Resliance Monitoring-Flood 

Waves Physical Oceanography 

Drought Catastrophic Event Documentation 

The following list of SFAN ranked vital signs includes all water resources related vital signs. 

#1 Weather and Climate 

#3 Freshwater Quality 

#14 Freshwater Dynamics 

#15 Wetlands 

#16 Riparian Habitat 

#20 Erosion and Deposition 

#21 Marine Oceanography 

#31 Stream Channel and Watershed Characterization 

#33 Marine Water Quality 

#42 Groundwater Dynamics 

#49 Resiliance Monitoring-Flood 

#61 Aquatic Invertebrates 

The inclusion of these vital signs in the ranking list is indicative of the significance of aquatic 

resources in the network. Several NPS efforts to improve water resources within SFAN are 

underway; continued and augmented monitoring is needed to ensure that existing linkages 

among these vital signs remain viable. 

Because of the presence of threatened and endangered species, Section 303d listed waters, 

significant coastal waters, unstable geomorphology, and public water use and health issues, 

network watersheds receive substantial attention from the surrounding communities and 

government agencies. The San Francisco Bay Regional Water Quality Control Board identified 

both Lagunitas Creek and Tomales Bay (PORE/GOGA) as impaired by fecal coliform, sediment, 

and nutrients. San Francisquito Creek is also sediment-mpaired; one of its sub-watersheds is 
68

located within GOGA boundaries. Erosion is not only a significant issue for these sedimentimpaired waters, but it is also the major watershed issue at JOMU. 

The State Water Resources Control Board has established four coastal Areas of Special 

Biological Significance (ASBS) within the legislative boundaries of the SFAN parks. Because of 

the significance of these areas as high quality habitat and the need to protect human health (i.e., 

contact and non-contact recreation), marine water quality will remain an important aspect for the 

network. Monitoring groundwater dynamics will become more important at PINN as water 

demand (primarily related to viniculture surrounding the park) increases, thereby applying 

greater stress to the ecosystem. 

3.4 Connectivity Between Selected Vital Signs and the SFAN Conceptual 

Model 

Justification for selection of monitoring vital signs is ultimately dependent on a linkage between 

the selected vital signs and the network conceptual models. To ensure that the major conceptual 

model components are represented by the selected vital signs, vital signs were organized by 

resource realm, vital sign categories, and by dominant ecosystem types depicted in the models 

(Table 3.5; refer to Chapter 2: Conceptual Models). Vital signs in the top 18 of the ranked list are 

noted in bold. Linkages with habitat components, physical resources, and other vital signs will be 

presented as part of the individual conceptual models developed for each vital sign. (See Figure 

2.6 for an example.) 

Table 0.5 List of specific vital signs linked to conceptual models. Rank number is the priority 

number from the ranking procedure. Letters signify the application of a given vital sign to the 

ecosystem types: M=marine, T=terrestrial and W=wetland. Bolded vital signs ranked in the 

top 18 and will be implemented first. Resource Realm 

General Vital Sign Specific Vital Sign Rank Ecosystem 

Connections 

AIR QUALITY 

Chemistry – contaminants (persistent organic 

pollutants (POPs), mercury, lead, zinc, cadmium) 

Air Quality 4 MTW 

 Lichens 45 T 

Chemistry – nitrogen/ sulfur deposition Air Quality 4 TW 

Chemistry – ozone 

Air Quality 

4 

T 

 Ozone Sensitive Vegetation 54 T 

Physics - fine particles (human health, visibility 

concerns) 

Air Quality 4 MT 

LIGHT AND SOUND 

Dark night sky/ light pollution Natural Lightscape 53 MT 

Natural sound levels Natural Soundscape 29 MTW 

WEATHER and CLIMATE 

 ATMOSPHERE 

Weather/ climate change Weather and Climate 1 MTW 

OSP

SOIL BIOTA AND QUALITY 
69

Resource Realm 

General Vital Sign Specific Vital Sign Rank Ecosystem 

Connections 

Soil chemistry and contaminants 

Soil Structure, Texture and 

Chemistry 

62 MTW 

Soil structure and texture 

Soil Structure, Texture and 

Chemistry 

62 MTW 

Soil erosion and deposition Erosion and Deposition 20 MTW 

Soil biota Soil Biota 55 MTW 

DISTURBANCE EVENTS 

Coastal dynamics Coastal Dynamics 19 MW 

Mass wasting Mass Wasting (Landslide) 57 MTW 

Catastrophic event 

Catastrophic Event 

Documentation 

43 MTW 

HABITAT PATTERNS 

Physical Habitat changes—physical (terrestrial, 

stream substrate change, channel and drainage 

morphology, seabed change) 

Landform type 52 T 

Stream channel and 

Watershed Characterization 

31 W 

 Cave Communities 47 TW 

WATER QUALITY 

Chemistry--core elements (temperature, specific 

conductance, pH, DO) 

Water Quality 3 MTW 

Clarity (turbidity and sediment) Water Quality 3 MTW 

Nutrients, organic/ inorganic contaminants Water Quality 3 MTW 

Groundwater quality TW 

Indicator bacteria (fecal and total coliform, 

e.coli.) 

Water Quality 3 MW 

WATER QUANTITY 

Surface water dynamics (flow, discharge, use) Freshwater Dynamics 14 TW 

Groundwater dynamics (water tables, recharge, 

draw down, use) 

Groundwater Dynamics 42 TW 

OCEANOGRAPHY 

Physical parameters (sea level change, current 

patterns, upwelling intensity) 

Physical Oceanography 21 MW 

Marine water quality Marine Water Quality 33 MW 

DISTURBANCE EVENTS 

Resilience monitoring--floods 

Resilience Monitoring – 

Flood 

49 MTW 

HYDROSPHERE 

Catastrophic events 

Catastrophic Event 

Documentation 

43 MTW 

FAUNAL CHARACTERISTICS 

Species richness and diversity – selected 

communities 

Stream Fish Assemblages 5 W 

Amphibians & Reptiles 8 TW 

Pinnipeds 10 MW 

Raptors and Condors 18 T 

 Shorebirds 24 M 

 Seabirds 25 M 

 Waterbirds 26 M 

 Marine and Estuarine Fish 28 M 

BIOSPHERE 

 Medium to Large Carnivore 30 TW 
70

Resource Realm 

General Vital Sign Specific Vital Sign Rank Ecosystem 

Connections 

Small mammal and 

Herpetofauna 

36 T 

 Bat Guild 41 T 

Terrestrial Invertebrate 

Community (non-T&E) 

48 T 

 Pelagic Wildlife 50 M 

 Soil Biota 55 T 

 Cetaceans 60 M 

 Aquatic Invertebrates 61 W 

Native species of special interest (presence, 

population size, trends) 

Pinnipeds 10 MW 

Landbird Population 

Dynamics 

17 TW 

Raptors and Condors 18 T 

 Medium to Large Carnivore 30 TW 

Small Mammal and 

Herpetofauna 

36 T 

 Corvids 46 TW 

 Black-tailed Deer 56 T 

Faunal species at risk (presence, trends, 

population size, genetic diversity) 

Stream Fish Assemblages 5 W 

Northern Spotted Owl 7 T 

(See Appendix 2 for more complete list of Amphibians and Reptiles 8 TW 

species at risk.) Western Snowy Plover 9 M 

Pinnipeds 10 M 

T&E butterflies 13 T 

Landbird Population 

Dynamics 

17 TW 

Raptors and Condors 18 T 

 Seabirds 25 M 

 Tule elk 27 T 

 Marine and Estuarine Fish 28 M 

 Townsend’s Big-eared Bat 34 T 

 Bank Swallow 35 TW 

Small mammal and 

Herpetofauna 

36 T 

Exotic animal species/ disease (population size, 

area covered, rate of spread) 

Non-native Animals 23 MTW 

 Wildlife diseases 52 MTW 

INTERSPECIFIC INTERACTIONS 

Selected species’ interactions (herbivory, 

predation, competition) 

 

FLORAL CHARACTERISTICS 

Species richness and diversity – selected 

communities 

Wetlands 15 W 

Riparian Habitat 16 W 

Dune Vascular Plant 

Assemblages 

22 M 

 Rocky Intertidal Community 32 M 

Grassland Plant 

Communities 

37 T 
71

Resource Realm 

General Vital Sign Specific Vital Sign Rank Ecosystem 

Connections 

 Oak Woodlands 38 T 

 Subtidal Monitoring 44 W 

 Lichens 45 T 

 Sandy Intertidal Community 59 MT 

Native species of special interest (presence, 

population size, trends) 

Oak Woodlands 38 T 

 Ozone Sensitive Vegetation 54 T 

Floral species at risk (presence, trends, population 

size, genetic diversity) 

Rare Plant Species 6 TW 

Wetlands 15 W 

(See Appendix 2 for a more complete list of 

species at risk.) 

Dune Vascular Plant 

Assemblages 

22 T 

Invasive exotic plant species/ disease 

(#, area covered, rate of spread of selected 

species) 

Invasive Plant Species – 

early detection 

2 TW 

(See Appendix 2 for a more complete list of 

targeted exotic plant species.) 

Sudden Oak Death 39 T 

Plant community composition and structure - 

change at multiple scales 

Plant Community Change 

11 

TW 

Plant Species at the Edge of 

their Range 

58 TW 

LANDSCAPE PATTERNS 

Community assemblages (area/ distribution) Plant Community Change 11 TW 

Wetlands 15 W 

 Riparian plant community 16 TW 

Dune Vascular Plant 

Assemblages 

22 MTW 

Grassland Plant 

Communities 

37 T 

 Oak woodland community 38 T 

 Subtidal community 44 M 

Fragmentation and connectivity Landscape Dynamics 12 TW 

Landscape and land use change (urban, 

agriculture, residential, grazing) 

Landscape Dynamics 12 TW 

ECOSYSTEM PROCESSES 

Succession Plant Community Change 11 TW 

Nutrient dynamics 

DISTURBANCE EVENTS 

Fire Resilience Monitoring – Fire 40 TW 

ABIOTIC/ BIOTIC INTERFACE 

Resilience Monitoring – 

Flood 

49 MTW 

VISITOR USE 

SOCIAL Viewshed Viewshed 63 MT 
72
73

Chapter 4 Sampling Design 

4.1 Overview of Sampling Design 

This chapter outlines the overall statistical sampling design for all vital signs in the SFAN parks. 

The statistical sampling design describes how spatial locations are chosen for sampling and how 

sampling effort will be rotated among those spatial locations. Certain details of the sampling 

designs will not be included here. For example, detailed maps showing realized sample locations 

are included in each vital sign protocol. Data analysis plans are described generally in Chapter 7 

and specifically in the individual protocols. Here, we focus on the overall sampling designs that 

will permit statistical inferences to large areas. 

This chapter is organized as follows. In section 4.2, Sampling Concepts and Definitions, several 

statistical concepts and terms are defined for use later in the chapter. Section 4.3, an overview of 

the proposed sampling approaches, introduces and explains the sampling plans that follow. Later 

discussions are grouped into sections by the general type of sampling proposed for particular 

vital signs. These sections are 4.4 Grid-based Sampling, 4.5 List-based Sampling, and 4.6 Index 

Sites. Lastly, section 4.7 outlines protocols that use multiple types of sampling approaches. In all 

of these sections, the overall statistical design for vital signs to be monitored at the outset of the 

program will be described. The areas of inference and general considerations for each vital sign 

will also be given. 

4.2 Sampling Concepts and Definitions 

Subsequent sections of this chapter describe various sampling plans proposed for parks in the 

SFAN. These sampling plans rely on a few underlying concepts and use specific statistical terms. 

This section describes some of the background concepts behind the recommended designs and 

defines sample unit, panel, rotation design, and membership design. 

During development of the sample designs, our working definition of “monitoring” was the 

collection and analysis of repeated observations or measurements over a long period of time to 

document the status and trend in ecological parameters. Monitoring is usually designed to 

provide unbiased statistical estimates of status and trends in large areas or entire study units. 

Monitoring programs, in our minds, do not set out to investigate a single question or test a 

specific hypothesis; rather they attempt to collect objective and scientifically defensible data to 

answer wide-ranging broad hypotheses, some of which may not be finalized at the outset. Using 

data collected by monitoring programs, long-term correlations between management or natural 

changes and ecological parameters can occasionally be documented and can provide the most 

compelling and complete picture of ecosystems and ecosystem changes. Monitoring, however, 

will not establish cause and effect relationships between external changes and the status of 

ecological parameters. Because of its long-term nature, monitoring usually collects relatively 

quick and easy-to-measure field data that are repeatable in the sense that different people taking 

the same measurement will likely produce the same value. Successful monitoring programs 

produce compelling evidence of ecological status and change because they collect long-term 
74

data, the object of study is representative of ecosystem condition, and their inferences apply to 

large areas. Successful monitoring programs are difficult to implement, however, because they 

require data to be collected for many years, which requires consistent motivational and financial 

support. 

The monitoring plans proposed for SFAN rely on concepts in finite population sampling. In 

finite population sampling, the area for which inferences are desired (e.g., a park or ecoregion) is 

generally viewed as a finite collection of sample units (or just units). 

In general, sample units are the smallest entities upon which measurements are taken. The total 

collection of sample units is called the population. In some studies, sample units will be discrete 

entities such as stream segments, ponds, lakes, or individual animals. Sample units for remote 

sensing studies may be aerial survey routes, small areas, or pixels. Responses are defined to be 

measurements taken on the sample units. The subset of units from the population for which we 

collect responses is called the sample. If the sample is chosen using some type of random draw, 

the sample is said to be a probability sample. Whenever possible we have opted for a probability 

sample to monitor vital signs of the SFAN. 

 

In selecting a sample design for SFAN, we must select: 

1. a method of distributing the sample 

a. unstratified – all areas of the park are sampled at the same rate (number of 

sample sites per square mile), 

b. stratified – the park is divided into strata that do not overlap and that cover 

the entire park. Some strata are sampled at a higher rate than others, but 

the sampling rate is the same within a stratum, or 

c. unequal probability – The sampling rate varies continuously, rather than 

being set by discrete strata. 

2. a method of selecting the sample 

a. random 

b. systematic (grid), with a random start 

c. Generalized Random-Tessellation Stratified (GRTS) design (Stevens and 

Olsen 2004). 

Any method of distributing the sample can be combined with any method of selecting the 

sample. In addition, field sampling may rotate through various sets of sample units over time. 

Unstratified sampling samples each habitat type in the same proportion as it occur in the park. 

Stratified and unequal probability sampling allows one to increase the sample size in less 

common or more important habitat types. Unequal probability sampling is more flexible but 

more complex than stratified sampling. Random sampling is less precise than systematic or 

GRTS sampling, because sample points tend to clump and not be evenly distributed over the 

park. GRTS sampling has the advantage of combining the strengths of systematic and random 

sampling and unlike systematic sampling, GRTS sampling allowing the sample size to be easily 

changed, if for example some of the points selected may not be suitable for monitoring. 
75

If all sample points will not be observed every year, it is useful to define several panels of 

sample points. A panel is a group of sample points that are always all sampled during the same 

sampling occasion or time period (McDonald 2003). For example, panel 1 points might be 

observed every year and panel 2 points every 5 years. The way in which units in the population 

become members of a panel will be called the membership design and pattern of visits through 

time to all panels is the revisit design (McDonald 2003). For example, if two panels are to be 

constructed from a systematic sample of points, every other point could be placed into panel 1, 

starting with the first and every other unit starting with the second could be placed in panel 2. If 

the sample points are to be observed annually for 10 years, the revisit design might specify that 

units in panel 1 be visited in years 1, 3, 5, ..., 9, and the units in panel 2 be visited during years 

2, 4, 6, ..., 10. An alternative revisit design might specify that units in panel 1 be visited every 

year, while those in panel 2 are to be visited every third year. 

McDonald (2003) proposed a notation system for revisit designs that may help with describe the 

sampling design. Under this notation, the revisit plan is represented by a pair of digits, the first of 

which is the number of consecutive occasions that a panel will be sampled, the second of which 

is the number of consecutive occasions that a panel is not sampled before repeating the sequence. 

The total number of panels in the rotation design is normally the sum of digits in the notation. 

For example, using this notation the digit pair [1-2] means that members of three panels will be 

visited for one occasion, not visited for two occasions, then visited again for one occasion, not 

visited for two occasions, and so on. If a single panel is to be visited every sample occasion, its 

revisit design would be [1-0]. The notation [1-1] means a panel is to be sampled every other 

sampling occasion. The notation [1-n] means a panel is to be visited once and never again. The 

notation [1-0,1-5] means that units in one panel will be visited every occasion, while units in 6 

other panels will be visited once every 6 years. The schematic representation and notation for 

five example revisit designs appears in Table 4.1. 

4.3 Sampling Approaches 

Historically, monitoring efforts at parks in SFAN consisted of: 

- Weather and air quality data collected throughout the parks 

- Landbird population dynamics 

- Northern Spotted Owl productivity 

- Pinniped productivity and distribution 

- Prairie Falcons productivity and distribution 

- Western Snowy Plover productivity and distribution 

- Stream fish productivity 

At the beginning of the planning process, the SFAN monitoring program attempted to integrate 

all of the vital signs studies under a single overarching survey design. This included many 

historical monitoring programs for which survey designs already existed, such as monitoring of 

stream fish, water quality, landbirds, and snowy plovers. A single overarching sample design, 

however, was impossible given the different fundamental types of sampling required by each 

study. 
76

Certain ecological parameters, such as vegetation composition or landbird abundance, 

were specific to two-dimensional locations and required a sample of two-dimensional 

landscapes. Certain other parameters, such as those measured in freshwater systems 

or on spotted owls, were specific to an entity that existed only as an identity, and 

those identities were amenable to placement in a one-dimensional list. Still other 

parameters, such as air quality or climactic measurements, were more-or-less constant 

at the scale of a single park and could be adequately monitored by collecting data at 

one or two sites. In the end, we relaxed our 

Table 0.1 Notational representation of five revisit designs. An ‘X’ in a cell indicates that all 

members of the panel are visited that occasion. 

Sample Occasion 

Panel 1 2 3 4 5 6 7 8 9 10 

 Design [1-0] 

1 X X X X X X X X X X 

 

 Design [1-9] 

1 X 

2 X 

3 X 

4 X 

5 X 

6 X 

7 X 

8 X 

9 X 

10 X 

 

 Design [2-8] 

1 X 

2 X X 

3 X X 

4 X X 

5 X X 

6 X X 

7 X X 

8 X X 

9 X X 

10 X X 

 

 Design [2-3] 

1 X X X X 

2 X X X X 

3 X X X X 

4 X X X X 

5 X X X X 

 

 Design [1-0, 2-3] 

1 X X X X X X X X X X 

2 X X X X 

3 X X X X 

4 X X X X 

5 X X X X 

6 X X X X 
77

requirement that all monitoring utilize a single sampling scheme in favor of separate survey 

designs that shared a common sample design when at all possible. 

Although a shared overall sampling design was not possible, co-locating of some sampling sites 

was still possible in order to enhance efficiency during field sampling and for correlation 

analyses. For example, some stream fish assemblage and water quality sampling sites are located 

at the same sites. Data analysis will also correlate results from the different vital signs. For 

example, there is an interest to correlate Northern Spotted Owl reproductive success with 

climatic variation. Likewise, landbird population data may be correlated with vegetation 

monitoring of riparian or chaparral/scrub habitat. 

During development of the sampling plans for SFAN, many milestones were passed and 

decisions made that influenced the ultimate plan. One of the key milestones was overcoming the 

aversion to judgment sampling. Initially, a number of lead investigators, statisticians and 

consultants recommended against judgment sampling (judgment sampling = non-probability 

sampling). We found, however, that probability sampling was not economically realistic in some 

cases, and eventually adopted judgment sampling for a few studies. In these cases, judgment 

samples were justified either because the vast majority of the entities under study were to be 

sampled, or because the spatial variation in responses at the scale of a park were inconsequential 

to long-term monitoring. 

The second milestone was based on the advent of the “grid” approach and GRTS based site 

selection. This was a milestone because it was the first feasible sample design under which it was 

possible to fully realize the utility of probability samples for making inferences to large expanses 

of a park. The SFAN, however, deemed that a simple random sample was not appropriate for 

selecting points. A simple random sample might result in some parts of the network being 

heavily sampled while other parts have few samples, which could skew the conclusions drawn 

from the monitoring. 

 

Finally, the concepts of rotation design and membership design were introduced and discussed. 

Prior to these discussions, it was unclear when and how field efforts were to be employed. In the 

end, three fundamentally different schemes for collecting measurements in the field were 

adopted for the SFAN monitoring studies. The first scheme (grid-based sampling) constructs a 

grid of either points or cells to use as sample units and draws a probability sample. The second 

scheme (list-based sampling) constructs a list of sample units and either draws a probability 

sample or attempts to census all units. The third scheme collects information on areas or at points 

(index sites) that were hand-picked by lead investigators to yield adequate data on a particular 

vital sign. Some sampling designs capitalize on multiple approaches that combine, for example, a 

grid based approach within an index site (area handpicked by investigator). The remainder of this 

chapter contains one main section for each of the three types of sample schemes, and the 

schemes are summarized in Table 4.2. 

4.4 Grid-based Sampling 

Although the plant community change protocol has not yet been established, grid-based 

(systematic) sampling is being considered. Grid-based sampling may also be considered as one 
78

part of a multi-pronged approach to monitor specific habitats including riparian, wetland, or oak 

dominated forests. Grid sizes have not yet been established. 

4.4.1 Plant Community Change 

The plant community change protocol has not yet been developed but will likely take a gridbased approach. Stratification of natural elements such as the underlying geology or elevation 

Table 0.2 The overall sample design approach, methods for spatially allocating samples, and the 

revisit plan for vital signs monitoring. 

Level 1 Level 2 Level 3 Network Vital 

Sign Name 

Overall 

Sample 

Design 

Approach 

Spatial 

Allocation 

Revisit 

Plan 

Ozone Air Quality Index Judgment Continuou

s 

Wet and Dry 

Deposition Air Quality Index Judgment Continuou

Air Quality s 

Visibility and 

Particulate 

Matter 

Air Quality Index Judgment Continuou

s 

Air and 

Climate 

Weather 

and Climate 

Weather 

and Climate Weather Index Judgment Continuous 

Hydrology Surface Water 

Dynamics 

Freshwater 

Dynamics List-based Criteria Monthly 

Water 

Water Chemistry Water Quality List-based Criteria Monthly Water 

Quality Nutrient 

Dynamics Water Quality List-based Criteria Monthly 

Landscape 

(Ecosyste

m Patterns 

and 

Proceses) 

Landscape 

Dynamics 

Land cover 

and use 

Landscape 

Dynamics TBD TBD TBD 

Invasive 

Species 

Invasive/ Nonnative Plants 

Invasive Plant 

Species (early 

detection) 

Grid, 

Listbased, or 

Index 

TBD TBD 

Wetland 

Communities Wetlands TBD TBD TBD 

Riparian 

Communities Riparian Habitat TBD TBD TBD 

Fishes Stream Fish 

Assemblages 

Listbased Complete 

census Monthly 

Amphibian 

and Reptiles 

Amphibian and 

Reptiles TBD TBD TBD 

Landbird 

Population 

Dynamics 

Index Judgment Annual 

Birds 

Raptors and 

Condors 

Listbased Complete 

census 

Annual 

Biological 

Integrity 

Focal 

Species or 

Communitie

s 

Mammals Pinnipeds Listbased 

Complete 

census 

Annual 
79

Level 1 Level 2 Level 3 Network Vital 

Sign Name 

Overall 

Sample 

Design 

Approach 

Spatial 

Allocation 

Revisit 

Plan 

Vegetation 

Community 

Plant 

Community 

Change 

Gridbased GRTS Panel 

Rare Plants 

Grid-, 

Listbased, or 

Index 

Random 

transect Annual 

Northern 

Spotted Owls Index Random 

sample Annual 

Western Snowy 

Plover 

Listbased Complete 

census 

Annual 

 

Threatened 

and 

Endangered 

(T & E) 

Species and 

Communiti

es 

T & E Butterlies Listbased 

Random 

transect Annual 

may also be considered. A spatially balanced (GRTS) as described above will also be considered 

to ensure that all communities of interest are sampled adequately. Grid size has not yet been 

determined. Panel designs with various membership schemes will also be considered in order to 

ensure a cost efficient design and to interpolate over the entire parks. 

4.5 List-based Sampling 

List-based sampling will be the primary sampling method for monitoring freshwater quality, 

stream fish assemblages, Western Snowy Plovers, pinnipeds, threatened and endangered 

butterflies, and raptors and condors. Snowy plover and pinniped monitoring will maintain a list 

of breeding beaches and haul outs where complete counts will be made every year. Rare 

butterflies will be sampled at known habitats. Prairie falcons will be sampled in known nesting 

areas annually. 

4.5.1 Freshwater Quality 

The SFAN approach to water quality monitoring focuses on collecting water quality parameters 

in freshwater streams. Basic freshwater quality monitoring includes the collection of a core set of 

parameters (e.g., pH, dissolved oxygen, specific conductance, flow, and temperature) at the same 

location. 

In order to select sample sites for freshwater quality sampling, SFAN will employ a list or framebased sampling design, much like the EPA Environmental Monitoring and Assessment Program 

(EMAP). The first step included identification of sites that were listed as Category 1 (including 

Section 303d listed streams and significant water bodies) and Category 2 (streams lacking 

baseline data) as established by the NPS WRD guidance from the freshwater work group 

subcommittee (NPS 2002). Additional criteria were used to narrow the field of potential 

sampling sites to include areas of concern for individual parks that did not necessarily fall within 

categories established by WRD. These additional criteria included: 1) past data indicated 

pollutant/parameter levels of concern, 2) sites where public health was an issue, 3) sites where 
80

land use impacts were suspected or point sources were known (e.g., faulty septic systems, 

agricultural use, pet waste, outfall pipe), 4) site access/private property issues; and 5) wadeable. 

Once all of the potential streams were mapped out, the selection narrowed to particular habitats 

of interest. The habitats included pools, riffles, and runs which represent the greatest importance 

to species of concern including California freshwater shrimp (Syncharis pacifica), coho salmon 

(Oncorhynchus kisutch), steelhead trout (Oncorhynchus mykiss), the California red-legged frog 

(Rana aurora), or Western Pond Turtle (Clemmys marmorata). Upon applying all of the criteria, 

30 sites were identified at watersheds in GOGA, JOMU, PINN, and PORE. Watersheds will be 

monitored on a two-year rotating schedule; one set of watersheds will be monitored the first two 

years and a different set will be monitored the following two yeares. Sites will be sampled 

monthly within the two-year time period. Randomization occurs at the sampling site in order to 

identify where at each sampling site the probes are placed. If new areas meeting the site 

selection criterion are identified they will be considered for inclusion in the sampling design. 

In addition to the overall sampling design, Olema Creek, which flows into Tomales Bay, will be 

tested for fecal coliforms where as part of the Tomales Bay Pathogen Total Maximum Daily 

Load (TMDL) program. Additional information about the sampling design including a 

discussion of sampling frequency and detailed maps of all sampling locations can be found in the 

protocol (SFAN 2005).

4.5.2 Stream Fish Assemblages 

The stream fish assemblages protocol calls for monitoring of species of concern which includes 

California freshwater shrimp, coho salmon, and steelhead trout. Sampling sites are collocated 

with freshwater quality sites described above. The aim of the protocol is to census the entire 

population at each sampling site. The assumption that all parameters are accurately counted, such 

as number of fish or redds, will be tested by conducting a pilot project using a double-observer 

approach. 

4.5.3 Western Snowy Plovers 

Snowy plovers have been monitored at GOGA and PORE for more than 20 years. The beaches 

used by the small birds are well known. The monitoring consists of two components. One 

component will consist of total counts on accessible beaches at GOGA (Ocean Beach only) and 

PORE during the winter season. The second component consists of nest searches at PORE 

during the breeding season. Although all beaches are known where plovers occur, if new habitats 

are found, they will be added to the sampling population. Observers receive training in order to 

ensure that no birds are missed. In order to ensure that all birds are counted, detectability will be 

tested with double observer counts. 

4.5.4 Pinnipeds 

Like snowy plovers, pinniped monitoring has a long history at GOGA and PORE in 

collaboration with other agencies and organizations. Monitoring is conducted during the 

breeding season and on a year round basis. During the breeding season, complete counts of 

adults and pups are conducted at known haul out sites. Locations of haul out sites are well 

established; however, if new haul out sites are identified, they will be added to the sampling 
81

population. Bi-monthly counts are made only at PORE year round. Observers receive training in 

order to ensure that no seals are missed or misidentified. 

4.5.5 Threatened and Endangered Butterflies 

This protocol focuses on the Mission blue butterfly and the Myrtle’s silverspot butterfly. 

Potential habitats with lupine host plants have been mapped. Transects will be placed randomly 

through each species habitat in order to count adults. In addition, stems of larval host plats and 

nectar sources are counted along the transect. Data can be extrapolated for the known habitat. In 

addition, new surveys will be conducted to identify new potential habitats every five years. If 

new habitats are found, they will be added to the sampling population. 

4.5.6 Raptors and Condors 

Prairie Falcons have been monitored at PINN for more than 20 years and historic nesting sites 

are well established. All known nest locations will be monitored in order to track annual 

productivity. New areas are inventoried as time allows to find new potential nest sites. If new 

nests are found they will be added to future nest surveys. 

4.6 Index Sites 

Weather and climate, air quality, and landbird monitoring components in SFAN will collect data 

at a small number of representative sites located in the parks. This focus on index areas or sites is 

justified due to the high costs of the surveys or equipment involved in the measurements. 

Technically, statistical inference to a larger area, such as a park or a portion of a park, is not 

possible using data collected in areas or at sites that were not chosen by a probability sample. 

However, monitoring of parameters in specific areas or at specific sites is adequate for these 

studies because either the index area contains the vast majority of the population of monitored 

subjects, or the spatial fluctuation in measurements across a park is inconsequential for long-term 

monitoring purposes. 

4.6.1 Weather and Climate 

The weather and climate monitoring at SFAN will maintain or establish several different types of 

climate and precipitation monitoring stations. One component of the climate monitoring study 

will maintain data collected at stations that represent a broad range of climate gradients and 

where data have been collected for a number of years. A full set of weather parameters will be 

collected at these sites. SFAN will minimally support data management at secondary sites where 

a full set of weather parameters are not collected but the stations represent park interests, such as 

rainfall patterns. 

4.6.2 Air Quality 

At present, air quality monitoring is only occurring at Class 1 parks including PINN and PORE. 

Monitoring is implemented by the NPS Air Resources Division (ARD). SFAN will continue to 

work with ARD and will maintain and archive data, and report results. 

4.6.3 Landbird Population Dynamics 

Monitoring of landbird populations has a long history at SFAN extending over 30 years. Point 

counts with variable point count distance sampling, and Monitoring Avian Productivity and 
82

Survivorship (MAPS) have been established by PRBO Conservation Science (PRBO). The point 

count and MAPS stations represent an index of all landbirds in habitats of interest which include 

riparian and coastal scrub/chaparral. MAPS stations were established based on the best judgment 

of experienced bird banders. Survey areas for point counts were also selected based on judgment. 

The actual points where the counts are made, however, were established by a systematic grid 

superimposed over the MAPS stations. Because of the use of judgment sampling, interpolation to 

areas beyond those sampled is not possible. 

Current priorities for GOGA and PORE are to: (1) continue mist-netting at all previously 

established / currently monitored mist-netting study sites year-round at Palomarin, Muddy 

Hollow, and Pine Gulch, and only during the breeding season at Lagunitas Creek and Redwood 

Creek; (2) continue nest monitoring at Palomarin; (3) conduct point count surveys annually at all 

previously established / currently monitored stations in coastal scrub / chaparral and riparian 

habitats; 

Current priorities for JOMU and PINN are to conduct point count surveys annually at all 

previously established stations. 

4.6.4 Northern Spotted Owl 

Spotted owls have been monitored at SFAN parks as part of the Northwest Forest Management 

Plan. Sites occupied by owls are well known. Among the 80 historically occupied sites, 46 sites 

are monitored annually for occupancy. A random subset of 30 sites are monitored for 

reproductive success. Sample site selection is based on those that are easily and safely accessible 

or have management concerns. These sites represent an index and data can not be interpolated to 

a larger area. In the future, it is proposed to randomly select monitored sites and to monitor for 

new sites in potential habitat. This would allow for interpolation to larger areas. 

4.7 Multi-Pronged Approaches 

Because some of the protocols are broad and may include multiple species, this section will 

summarize protocols that may incorporate multiple approaches listed above including grid, list, 

and index based. The protocols for invasive species and for rare plant species include species 

specific standard operating procedures (SOP). Each SOP, for example, may describe a different 

sampling approach based on life history, location, and monitoring objective. 

4.7.1 Invasive Species 

Although the invasive species monitoring protocol has not yet been developed it is envisioned 

that a list based monitoring scheme will be a significant component. One of the first steps is to 

generate a list of priority species for which monitoring will be conducted. The next step is to map 

known locations supplemented with predictive modeling which incorporates potential vectors to 

identify areas where the species occurs or is expected to occur. For some species it may be 

possible to monitor the entire population while in other cases monitoring will only focus on 

index sites. The index sites may be identified as those that are the most susceptible to invasion or 

areas that contain rare species where managers wants to keep all invasive species out. If too 

many priority areas are identified or a species covers too large of an area to track the entire 

population, a probabilistic design will be considered so that a certain portion of the known and 
83

expected population is sampled at random. In this case, a grid based approach may be most 

appropriate. 

A pilot program is in place for monitoring Yellow starthistle in order to test the possibility of 

using park staff and volunteers to assist monitoring. 

4.7.2 Rare Plant Species 

One protocol will be established for monitoring rare species and each species specific standard 

operating procedures may take a variety of approaches depending the species phenology, life 

history, detectability and habitat. The first step for developing this protocol was to develop a list 

of priority species for each park based on a matrix which incorporated a species’ rarity and 

management potential. For example,a species for which management is possible, has a higher 

rank than a species for which there are no known management options. PORE has over 50 plant 

species with federal, state or local status. GOGA has over 35 plant species with federal, state or 

local status. The inventory for PINN needs to be refined and better documented, but there is 

currently evidence for over 10 species. 

For some rare plant species, it may be possible to conduct counts of the entire population. Tests 

will have to be made to account for detectability with double observers. We want to make sure 

that we understand the likelihood of missing stems or misidentifying species of interest. 

To date, one SOP has been developed for the rare plant protocol. The SOP was written for the 

Chorizanthe valida. Based on previous inventories, the entire population has been mapped. 

Within the mapped area, a 40x100 m permanent plot was establish which covers about 40% of 

the known population. A randomly placed transect is placed through the known population to 

cover at least 5% of the mapped area. Stem counts are made along the transect to detect changes 

in the population. In addition, the plant will be surveyed for regularly and the population mapped 

to ensure that we are documenting changes in aerial extent of the population. 

4.7.3 Habitats of special interest (wetlands, riparian) 

Park managers are especially interested in a variety of habitats that may be rare, contain rare 

species or represent a unique ecological function. These include wetlands, riparian habitats, and 

oak woodlands, among other habitats. Protocols and parameters to be measured have not yet 

been identified but sampling may include a multi - pronged approach. Remote sensing may be 

used to develop polygons of priority habitats. A grid based approach may be used to collect 

certain parameters such as plant species composition, soil water retention, etc. in order to 

validate remote sensing techniques or to provide more information. Before a full sampling design 

can be developed, monitoring objectives need to be refined. 
84
85

Chapter 5 Sampling Protocols 

5.1 Overview of High Priority Vital signs 

This chapter includes more detail regarding the top 18 protocols the network prioritized for 

development, and in some cases implementation, within the next 5 years. Table 5.1 shows the 

suite of SFAN protocols, the parks in the Network in which they will be monitored and the 

monitoring objectives for each vital sign. Complete protocol development summaries can be 

found in Appendix 4. 

Protocols will follow guidelines published by Oakley et al. (2003) and will specify sampling 

units and sampling methods. The protocols will also define target populations for monitoring and 

discuss the level of inference that a park will be able to make from analysis of monitoring data. 

Data management, analysis, and reporting make up significant portions of the protocols. 

Protocols for two of the 18 vital signs have been completed and are undergoing peer review. 

Both of these (water quality and streamfish assemblages) will be implemented in FY06. 

Protocols for spotted owls and pinnipeds are still being reviewed and will be completed in FY06. 

Five protocols are still in the process of being drafted including weather, raptors and condors, 

freshwater dynamics, landbirds and snowy plovers. The remaining set of protocols are slated for 

development beginning in late FY06 and beyond. Specific monitoring questions and objectives 

are still being explored and refined. 

 

As protocols are completed they will become stand alone documents and posted to the SFAN 

webside: http://www1.nature.nps.gov/im/units/sfan. 
86

Table 0.1 Key information from Protocol Development Summaries (PDS) for each of the top 18 vital signs (see A

Vital sign Name (rank) 

Justification Monitoring Objectives 

Weather and Climate (1) 

The Weather/Climate vital sign is ranked first among all of the potential vital signs evaluated by the SFAN. Knowledge about weather and climate is critical because they affect not just geophysical and biological resources but ecosystem drivers and processes. Key reasons for monitoring weather and climate in network parks are because the effects can be long-lasting on (1) plant and animal populations, some of which are listed as endangered or threatened species, (2) on air and water quality, and (3) on drought and flood cycles, fires, mass wasting and other catastrophic events. Long-term weather data can also contribute to the understanding of global climate change and its effects on Network ecosystems. 

Determine variability and long-term trends in climmonthly and annual summaries of selected weatheparameters (temperature and precipitation). Identify and determine frequencies and patterns of climatic conditions for common weather parameter

Invasive Plant Species (early detection) (2) 

Invasive plant species ranked second in the prioritized list of vital signs to be monitored for ecosystem changes and trends. Early detection of invasive plant species is a proven method for preventing the establishment of new species and limiting the spread of existing species into uninfested areas. This protocol provides information that can be used immediately by park managers to target new or expanding infestations. The data can also track long-term infestation patterns and potentially evaluate long-term effectiveness of invasive species management. 

Develop and maintain a list of target species that dcurrently occur in the parks, occur in localized areaor are extremely rare, but that would cause major eor economic problems if they were to become estaDetect new species and new populations of invasivbefore they become established in areas of high anmanagement importance. 
87

Vital sign Name (rank) 

Justification Monitoring Objectives 

Freshwater Quality (3) 

The SFAN has many unique aquatic resources that are significant in an ecological and economic context. Freshwater systems within the network support a variety of threatened and endangered species. Freshwater quality has direct impact on several other vital signs including: marine water quality, stream T&E species and fish assemblages, T&E amphibian and reptiles, riparian habitat, wetlands, and aquatic macroinvertebrates. Freshwater quality also indirectly impacts plant and animal life. In addition, Tomales Bay is a major commercial shellfish growing area. The Tomales Bay Pathogen Total Maximum Daily Load (TMDL) program requires NPS to conduct fecal coliform analysis of streams entering the bay to ensure that allowable standards are not exceeded. 

Determine variability and long term trends quality through monthly summaries of seleparameters (temperature, pH, conductivitydissolved oxygen, total nitrogen, nitrate, aflow, fecal and total coliforms), in priority freshwater sites. Determine the existing ranges and diurnal variabilitemperature, pH, conductivity, and dissolved oxygselected sites in priority streams within SFAN. Determine the extent that priority streams within Sfederal and state water quality criteria for fecal indbacteria, un-ionized ammonia, dissolved oxygen, athrough monthly sampling. Determine the annual, seasonal, and 30-day mean coliform load to Tomales Bay (in impaired water bOlema Creek as required by the San Francisco Bay Water Quality Control Board's Tomales Bay PathoProgram. 

Air Quality (4) 

Clean unpolluted air is essential for all life on earth. Air quality is linked to many natural processes, i.e. soil and water nutrients, photosynthesis, acidification of lakes and streams. PINN and PORE are rated as Class 1 areas by the Clean Air Act and are protected by strict air quality regulations. The rest of the parks in the SFAN are Class 2 areas and pollution regulations are less strict. However, in some instances federal land managers apply the “precautionary principle” and treat Class 2 areas with the same standards as Class 1 Areas. 

Report on seasonal and annual status and trends of concentration and deposition in precipitation at eximonitoring stations in SFAN parks. Report on seasonal and annual status and trends of particle concentrations and composition at existing monitoring stations in SFAN parks. Report on seasonal and annual status and trends of concentrations in NCRN parks using metrics that aindicative of human health (e.g., 8-hour average) aresponse (e.g., SUM06). 
88

Vital sign Name (rank) 

Justification Monitoring Objectives 

Stream Fish Assemblages (5) 

As an indicator of ecological health of freshwater stream systems, this vital sign category includes monitoring for a suite of species and conditions within stream aquatic habitat including habitat condition, fish assemblage, population, and community structure, as well as three threatened and endangered species: coho salmon (Oncorhychus kisutch); 

steelhead trout (O. mykiss); and the California freshwater 

shrimp (Syncharis pacifica). 

Coho salmon and steelhead are anadromous and the life stage requirements demand year-round, high-quality cold water, continuous riparian cover, and complex habitat and structure to accommodate development from egg to smolt stage. 

Monitoring of these species at multiple life stages is valuable to the understanding of aquatic conditions and a good measure of watershed health. Because coho salmon and steelhead live for more than a year in freshwater, and the 

conditions required to support them are highly restrictive, they are susceptible to anthropogenic impacts to the stream and riparian systems. Because salmonids are sensitive to watershed and habitat impacts, they are effective indicators of 

stream and aquatic health. The California freshwater shrimp are also highly sensitive to water quality and changes to habitat. 

Determine long-term trends in size and age class d

and production of salmonid smolts through spring select streams at PORE, MUWO, and GOGA. Determine long-term trends in timing and distributsalmonid spawning, adult sex ratios, and escapemestreams at PORE and GOGA. Track the distribution and relative abundance of Cfreshwater shrimp within known freshwater shrimp SFAN. Determine the trends in distribution, abundance, coand size/age structure of fishes at summer index reSFAN streams of PORE, MUWO, and GOGA. Measure the long-term trends in distribution and asof fish species through annual spring surveys of ChCreek at PINN. Measure the long-term trends in the annual fish assdistribution and abundance through fish surveys wNPS managed section of Franklin Creek at JOMU
89

Vital sign Name (rank) 

Justification Monitoring Objectives 

Rare Plant Species (6) 

PORE has over 50 plant species with federal, state or local status. GOGA has over 35 plant species, including those at PRES, with federal, state or local status. The inventory for PINN needs to be refined and better documented, but there is currently evidence for over 10 sensitive species. In the summer of 2004, a ranking system was developed to help the parks determine which species are the “most rare” within the park boundaries regardless of official listing status. A different version of the ranking matrix will be used to determine which species are the most appropriate for longterm monitoring for trends and ecosystem health. We are developing a systems approach to monitoring rare plants, while also addressing management needs. This vital sign is also part of a hierarchy of vegetation monitoring being developed by the working group, in which some rare species will be monitored via the plant community change protocols. 

Develop and maintain a list of target rare species bregional rarity matrix and in order to prioritize RTE monitoring efforts. Determine long-term trends of population abundanconducting species specific surveys as needed of mpopulations. Identify potential threats (e.g. visitor trampling, prencroachment of invasive plant species, pest infestestimate degree of threat to rare species at mapped in order to identify management needs. Monitor suitable habitats every 5-10 years in order presence/absence of target species and incorporate annual abundance estimates. 

Northern Spotted Owl (7) 

The federally threatened status of this species requires the NPS monitor the long-term status and trend of the population and maintain stable or increasing populations of spotted owls. Owls are also good indicators of forest ecosystem condition because they area associated with multi-tiered, old growth forests. This monitoring program provides the data required to accurately assess the status and trend of this isolated, potentially vulnerable spotted owl population, where it occupies a land use matrix strikingly different from that found throughout most of the owl’s range. Our monitoring program contributes to the Northwest Forest Plan which is working to arrest the downward trend in spotted owl populations and in maintaining and restoring the habitat conditions necessary to support viable populations of the northern spotted owl. The program has an eight-year history of monitoring spotted owls in the SFAN parks, which contributes to region and rangewide monitoring programs and park management activities. 

Monitor changes in spotted owl abundance and repsuccess at known owl activity sites within the NPS boundaries of Marin County, California. Determine the long-term changes of nest site chara(e.g. tree species selected for nest sites, vegetation selected for nest sites) at Northern Spotted Owl at activity sites in order to evaluate habitat selection. Monitor suitable habitats every 5-10 years in order population expansion of target species and incorpointo annual abundance estimates. 
90

Vital sign Name (rank) 

Justification Monitoring Objectives 

Amphibians and Reptiles (8) 

Due to their habitat and physiology, these taxa are particularly sensitive to environmental degradation, such as air and water pollution. The number of species and populations of amphibians are declining worldwide. Because they are midlevel predators, population trends in these taxa may indicate trends in populations of animals at both higher and lower trophic levels. Standard protocols are available for sampling these animals in the San Francisco Bay Area, in some cases long-term data sets already exist. In addition to monitoring the two federally protected herptile species found in the network, the protocol will also address monitoring of terrestrial amphibian and reptile assemblages. 

Determine variability and long-term trends in amphreptile assemblages in key terrestrial habitats. Determine relative abundance of populations of kethreatened and endangered amphibians and reptilesCalifornia red-legged frogs (Rana aurora draytoni

San Francisco garter snake (Thamnophis sirtatlis tewithin the network parks. Determine distribution of populations of key threatendangered amphibians and reptiles within the netwMonitor habitat variables at breeding sites for the kthreatened and endangered species. 

Western Snowy Plover (9) 

Western snowy plovers are listed as federally threatened under the Endangered Species Act. They are also part of the coastal dune ecosystem, which is identified in the PORE enabling legislation. Western snowy plovers are good indicators of the condition of the coastal dunes ecosystem and are the only nesting shorebird in the coastal strand. There is a long history of monitoring snowy plovers at PORE and GOGA. in collaboration with other organizations and agencies. Several park management actions, including major dune habitat restoration projects to enhance the recovery of snowy plovers. 

Determine long-term changes in the breeding popudistribution, and reproductive success of snowy ploknown breeding beaches at PORE. Determine changes in wintering population size andistribution of snowy plovers at known wintering b

GOGA and PORE. Determine trends in pollutant loads (e.g. mercury aselenium) in plover eggs, chicks, and adults, as funavailable in order to evaluate potential hazards. Monitor suitable habitats every 5-10 years in order population expansion of target species and incorpointo annual abundance estimates. 
91

Vital sign Name (rank) 

Justification Monitoring Objectives 

Pinnipeds (10) 

Pinnipeds come under the legal mandates of the Endangered Species Act and Marine Mammal Protection Act. They are also specifically identified in the enabling legislation of and management objectives of PORE. Pinnipeds are good indicators of the condition of the marine ecosystem and global climate change because they respond quickly to oceanic conditions and food resources, such as El Nino events. There is a long history of monitoring pinnipeds at PORE and GOGA in collaboration with other agencies and organizations. Identifying natural and anthropogenic threats and quantifying the level of disturbance to harbor seals will also be critical in order to effectively manage and protect pinnipeds. 

Determine long-term trends in annual population sannual and seasonal distribution of pinniped populPORE and GOGA. Determine long-term trends in reproductive succeselephant seals and harbor seals populations through estimates of productivity at PORE and GOGA. Identify potential threats (i.e. presence of hikers, mor airplanes presence), and estimate degree of threaseal haul outs in order to identify management nee

Plant Community Change (11) 

Numerous biotic and abiotic factors have altered and continue to threaten plant communities within SFAN. As plant communities continue to recover from past resource extraction and grazing, there is a need to understand how current activities are effecting this recovery. It is also important to monitor and evaluate changes to the composition of plant communities and type changes occurring on the landscape. The monitoring program proposed assimilates multiple vital signs including invasive plant species, threatened and endangered plant species, wetlands, grassland plant communities, oak woodlands, and plant species at the edge of their range. There are also significant ties between plant community change and almost all of the faunal indicators being monitored such as landbirds, Northern spotted owls, endangered butterflies, etc. 

Develop and maintain a list of priority plant commbased on their rarity and degree of protection. Detect long-term trends in native and non-native aband distribution within selected plant communitiesDetect changes in overall vegetation cover, vegetatand species composition of selected SFAN plant cothrough monitoring every 7-10 years. 
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Vital sign Name (rank) 

Justification Monitoring Objectives 

Landscape Dynamics (12) 

Key reasons for monitoring regional landscape & land use change are (1) the rapid development of neighboring lands (2)the fragmentation of wildlife habitat (3) the need to detect life-form change within parks, and (4) to provide early warning of large-scale community shifts. 

Determine status and trends in the areal extent and configuration of land-cover types (Anderson Level lands in order to evaluate large scale changes affecresources. Determine status and trends of key landscape metrproportion of area in different cover types, number 

density of patches, mean patch size) of park lands mile buffer in order to determine land use patterns parks. 

Threatened and Endangered (T & E) Butterflies (13) 

The protected legal status of these taxa require the NPS to evaluate the condition of these populations. Because they are closely tied to host and nectar plants, butterfly populations are good indicators of general health of habitat. 

Determine the trends in population distribution and abundance of threatened and endangered butterflieknown habitats in GOGA and PORE. Detect changes in acreage of habitat available for bpopulations at GOGA and PORE such that potention the butterfly populations may be identified. Predict and identify new lupine habitat annually in identify new butterfly populations. 

Freshwater Dynamics (14) 

Freshwater Dynamics is ranked 14th among all of the potential vital signs evaluated by the SFAN. Streamflow characteristics offer some of the most appropriate and useful indicators for assessing river ecosystem integrity over time. The hydrologic output of a watershed is a function of the land characteristics and human use, the weather and climate conditions, urbanization and soil characteristics. Hydrologic variation plays a key part in structuring the biotic diversity within river ecosystems by controlling critical habitat conditions within the river channel, the floodplain, and hyporrheic zones. Stream hydrology data provides key “support” data for vital signs including stream T&E species and fish assemblages, T&E amphibians and reptiles, wetlands, and riparian habitat. 

Monitor the variability and long-term trends in strebased on monthly and storm event-related dischargmeasurements at fixed stations in GOGA, JOMU, PINN, and PORE. Monitor the frequency, magnitude and duration of events at fixed water level monitoring stations by pinstantaneous peak, hourly, daily, monthly and annsummaries of stage height and discharge in GOGAMUWO, and PORE. Monitor the frequency, magnitude and duration of or extreme low water/low flow events in stream re

known to support threatened and endangered aquatin the dry season at GOGA and PORE.
93

Vital sign Name (rank) 

Justification Monitoring Objectives 

Wetlands (15) 

Wetlands are keystone ecosystems in the San Francisco Bay Area. Some ecologists call wetlands "the kidneys of the landscape" as they provide water quality protection, flood and drought mitigation, erosion control, and groundwater recharge functions. Wetlands support complex food webs, housing a rich biodiversity of wetland-endemic species, and providing habitat functions for many aquatic and terrestrial species. An estimated 46% of US endangered and threatened species and 50% of all bird species require wetland habitat (USFWS). Wetland habitats are vulnerable to alteration due to global climate change and associated potential temperature, hydrology, and salinity regime changes. Understanding the condition of wetlands may be a good proxy for understanding the condition of many taxa of concern in the network. 

Determine if the extent, type, condition and functiowetlands is changing. 

Riparian Habitat (16) 

Riparian habitat is closely tied to the health of wetlands, streams and stream fish assemblages. Characteristics of riparian habitat structure such as the ratio of edge to interior, the degree of canopy complexity within riparian strata (e.g., herb/forbs, shrubs, sub-canopy tree, and overstory tree), and the degree of fragmentation is highly associated with amount and type wildlife use. 

Determine status and trend of riparian habitat by mspecies composition, habitat structure, and width astreams in SFAN parks. 

Landbird Population Dynamics (17) 

Landbirds are good indicators of terrestrial ecosystems and numerous dynamic processes interacting together have the potential to affect their abundance and distribution. Landbird monitoring is focused in priority areas including riparian and coastal scrub/chaparral habitats. Changes in species abundance, distribution, reproductive success, and annual survival may be caused by changes in habitat, food supply, park management strategies, disturbance to nesting areas by recreational users, or environmental factors on multiple scales (localized storm events to decadal shifts in climate). 

Determine the annual changes in species compositdistribution, and abundance for landbirds in prioritincluding riparian and coastal scrub / chaparral habDetermine long-term changes in reproductive succlandbirds in priority habitats including riparian and scrub / chaparral habitats. Determine long-term changes in annual survival foin priority habitats including riparian and coastal schaparral habitats. 
94

Vital sign Name (rank) 

Justification Monitoring Objectives 

Raptors and Condors (18) 

Long-term trends in the nesting success and productivity of prairie falcons provide a means for assessing the park’s ability to adequately manage climbing use and the overall ecological integrity and sustainability of the rock/cliff ecosystem. Longterm patterns in population size and breeding behavior (e.g. feeding rates of chicks) are compared to long-term climate change, effects of conversion and development of agricultural lands surrounding the monument, and visitor use of the monument. This information will improve the understanding of raptor ecology and the effects of park management decisions. 

Determine annual nesting success at Pinnacles NM measured by territories occupied, number of chick and number of chicks fledged. Monitor potential threats (i.e. presence of hikers or and estimate degree at nesting sites in order to idenmanagement needs. 
95

Chapter 6 Data Management 

6.1 Overview of Data Management 

Collecting natural resource data is the first step toward understanding the ecosystems within the 

national parks. These ecosystems are evolving, as is the knowledge of them and how they work. 

Researchers use these “raw” data to analyze, synthesize, and model aspects of ecosystems. In 

turn, the results and interpretations are used to make decisions about the parks’ vital natural 

resources. Thus, data collected by researchers and maintained through sound data management 

practices will become information through analyses, syntheses, and modeling. This 

transformation can only be achieved through the development of a modern information 

management infrastructure (e.g., staffing, hardware, software) and procedures to ensure that 

relevant natural resource data collected by NPS staff, cooperators, researchers, and others are 

entered, quality-checked, analyzed, reported, archived, documented, cataloged, and made 

available to others for management decision making, research, and education. 

This chapter summarizes the SFAN data management strategy, which is more fully presented in 

the SFAN Data Management Plan (DMP; Press 2005). The SFAN DMP serves as the 

overarching strategy for achieving the goals noted above. The plan supports I&M program goals 

and objectives by ensuring that program data are documented, secure, and remain accessible and 

useful indefinitely. 

6.1.1 Data Management Strategy 

The SFAN data management strategy holds that all data and derived information generated or 

otherwise used by the program will meet a high level of quality standards. Further, all data and 

information the SFAN program deems necessary to meet objectives, and that are not otherwise 

maintained, will be archived, documented, and made easily available and accessible. Data and 

information will be managed in a transparent manner such that all components may be easily 

compared by location, time and subject. Data and information will be accompanied by 

supporting documentation (metadata) that provide context, value, utility, and longevity, thereby 

facilitating broad understanding of SFAN program output to current and future end users. 

The overarching goals of SFAN data management are to: 

• ensure the highest quality and accuracy of program data 

• fully qualify, document, and catalog all data to ensure their proper interpretation and use 

• maintain data in an environment that ensures the long-term security and integrity of data 

• ensure the longevity of data by keeping data formats standardized and current 

• provide data in a variety of formats and venues to reach all potential users 

The following objectives of the SFAN Data Management Plan help frame the strategy to meet 

SFAN data management goals: 
96

Overall objectives: 

• Outline the long-term goals of a comprehensive data management strategy for the SFAN 

I&M program 

• Associate data management goals with the long-term goals of the network and servicewide I&M program 

• Outline the procedures and work practices that support effective data management 

• Guide current and future staff of the SFAN to ensure that sound data management 

practices are followed 

• Guide the enhancement of legacy data to match formats and standards put forth in this 

plan 

• Encourage effective data management practices as an integral part of project management 

so all data are available and usable for park management decisions now and into the 

future 

Specific Objectives: 

• Establish roles and responsibilities of SFAN program staff for managing data 

• Identify necessary elements for a functional data management program and describe any 

anticipated changes to those elements 

• Establish an organizational scheme for SFAN program data and information so that they 

are retrievable by staff, cooperators, and the public 

• Establish basic quality control standards 

• Establish standards for data, data distribution, and data archiving to ensure the long-term 

integrity of data, associated metadata, and any supporting information 

6.1.2 Types of Information Managed by the SFAN 

The term “data” is frequently used in a way that also encompasses other products that are 

generated alongside the tabular and spatial data that are the primary targets of data management 

efforts. These products fall into five general categories: raw data, derived data, documentation, 

reports, and administrative records (Table 6.1). 

These data categories can contain one or more of the following data formats: 

• hard-copy documents (e.g., reports, field notes, survey forms, maps, references, 

administrative documents) 

• objects (e.g., specimens, samples, photographs, slides) 

• electronic files (e.g., Word files, email, websites, digital images) 

• electronic tabular data (e.g., databases, spreadsheets, tables, delimited files) 

• spatial data (e.g., shapefiles, coverages, remote-sensing data) 

Each of these data formats has specific requirements for ongoing management and maintenance, 

which are addressed in the SFAN DMP. 
97

Table 0.1 Categories of data products and project deliverables. 

Category Examples 

Raw data GPS rover files, raw field forms and notebooks, photographs and sound/video 

recordings, telemetry or remote-sensed data files, biological voucher 

specimens 

Compiled/derived data Relational databases, tabular data files, GIS layers, maps, species checklists 

Documentation Data collection protocols, data processing/analysis protocols, record of 

protocol changes, data dictionary, NPS- Federal Geographic Data Committee 

(FGDC) standard metadata, database design documentation, quality assurance 

report, catalog of specimens/photographs 

Reports Annual progress report, final report (technical or general audience), periodic 

trend analysis report, publication 

Administrative records Contracts and agreements, study plan, research permit/application, other 

critical administrative correspondence 

6.2 Data Management Roles and Responsibilities 

For the SFAN I&M program to work effectively, everyone within the network will have 

stewardship responsibilities in the production, analysis, management, and/or end use of data and 

information. The SFAN Data Management Plan specifies basic roles and responsibilities 

spanning the spectrum of data handling from collection to archiving. This spectrum includes 

field technicians, projects leaders, GIS specialists, and data managers. More detailed roles and 

responsibilities are given in the protocol for each monitoring project. Table 6.2 lists these basic 

roles and principal responsibilities. 

Chief personnel involved with data management include project leaders and data managers. 

Figure 6.1 illustrates the core data management duties of the project leader and data manager and 

where those duties overlap. The Network coordinator interacts with project leaders to ensure that 

timelines for data entry, validation, verification, summarization/analysis and reporting are met. 

6.2.1 Project Leaders 

Project leaders oversee and supervise all phases of a monitoring project and are the point of 

contact for that project. Each project has two project leaders (one lead, one backup), which may 

consist of network, park or regional staff. They are responsible for the coordination and 

supervision of all phases of the project, from raw data collection to data validation and 

documentation to data analysis and reporting. They are also responsible for complying with the 

protocol methods and data management plan. They are responsible for the final submission of all 

products and deliverables. For projects involving contractors and/or cooperators, the project 

leader is also the Contracting Officers Technical Representative (COTR), and must insure that 
98

Table 0.2 Summary or programmatic roles and responsibilities for data stewardship. 

Role Data Stewardship Responsibilities 

Network Coordinator 

Ensure programmatic data and information management requirements are met 

as part of overall Network business. 

Communicate with Network staff, park staff at all levels, and other appropriate 

audiences to support and emphasize data management as a critical aspect of 

network business. 

Lead Data Manager 

Serve as Point of Contact for National Park Service database applications 

(NPSpecies and NatureBib). 

Communicate with national-level I&M Program for updates on NPS database 

applications and data standards. 

Project Leader 

Ensure useful data is collected and managed by integrating natural resource 

science in network activities and products, including objective setting, sample 

design, data analysis, synthesis, and reporting. 

Develop, document and implement standard procedures for field data collection 

and data handling. 

Supervise and certify all field operations. 

Produce regular summary reports and conduct periodic trend analysis of data. 

Project Data Manager 

Develop and maintain the infrastructure for metadata creation, project 

documentation, and project data management. 

Create and maintain project databases in accordance with best practices and 

current program standards. 

Establish and implement procedures to protect sensitive data. 

GIS Specialist 

Coordinate and integrate local GIS and resource information management with 

Network, regional, and National standards and guidelines. 

Project Technician 

Record, enter and verify measurements and observations based on project 

objectives. 

Information Technology/ 

Systems Specialist 

Provide and maintain an information systems and technology foundation to 

support data management 

I&M Data Manager (National 

Level) 

Provide servicewide database support and services. 

End Users 

(managers, scientists, public) 

Provide necessary and requested feedback, review, and comments in order to 

sustain the continuous improvement of network operations and services. 

the contractor complies with the terms of the contract or cooperative agreement. Their active 

involvement in data management determines the quality and usefulness of the project data and 

overall success and longevity of the I&M Program. 

6.2.2 Data Manager 

Data Managers oversee the development, implementation, and maintenance of data infrastructure 

and standards for specific parks. Each I&M project is assigned a Data Manager for the duration 

of the project. Data Managers facilitate coordination between projects and protocols to allow for 
99

interchange of information wherever possible. Data Managers work with project leaders to 

design databases and software applications, facilitate data dissemination and coordinate longterm storage and maintenance of the data 

Figure 0.1 Core project data stewardship duties of project leaders and data managers. 

6.3 Data Management Infrastructure 

The information system architecture necessary to fulfill the role of program data management 

includes national, regional, and park level infrastructure. Systems architecture signifies the 

applications, database systems, repositories, and software tools that make up the framework of 

the data management enterprise. The national level I&M data management infrastructure and 

strategy are used as a basis for data management in the SFAN. 

6.3.1 National Level I&M Data Management Infrastructure 

The NPS Natural Resource Program Center (NRPC) and the I&M Program actively develop and 

implement a national-level, program-wide information management framework. NRPC and I&M 

staff integrate desktop database applications with internet-based databases to serve both local and 

national-level data and information requirements. Centralized data archiving and distribution 

capabilities at the NRPC provide for long term data security and storage. 

To achieve an integrated information management system, three of the national-level data 

management applications (NatureBib, NPSpecies, and NR-GIS Metadata Database) used by the 

SFAN utilize a distributed application architecture with both desktop and internet-accessible 

(master) components (Figure 6.2). In addition, the SFAN has adopted relational database design 

standards in accordance with the Natural Resource Database Template, a relation database model 

developed in MS Access by the NRPC (Figure 6.2). 

Joint 

Responsibilities 

• project data design

• data maintenance 

• generate data 

products 

• catalogue and post 

data, metadata and 

th d t

Data Manager 

• develop and 

support data 

management 

system 

• project database 

development and 

support 

• ensure compliance 

with data standards 

• improve data 

accessibility and 

transparency 

• provide training

Project Leader 

• project schedule 

• contract 

management 

• supervise field 

operations 

• data collection 

and entry 

procedures 

• project 

documentation 

• main project 

contact, 

including for
100

Figure 0.2 Model of the national-level application architecture. 

6.3.2 Network and Park Level Data Management Infrastructure 

An important element of a data management program is a reliable, secure network of computers 

and servers. The SFAN digital infrastructure has three main components: servers maintained at 

the national level, park-based local area networks (LAN) nested within the Pacific West Region 

wide area network (WAN), and a Network directory nested within the GOGA LAN (Figure 6.3). 

This infrastructure is maintained by park, regional, and national IT specialists, who administer all 

aspects of system security and backups. 

These components each host different parts of the natural resource information system. 

Park LANs 

• Local applications – desktop versions of national applications such as NPSpecies, Dataset 

Catalog, and NPS Metadata Tools and Editor 

• Working files – working databases, draft geospatial themes, drafts of reports, administrative 

records 

• Park digital archives – base spatial data, finalized datasets, and finished versions of park 

project deliverables 

• Park GIS files – base spatial data, imagery, and project-specific themes 

Master Applications

(Client-server RDBMS 

– Internet 

Desktop 

Applications 

(NatureBib, 

NPSpecies Dataset

Natural 

Resource 

Database 

Template

Data 

Dissemination 

(Public and NPS-only: 

via NPSFocus NR

Data/Application 

Download 

Data 

Upload 

Network and 

Park Users 

(data 

GIS / 

GeoDatabase 

(base GIS layers, 
101

Network Directory 

• Master project databases – compiled data sets for monitoring projects and other multi-year 

efforts that have been certified for data quality 

• Network digital archives – network repository for finished versions of project deliverables 

for I&M projects (e.g., reports, methods documentation, data files, metadata, etc.) 

Figure 0.3 Schematic representing the layout and connectivity of SFAN computer resources. 

The Marin Headlands GOGA server is a critical component of the SFAN computer 

infrastructure. A separate directory on this server houses the Network directory, which includes 

all of the SFAN central files and digital archives. The server has power supply and storage 

redundancy built to ensure data are kept safe. A tape drive is also connected to back up data on a 

regular weekly schedule. The last tape of the month is taken offsite to further protect the data. 

6.4 Data Management Standards 

The SFAN will conform to NPS standards and policy in all aspects of program data management 

operations in the interest of program integration and information sharing. The SFAN DMP 

specifies the standards by which data will be handled. Data management elements or principles 

common to more than one vital sign will be managed in a conventional manner to allow for 

greater comparison of data across the network, as well as to ensure further general data integrity. 

6.5 Data Acquisition and Processing 

The NPS I&M Program is responsible for acquiring the necessary information required by park 

managers to properly manage and maintain the natural resources of their park. To successfully 

Park 

LANs 

National 

servers 

Regiona

l server 

Regional 

park 

workstatio

Network 

workstatio

Networ

k 

director

GOGA 

LAN 
102

accomplish this task, information from multiple sources is collected by the SFAN I&M Program 

and processed to ensure that it meets the data standards established by the SFAN. The DMP 

describes the general procedures the SFAN follows for acquiring and processing natural 

resource-related data. Procedures will vary depending on the data source, which can be placed 

into three general categories: 

• SFAN data: data resulting from projects that are initiated, sponsored, or funded by the 

San Francisco Bay Area Network. 

• Other NPS data: data resulting from projects that are initiated, sponsored, or funded by 

park units, or by regional or national NPS programs. 

• External data: data produced or managed by agencies, organizations, or individuals 

other than the NPS. 

The collection of programmatic data under the purview of the SFAN I&M Program is connected 

to either natural resources inventories or to vital signs monitoring. Data for each of these projects 

will enter and flow through the system illustrated in Figure 6.2. 

Information and data sets available from other NPS (i.e., Exotic Plant Management Teams, Joint 

Fire Science Program) and external programs (USGS, NOAA) are utilized by the SFAN to 

strengthen and support its inventory and monitoring programs. These data sets can help to 

establish base resource conditions and aid in the detection of long-term monitoring trends. 

6.6 Quality Assurance/Quality Control 

The network will establish and document protocols for the identification and reduction of error at 

all stages in the data lifecycle. Although specific QA/QC procedures will depend upon the 

individual vital signs being monitored and must be specified in the protocols for each monitoring 

vital sign, some general concepts apply to all network projects. 

Each vital sign protocol will include specifics that address quality control. These may include: 

• Field crew training 

• Standardized data sheets 

• Use of handheld computers 

• Equipment maintenance and calibration 

• Procedures for handling data (including specimens) in the field 

• Data entry, verification and validation 

Data entry after the field season represents a critical data life stage in terms of QA/QC. To 

facilitate data entry, data for each vital sign will be entered via customized MS Access 

applications modeled after the Natural Resources Database Template developed by the National 

I&M Program. These applications help enforce data standards by constraining the type, value, 

and format of data as appropriate to each vital sign. 
103

The SFAN DMP presents several options for carrying out data verification (ensuring data on 

field sheets match data entered into a database) and validation (ensuring that the data make 

sense). Each vital sign protocol specifies procedures for completing proper verification and 

validation of data. 

6.6.1 Documentation of Quality 

The final step in data QA/QC is the preparation of summary documentation that assesses the 

overall data quality. A statement of data quality will be composed by each vital sign project 

leader and incorporated into formal metadata, as well as the SFAN primary data repository. 

Metadata for each data set/database will also provide information on the specific QA/QC 

procedures applied and the results of the review. Metadata and data will be available via the NPS 

NR-GIS Data Store. 

6.7 Data Documentation 

Data documentation is a critical step towards ensuring that data are useable for its intended 

purposes well into the future. This involves the creation of metadata. Metadata can be defined as 

data about the content, quality, condition and other characteristics of data. Additionally, metadata 

provide the means to catalog datasets, within intranet and internet systems, thus making these 

datasets available to a broad range of potential data users. 

Metadata for all SFAN monitoring data will conform to the NPS Metadata Profile, which 

combines the FDGC standard, elements of the ESRI metadata profile, the Biological Data 

Profile, and NPS-specific elements (FDGC 1998). The SFAN metadata plan is limited to four 

recommended desktop applications for collecting metadata. These include Dataset Catalog and 

the NPS Metadata Tools and Editor, both developed by the NPS I&M Program, and two 

commercial off the shelf metadata tools, ArcCatalog and SMMS. 
104

Figure 0.4 Diagram of the typical project data life cycle. 

Data upload

Working 

databas

Certified 

data and 

metadat

Acquire data

Raw 

data

Products

Reports, 

maps

Data entry/import

Archive raw data

Verification, 

processing, 

validation 

Documentation 

and certification

Archives & Digital 

Library

• Digital library on file 

server 

• Document archives 

(analog) or off-line 

archival media

Master 

databas

e

Distribute data 

and information 

Track 

changes 

Reporting 

and analysis 

Archive versioned 

data set

Short-term 

projects 

Edit 

log

Store products 

according to 

demand

National databases

• NR-GIS Data Store 

• NR-GIS Metadata 

Database 

• NPSpecies 

• NPSTORET 

Post & 

update 

National databases

• NatureBib 

• NR-GIS Data Store 

• NR Data Image Server 

Post & update

Update 
105

All relevant data products and associated metadata generated through the SFAN I&M Program 

will be posted to the NR-GIS Data Store. Launched in June 2005, the NR-GIS Data Store is a 

web-based system designed to integrate data dissemination and metadata maintenance for 

Natural Resource, GIS, and other program data sets, digital documents, and appropriate digital 

photos. The NR-GIS Data Store provides two functions: the NR-GIS Metadata Database and the 

NR-GIS Data Server. The NR-GIS Metadata Database is a repository of and search engine for 

metadata describing natural resource and GIS data. The NR-GIS Data Server hosts natural 

resource and GIS data (documented by the metadata in the NR-GIS Metadata Database) for 

download. 

6.8 Data and Information Dissemination 

Access to SFAN monitoring products will be facilitated via a variety of data and information 

systems employing tools that allow potential users to browse, query, and obtain data, 

information, and supporting documents easily. 

Providing well-documented data in a timely manner to park managers is especially important to 

the success of the program. The SFAN will make certain that: 

• Data are easily discoverable and obtainable 

• Data that have not yet been subjected to full quality control (legacy data, unknown data 

quality, Freedom of Information Act (FOIA) requests will be released with a disclaimer 

stating as such 

• Distributed data are accompanied by metadata that clearly establishes the data as a 

product of the NPS I&M Program 

• Sensitive data are identified and protected from unauthorized access and inappropriate 

distribution 

• A complete record of data distribution/dissemination is maintained 

The network’s main mechanism for distribution of I&M data will be the internet. Use of the 

internet will allow the dissemination of data and information to reach a broad community of 

users. As part of the NPS I&M Program, web-based applications and repositories have been 

developed to store a variety of park natural resource information. Table 6.3 outlines the 

applications and repositories that the SFAN will use to distribute data developed by the program. 

6.8.1 Data Ownership, FOIA, and Sensitive Data 

SFAN products are considered property of the NPS. However, the FOIA establishes a general 

right for any person to access federal agency records that are not protected from disclosure by 

any exemption or by special law enforcement record exclusions. The SFAN complies with all 

FOIA strictures regarding sensitive data. Each vital sign project leader, as the chief data steward, 

determines data sensitivity in light of federal law and stipulates conditions for release of the data 

in the project protocol and metadata. 
106

Table 0.3 Repositories for SFAN products. 

Repository Product

SFAN Digital Archive Project data, metadata, and other products 

Raw and certified data sets 

Metadata, protocols, SOPs 

Reports and administrative records 

Digital photographs, derived products 

SFAN Project Databases Comprehensive data for multi-year projects 

Park Collections, Museums, Herbariums, and/or 

National Archives 

Administrative records, voucher specimens, raw data 

forms, hard copy reports 

National Databases 

- NPSTORET, NPSpecies, NatureBib 

Compiled information about water quality, park species 

lists and taxonomic documentation, park resource 

bibliographies 

NR Data Image Server Copies of digital reports and other documents (catalogued 

in NatureBib) 

NR-GIS Data Store Metadata and data sets (spatial and non-spatial and 

products) 

SFAN Website Protocols, SOPs, and reports for all I&M data produced 

by the network. 

6.9 Data Maintenance, Storage, and Archiving 

The SFAN DMP describes procedures for the long-term management and maintenance of digital 

data, documents, and objects that result from SFAN projects and activities. The overall goals of 

these procedures are: 

• to avert the loss of information over time 

• to ensure that information is properly interpreted by a broad range of users 

• to ensure that information can be easily obtained and shared through future decades 

6.9.1 Digital Data Maintenance 

In general, digital data maintained over the long term will be one of two types: short-term data 

sets, for which data collection and modification have been completed (i.e., inventory projects); 

and long-term monitoring data sets, for which data acquisition and entry will continue 

indefinitely. 

Maintaining digital files involves managing the ever-changing associated infrastructure of 

hardware, software, file formats, and storage media. As software and hardware evolve, data sets 

must be consistently migrated to new platforms. 

Data sets created or managed by the SFAN will be archived in read-only format with 

accompanying metadata, other data documentation, protocols, and final reports according to a 

specified project schedule (monitoring) or upon project finalization (inventory). All finalized 

files will be stored in the SFAN archive directory on the GOGA Headlands server.. 
107

6.9.2 Storage and Archiving Electronic Data and Documents 

Digital archives of completed I&M products, including SOPs, reports, and data sets, will be 

maintained at the park and Network levels. For long-term monitoring projects, data sets will be 

uploaded to both digital archive locations on an annual basis according to schedules outlined in 

the SOPs. 

Final digital products, including SOPs, final reports, and data sets will be placed in a read-only 

format in the SFAN digital archives located on the Headlands server, Network I&M directory. 

Only final documents will be archived – no drafts or works in progress. Only the lead data 

manager will archive data sets. Data sets must be validated and verified, must represent a 

complete set of records, and must have accompanying metadata and readme text files. Archived 

digital documents will then be entered online into NatureBib. 

To ensure long term management of and protection for the work that is generated by the I&M 

program, a hardcopy of final products will be sent to the GOGA Records Center located in the 

Presidio of San Francisco and to individual park’s archives as necessary. 

6.9.3 Storage and Archiving Hardcopy Documents and Objects 

Documents that are not available in digital format will either be scanned and saved as PDF files 

in the SFAN archive directory or saved in hardcopy format for larger documents. Scanned 

documents will then follow procedures outlined for electronic digital archives, which include 

entering the document into NatureBib and forwarding the original document to the GOGA 

Records Center and individual park’s archives. Hardcopy documents will be maintained in a 

local library being developed at GOGA’s Fort Cronkhite, with original copies forwarded to the 

GOGA Records Center and a record entered into NatureBib. 

Specimens collected under the auspices of SFAN I&M program will be cataloged and 

maintained according to NPS Director’s Order #24: NPS Museum Collections Management. 

Specific repositories for specimens are detailed in the inventory contracts or study plans, 

monitoring protocols and SOPs, and collection permits. 

Several of the SFAN I&M projects incorporate digital, film (slides or negatives), and/or print 

photography into their protocols. Archiving procedures for digital and print photos will follow 

guidelines previously established for digital and hard-copy documents, respectively. 

6.10 Water Quality Data 

Water quality data collected to meet regulatory requirements is managed according to guidelines 

from the NPS WRD. This includes using the NPSTORET desktop database application at the 

parks to help manage data entry, documentation, and transfer. The network oversees the use of 

NPSTORET according to the network’s integrated water quality monitoring protocol and ensures 

the content is transferred at least annually to NPS WRD for upload to the STORET database 

maintained by the U.S. Environmental Protection Agency (Figure 6.5). 
108

Figure 0.5 Data flow diagram for water quality data. 

NPSTORET

SFAN copy 

(MS Access)

STORET National 

Data Warehouse

EPA, Washington, 

D.C. 

/

NPSTORET

NPS-WRD 

Fort Collins

Annual 

upload

Monthl

y 

Edits or 

change
109

Chapter 7 Data Analysis and Reporting 

7.1 Overview of Data Analysis and Reporting 

Sound data management practices are a key component to having a credible monitoring program 

that provides data to managers. In order to be meaningful, however, data must be analyzed, 

synthesized, interpreted, and provided to managers, decision-makers, or other interested parties 

in a usable form at regular intervals. Different types of reports are needed to provide information 

to multiple audiences. This chapter presents an overview of the types of analyese that the I&M 

program will produce and the resulting reporting mechanisms. 

In Table 7.1, we present an outline of data management tasks (data collection, data entry, and 

archiving), types of analysis and reporting, the position(s) responsible for the analysis and 

reporting, and the frequency for the long-term trend analysis reports. All of these considerations 

are important to clarify not only the nature of and logistics required for these analyses and 

reports, but also to ensure that there is sufficient program accountability, documentation, and 

evaluation. 

7.2 Data Analysis 

Many of the monitoring programs utilize summary statistics (mean, median, range, standard 

deviations, etc.) in the annual report to provide results such as, population size estimates, 

reproductive rates, and annual precipitation. In addition, geographic information systems (GIS) 

analysis is an important component of annual monitoring. GIS analyses include measuring 

invasive species rates of spread, population density, and changes in land use over time. The vital 

sign protocol explains the type of data analyses used in annual and long-term trend data analysis. 

7.2.1 Water Quality Data Analysis 

Non-parametric statistical tests will primarily be used to describe water quality data. The median 

and interquartile range (IQR) (middle 50% of data points) will be used in addition to the mean 

and standard deviation. Confidence intervals (95%) will be used to bound uncertainties in means 

and medians. Summary statistics and correlation techniques will be used to quantify relationships 

between water quality variables. To limit seasonal variability, statistical tests will be performed 

on each of the different seasons. The Seasonal-Kendall test will be used for trend analyses. 

For each monitoring question, individual station data will be summarized seasonally and 

annually. Data from all stations within each watershed will also be summarized seasonally and 

annually. All data will be compared with water quality standards by graphing the data along with 

a “criteria line” on the graph that clearly shows which measurements fall above or below the 

standards. Within each watershed, data from stations upstream and downstream of a suspected 

pollution source or tributary will be compared. Summary tables, histographs, and box and 

whisker plots will be used to show median and interquartile ranges, mean and standard deviation, 

and 95% confidence intervals for means and medians. Summary reports and an updated 

NPSTORET database will be sent to WRD annually. 
110

7.3 Reporting 

The I&M program has multiple audiences that need to receive and understand the information 

learned through the monitoring program. Congress, the Office of Managemend and Budgets 

(OMB), national and regional offices, superintendents, resource managers, park interpreters, 

cooperators, volunteers, friends groups, and the public all need to be provided the opportunity to 

learn about and understand the SFAN Vital Signs Monitoring Program. Each group will require a 

different level of information and a different method of delivery. Within the next year, the SFAN 

will develop an explicit communication strategy to explore, plan and prioritize the types of 

information and communication tools to use for the different audiences. A variety of reporting 

tools are already being considered. 

• Annual Reports 

• Annual Briefings to Park Managers 

• Analysis and Synthesis Reports 

• Program and Protocol Reviews 

• Scientific Journal Articles 

• Internet and Intranet Websites 

7.3.1 Annual Reports 

The major purpose of annual reports is to: 

• Summarize public interest highlights, 

• Archive annual data and document monitoring activities for the year, 

• Describe current condition of the resource, 

• Detect change in resource condition outside of normal range of variation, 

• Increase communication within the park and network, 

• Provide summary reports and updates to region and national levels, and 

• Provide summary reports and updates to collaborators. 

7.3.1.1 Annual Project Reports: Many monitoring programs will be active each year, and those programs will 

generate annual reports; however, some sampling regimes do not require annual activity. Those programs will 

produce “annual” reports only during those years where there are significant monitoring activities to document. For 

those protocols, which require multi-year implementation or pilot testing, an annual report will be created that 

summarizes the protocol development steps accomplished during that year. 

With a higher level of database design and effort applied to the vital signs, one of the goals is to 

develop databases with automated summary reports and data analysis capabilities. The standard 

use of Microsoft Access software, the standardization of database design, and the automation of 

data summaries and reporting all contribute to a more efficient reporting ability. With proper 

metadata available for each vital sign dataset and GIS component as outlined in Chapter 6 and 

the Data Management Plan, raw data could be provided to collaborators for additional data 

analysis (Press 2005). 
111

All reports will be written using language understandable to a general audience not conversant 

with the specific technical details of the subject matter. Main sections will include: 

• Executive Summary 

• Overview 

• Study Area 

• Methods 

• Significant findings 

• Public Interest Highlights 

• Management Recommendations 

• Research Recommendations 

• Photographs 

The executive summary will be written in the form of a 1- or 2-page “briefing statement” that 

summarizes the key findings and recommendations for their protocol or project; these written 

briefing statements will then be integrated into project specific annual reports and the Annual 

Administrative Report and Work Plan. 

7.3.1.2 Water Quality Annual Reports: Water quality monitoring will occur on an annual basis. Data will be 

provided to the Water Resources Division annually following. In addition, a summary report will be provided that 

includes a paragraph summary for each parameter plus summary graphs of each site; and, summary paragraphs will 

be provided for each watershed including any proposed management activities related to water quality 

improvements. Recommendations for revising the protocol (changing monitoring intervals and timing, 

moving/adding sites, etc.) will also be proposed. 

7.3.2 Annual Administrative Report and Work Plan 

Each year, the Monitoring Program will produce an annual report in the form of the Annual 

Accomplishments Report and Work Plan (AARWP) as required by the national I&M office. The 

purpose of the report is to account for funding and program personnel expenditures, describe 

objectives, tasks, accomplishments, and products of the monitoring effort for the past year. The 

report serves as an administrative record of the program as well as a tool that informs the park, 

network and regional staff on the progress of the SFAN Vital Signs Monitoring Program. 
112

Table 0.1 Data analysis and reporting schedule for SFAN vital signs monitoring program. 

Level 1 Level 2 Level 3 Network Vital Sign Name Data Analysis / Reporting Type of Data Analysis Person Responsible for Data Analysis & Reporting Data Archival Long-te

Trend

Reporti

Ozone Ozone Annual Summary statistics ARD Continuous 10 yea

Wet and Dry Deposition Wet and Dry Deposition Annual Summary statistics ARD Continuous 10 yea

Visibility and Particulate 

Matter 

Visibility and 

Particulate Matter Annual Summary statistics ARD Continuous 10 yea

Air Quality 

Air Contaminants Air Contaminants Annual Summary statistics ARD Continuous 10 yea

Air and Climate 

Weather 

and 

Climate Weather and Climate Weather and Climate Annual Summary statistics 

Western 

Regional 

Climate Center, 

Network 

Coordinator 

Continuous 10 yea

Hydrology Surface water dynamics Freshwater Dynamics Annual Hydrographs, rating curves, other hydrologic summaries GOGA Aquatic Ecologist, Network Coordinator Annually 5 year

Water 

Wat

er 

Qual

ity Water Chemistry Freshwater Quality Annual 

Summary 

statistics, 

seasonal trends 

Network WQ 

Specialist Annually 5 year

Invasive 

Species Invasive/Exotic Plants Invasive Plant Species (early detection) Annual GIS analysis, summary statistics Network Veg. Ecologist Annually 5 year

Wetland Communities Wetlands TBD TBD TBD TBD TBD 

Riparian Communities Riparian Habitat TBD TBD TBD TBD TBD 

Fishes Stream Fish Assemblages Annual Population estimates PORE Hydrologist Annually 3 year

Biological Integrity 

Focal Species or Communities Amphibians and Reptiles Amphibians and Reptiles TBD TBD TBD TBD TBD 
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Level 1 Level 2 Level 3 Network Vital Sign Name Data Analysis / Reporting Type of Data Analysis Person Responsible for Data Analysis & Reporting Data Archival Long-te

Trend

Reporti

Birds Landbirds Annual 

Summary 

statistics, 

population 

trends 

PRBO Annually 5 year

Birds Raptors and Condors Annual 

Nesting success, 

locations, 

summary 

statistics 

PINN Wildlife 

Biologist Annually 5 year

Mammals Pinnipeds Annual Summary 

statistics 

PORE I&M 

Coordinator Annually 5 year

Vegetation 

Communities 

Plant 

Community 

Change 

TBD TBD 

PORE GIS 

Biologist, 

Network Veg. 

Ecologist 

TBD TBD 

T&E Species and 

Communities 

Northern Spotted 

Owl Annual Summary statistics PORE I&M Coordinator Annually 5 year

T&E Species and 

Communities 

Rare, T&E Plant 

Species Annual 

Summary 

statistics, 

population 

trends 

Park Plant 

Ecologists Annually 3 – 5 years 

T&E Species and 

Communities T&E Butterflies Annual 

Nectar source 

density trends, 

relative 

population 

estimates 

PORE I&M 

Coordinator, 

GOGA Wildlife 

Ecologist 

Fall./ 

Annually l 6-8 yea

At-risk Biota 

T&E Species and 

Communities 

Western Snowy 

Plover Annual 

Population and 

productivity 

estimates, 

summary 

statistics 

PRBO, 

PORE I&M 

Coordinator, 

GOGA Wildlife 

Ecologist 

Fall./ 

Annually 5 year

Ecosystem 

Patterns and 

Processes 

Land Cover 

and Use Land Cover and Use Landscape and Land Use Change TBD TBD TBD NA TBD 
7.3.3 Annual Briefings to Park Managers 

Each year, in an effort to increase the availability and usefulness of monitoring results for park 

managers, the network coordinator will take the lead in organizing annual briefings to the park 

managers. The briefings will include visits to each park to present highlights and results from 

ongoing monitoring efforts to all park staff. Project leads and principal investigators will be 

encouraged to participate. Highlights will include discussions of significant findings, public 

interest stories, and potential management action items. These briefings may include specialists 

from the air quality program, fire ecology program, Research Learning Center, and collaborators 

from other programs and agencies to provide managers with an overview of the status and trends 

in natural resources for their parks. 

7.3.4 Long-term Trend Analysis Reports 

The role of long-term trend analysis reports is to: 

• determine patterns/trends in condition of resources being monitored, 

• discover new characteristics of resources and correlations among resources being 

monitored, 

• detect change in resource condition outside of normal range of variation 

• analyze data to determine amount of change that can be confidently detected by this type 

and level of sampling, 

• provide context, interpret data for the park within a multi-park, regional or national 

context, 

• inform resource management programs (feedback for adaptive management), and 

• provide summary reports and updates to collaborators 

These reports can provide critical insights into resource status and trends, which can then be used 

to inform resource management efforts and regional resource analyses. This type of in-depth 

analysis typically requires several seasons of sampling data. Therefore, these reports are not 

written more frequently than every three to five years, for resources sampled annually. For 

resources sampled less frequently, or which have a particularly low rate of change and 

variability, intervals between reports may be longer. The target audiences for analysis and 

synthesis reports are superintendents, park resource managers, network staff, and external 

scientists. Trend analysis reports will generally be published in hardcopy and electronic formats, 

posted to the Network web site and shared with external scientists working on similar vital signs. 

7.3.5 Program and Protocol Reviews 

The purpose of program and protocol reviews is to: 

• Conduct periodic formal reviews of the monitoring program including program 

administration, staffing plan, budgets, and products in order to evaluate program 

effectiveness (every 5-10 years) 

• Conduct periodic formal reviews of individual monitoring protocols including objectives, 

design, operations, and products in order to evaluate new scientific information and 

determine if changes are needed (5-10 year intervals). 
115

The primary audience for these types of reviews includes superintendents, park resource 

managers, network staff, servicewide program managers, and external scientists. Program and 

protocol reviews will generally be initiated by the Regional I&M Coordinator or Network 

Coordinator. The program and protocol reviews will include peer review, either through 

participation in the process or review of a recommendations report. 

The following is an example of the sequence of events in a program review: 

• Program manager/network team summarizes program and activity to date. 

• Outside contractor or academic enlisted to conduct program assessment (e.g., power 

analyses of the data) and report findings. 

• Broad spectrum of peers invited to review the program’s products. 

• Peers invited to a workshop to discuss the program, the analyses it was subjected to, 

whether or not it is meeting program goals, how it might be improved, what should be 

changed, left behind, or tried anew, and what new partners might be enlisted to join. 

• Program manager or contracted personnel writes up results of this workshop, circulates to 

participants, and posts final report on SFAN web site, sends to NPS regional and WASO 

program offices. 

• Program manager develops strategy with SFAN team on implementing 

recommendations. 

Typical topics addressed are a general review of program efficacy, accountability, scientific 

rigor, contribution to park management and larger scientific endeavors, outreach, partnerships 

and products. These reviews are among the most in depth—not only will monitoring results be 

analyzed over a longer period of time, but the entire program, its structure, and function are 

evaluated to determine not only whether the program is achieving its objectives, but also whether 

the list of objectives is still relevant, realistic, and sufficient. 

7.3.6 Scientific Journal Articles 

This aspect of the program will be directed by the program managers or cooperators, and is more 

at the discretion of the individual investigators than any of the previous report types. Publishing 

scientific journal articles is primarily conducted to communicate advances in knowledge, and is a 

very important, widely acknowledged means of quality assurance and quality control, via the 

peer review process. Putting a program’s methods, analyses, and conclusions under the scrutiny 

of a scientific journal’s peer review process is basic to science and one of the best ways to ensure 

scientific rigor. Accordingly, the journal or book editor will conduct the peer review process. No 

coordination at the network level is required except for the Network Coordinator and other 

involved program managers to review the article before submittal to a journal. The SFAN 

Monitoring Program should be acknowledged as providing funding and support. 

The SFAN monitoring program tracks scientific journal articles produced by SFAN efforts; new 

publications are a standard part of the AARWP, which the network updates and sends to the 

regional and national offices each year. Additionally, all scientific journal articles, which are 

reported in the AARWP will be entered into the NatureBib database by network data managers. 
116

7.3.7 Internet and Intranet Websites 

Internet and (restricted) intranet websites are key tools for promoting communication, 

coordination, and collaboration among the many people, programs, and agencies involved in the 

network monitoring program. All written products of the monitoring effort, unless they contain 

sensitive or commercially valuable information that needs to be restricted, will be posted to the 

main network website: 

http://www1.nature.nps.gov/im/units/sfan

Documents to be posted to the network website include this monitoring plan, all protocols, 

annual reports, analysis and synthesis reports, and other materials of interest to staff at the park, 

network, regional, and national levels, as well of being of interest to our collaborators. 

In addition, to promote communication and coordination within the network, we will maintain a 

password-protected “team website” where draft products, works in progress, and anything that 

needs to have restricted access can be shared within the program. 

7.4 Interpretation and Outreach 

In is anticipated that a variety of interpretation and outreach products will be identified through 

the communication strategy. Parks in the SFAN have already developed a variety outreach tools 

upon which the I&M network can build. PORE, for example, has an informal “brown bag” 

program which brings network researchers and park staff together to share results of ongoing 

research. Presentations are often videotaped so interpreters or other park staff who were not 

available to participate can view them. Network staff may also get involved with annual 

Interpretive Docent Training sessions which are provided for interpreters and docents who lead 

tours. 

Interpretation and outreach is a perfect place for the SFAN Vital Signs Monitoring Program to 

team up with the Pacific Coast Science and Learning Center (PCSLC). The PCSLC promotes 

research in parks and acts as a bridge between science being conducted in parks and the public, 

particularly students. One of the successful programs initiated by the PCSLC employs high 

school students to assist with research that is being conducted at the park. 

In order to ensure that information is widely available, SFAN will encourage project leads to 

develop up to date fact sheets, brochures, or posters about their projects. Similar products are 

already being developed by park staff in order to share ongoing monitoring results. During the 

elephant seal breeding season, for example, weekly charts showing the numbers of seals are 

distributed to all visitor centers at PORE and posted on the park website between December 15 

and March 30. During the plover breeding season, park staff receives weekly electronic mail 

updates on the progress of the plover nesting season from a seasonal plover program park guide. 

Another example of using monitoring information for outreach to visitors occurs with the raptor 

monitoring program at PINN. Raptor updates are biweekly summaries of raptor observations and 

activity, documented by the raptor monitor in field notes, and by other park staff or visitors on 
117

wildlife observation cards (available in the Visitor Centers). Raptor updates are important as a 

communication tool, providing park staff with current information on the status of raptors in the park. 

This information allows rangers to more effectively enforce raptor advisories, and give more 

complete reports on observed raptor activity. In this sense, the updates help to ensure the success of 

the raptor monitoring effort, and the protection of breeding raptors at the park. The updates also 

support interdivisional relationships by letting other park employees know what raptor monitors are 

doing, and encouraging other staff to assist with the monitoring effort. 
118
119

Chapter 8 Administration/Implementation of the 

Monitoring Program 

8.1 Board of Directors 

The overall administration structure and implementation of the SFAN monitoring program was 

specified in the Charter of the San Francisco Bay Area Network for Inventory and Monitoring 

Board of Directors (BOD; SFAN 2001a). The BOD is comprised of park superintendents of the 

four park units that comprise the network (GOGA, PORE, PINN, JOMU/EUON). The Pacific 

West Region I&M Coordinator and the Network I&M Coordinator are ex officio members of the 

BOD. There will be no officers. Any park superintendent who cannot attend or otherwise 

participate in a meeting of the Board may assign an alternate. A park superintendent from the 

network may not serve as the alternate, or carry the proxy of, another park superintendent. Three 

BOD members constitute a quorum. 

The SFAN Board of Directors shall: 

• Promote accountability and effectiveness for the I&M Program by reviewing progress 

and results to ensure goals and targets are being achieved; 

• Assist in defining the vision, long-term goals, and objectives for the program; 

• Review strategies and procedures for utilizing both new and existing network resources 

(i.e., funding, staff, and tools) to best accomplish I&M Program goals; and 

• Assist with redefining objectives and realigning resources to meet new challenges and 

opportunities. 

All BOD decisions will be made by consensus. Consensus is defined as an outcome that all BOD 

members can live with even if not ideal from any one viewpoint. If the BOD cannot reach a 

consensus decision, the matter with all viewpoints represented, will be referred to the Deputy 

Regional Director of the Network. All decisions will be documented with responsible individuals 

and deadlines identified, as appropriate. Such decisions will be distributed to all BOD members 

as well as the Regional I&M and Network I&M Coordinator. 

To be most effective, the BOD will maintain a close working relationship with the Chief of 

Natural Resources of each park in the network, members of the Technical Steering Committee 

(TSC), and the Regional and Network I&M Coordinator. BOD members are encouraged to 

participate in and/or keep informed with respect to the work of the TSC. The Network I&M 

Coordinator will be expected to provide regular briefings (by memoranda, electronic mail or 

telephone conference) to the BOD. 

8.2 Technical Steering Committee 

The TSC is comprised the network coordinator and one representative each from GOGA, PINN, 

and PORE. JOMU and EUON have one joint representative. Decisions are made by concensus. 

Additional non-voting members include the PORE Senior Science Advisor, the Lead Data 

Manager, and any park staff that supervises an I&M technician (e.g. PORE Hydrologist). The 
120

Board will approve its composition as well as its charter and the Network I&M Coordinator will 

chair its meetings and coordinate its efforts. The TSC will be responsible for: 

• Acting as a liaison to their parks’ natural resource management and science division staff 

for communicating I&M program objectives and issues; 

• Compiling and summarizing existing information about park resources; 

• Participating in the identification of monitoring objectives; 

• Evaluating sampling designs, methods and protocols; 

• Reviewing annual monitoring reports and interpretation; 

• Participating in the preparation of the Monitoring Plan, Annual Work Plan, Annual 

Accomplishments Report and other Network documents; and 

• Developing materials for and facilitating the Five Year Program Review. 

The products and recommendations of the TSC will be presented to the BOD for approval. TSC 

meetings are open to any interested park staff. The Network I&M Coordinator will be 

responsible for maintaining the administrative record. Copies of all documentation will be made 

available to the Regional I&M Coordinator, BOD and TSC through emails, phone calls, or on the 

Network’s web site. 

8.3 Other Committees 

The BOD may form a standing Information and Education Committee comprised of 

interpretation, education and public affairs staff at a later date. When needed, the BOD, TSC, or 

Network I&M Coordinator may form groups of specialists to work on a particular task or a 

particular sub-program area. 

8.4 Network Staff 

Vital signs monitoring will be implemented by a combination of network and park staff. A lead 

will be selected to implement each protocol. In some cases, the lead may oversee and implement 

all aspects of a monitoring protocol from the design phase through the implementation phase 

including data collection, management, analysis, and reporting. Where opportunities for 

collaboration exist, the lead may be responsible for overseeing a contract or agreement (e.g., 

cooperative agreement or interagency agreement). Protocols will specify the roles and 

responsibilities of each project lead. 

The I&M Program currently supports 12 employees. This includes two permanent employees 

who are housed at GOGA (Network Coordinator and Lead Data Manager). The other positions 

consist of one natural resources specialist, six technicians, two data managers, and one Student 

Conservation Association (SCA) volunteer. Additional volunteers support data collection efforts 

whenever possible. PORE partially funds two of these positons. The I&M program also 

contributes to PORE in return for administrative support. 

The TSC and BOD have decided to make all new positions subject-to-furlough (STF) in order to 

build maximum flexibility into the program. It is expected that some STF positions will be 

reconsidered as the the program continues to move from protocol development to full 
121

implementation. Position management is a BOD responsiblility, but recommendations will be 

made to the BOD from the TSC when and how to fill any vacancies in network positions that 

occur. No position shall be converted from non-permanent to permanent status without the 

explicit written approval of the Board of Directors. 

8.4.1 Network Coordinator 

The permanent Network I&M Coordinator (GS-12; subject to furlough) is duty stationed at 

GOGA. The Network I&M Coordinator works closely with park biologists and physical 

scientists to plan and implement the vital signs long-term monitoring plan. The Coordinator is 

responsible for the overall SFAN I&M program administration (budget, property, staffing, 

reporting, project completion, and data archiving). The Coordinator seeks strategic partnerships 

to further the monitoring plan goals. The Coordinator may also conduct ecological studies 

concerning a range of resource attributes and associated habitats. The Network Coordinator is 

supervised by the GOGA Assistant Superintendent and takes direction from the BOD. 

8.4.2 Data Manager 

Data management is accomplished through a team of three data managers. 

8.4.2.1 Lead Data Manager: The permanent Lead Data Manager (GS-11; subject to furlough) is duty stationed at 

GOGA. The lead data manager provides programmatic oversight on all issues relating to data management. The 

incumbent serves as the liaison for the I&M Program to the national, regional, and network parks. The position 

provides oversight to all data management products. The position is supervised by the Network Coordinator. 

8.4.2.2 Park Data Managers: Two supporting Data Mangers are funded by the I&M program and are based at PORE 

and PINN. Both positions are funded at the GS-9 level. The PORE position is split among two employees and was 

raised to a GS-11 by the park. The positions are designed to provide assistance to the Lead Data Manager including 

database development and GIS support. As databases are populated and processes implemented to input, archive, 

and manage the databases, the data management staffing plan will be evaluated to determine if it still serves the 

Network needs sufficiently. 

8.4.2 Natural Resource Specialist 

The term, subject-to-furlough, Natural Resource Specialist (GS-9) is duty stationed at GOGA. 

The position serves as the lead biologist developing the protocols for the early detection of 

invasive plant species, rare plant species, and components of the plant community change 

protocol. The position is supervised by the Network Coordinator. 

8.4.3 Fisheries Biologist 

The Fisheries Biologist (GS-9) is responsible for field work associated with monitoring 

freshwater assemblages. In addition, at least 20% of the technician’s time is dedicated to 

maintaining accurate field data and entering data into appropriate databases in order to prepare it 

for analysis and reporting. The position is funded at the GS-7 level for 25 pay periods and is 

stationed at PORE. PORE has allocated additional funding to support the position at a GS-9 

level. 

8.4.4 Hydrologic Technician 

The term, subject-to-furlough, Hydrologic Technician (GS-7) is duty stationed at PORE and is 

supervised by the PORE Hydrologist. The position is responsible for implementing the Water 

Quality Monitoring Plan. 
122

8.4.5 Wildlife Biological Technician 

The Wildlife Biological Technician (GS-7) is responsible for field work associated with pinniped 

and spotted owl monitoring. In addition, at least 20% of the technician’s time is dedicated to 

maintaining accurate field data and entering data into appropriate databases in order to prepare it 

for analysis and reporting. The position is funded for 20 pay periods and is stationed at PORE. 

8.4.6 Vegetation Biological Technician 

The Vegetation Biological Technician is responsible for field work associated with invasive 

species monitoring. In addition, at least 20% of the technician’s time is dedicated to maintaining 

accurate field data and entering data into appropriate databases in order to prepare it for analysis 

and reporting. The position is funded for 16 pay periods during FY06. The number of people in 

this position may be increased and funded for more pay periods as the program moves toward 

implementation of both invasive species and rare species monitoring. 

8.4.7 Avian Biological Technician 

The Avian Biological Technician (GS-7) is responsible for field work associated with raptor and 

condor monitoring. In addition, at least 20% of the technician’s time is dedicated to maintaining 

accurate field data and entering data into appropriate databases in order to prepare it for analysis 

and reporting. The position is funded for 13 pay periods and is stationed at PINN. 

8.4.8 Student Conservation Association 

The I&M program will provide training opportunities through the Student Conservation 

Association (SCA) in exchange for assistance with field monitoring. SFAN is budgeting for at 

least one SCA volunteer annually to assist with a variety of projects including weather 

monitoring, freshwater dynamics, or other vital signs monitoring. Approximately 40% of the 

position will be dedicated to fieldwork and 40% to data management. 

8.5 Shared Positions 

8.5.1 Budget Analyst 

The I&M program contributes $15,250 to support a budget analyst for 0.25 FTE. The position 

helps track budgets including purchases and credit cards, vehicles, and assists with travel. The 

position is based at PORE. 

 

8.5.2 Administrative Support 

The I&M program contributes $10,000 to PORE for administrative support. This provides the 

program with assistance from contracting, procurement, and human resources. 

8.5.3 Regional Aquatic Ecologist 

The Regional Aquatic Ecologist (GS-12) is partially funded by the WRD. The I&M Program, 

however, has contributed amounts up to $14,000 toward the ecologist’s salary for assistance on 

various projects. In FY05, for example, the Aquatic Ecologist coordinated an amphibian and 

reptile monitoring workshop to identify appropriate monitoring questions and to develop 

monitoring goals and objectives. She also assisted with establishing a robust experiental design 
123

for monitoring a rare plant species. It is anticipated that I&M will continue to contribute project 

specific funds to this position. 

8.6 The PWR Inventory and Monitoring Coordinator 

Program coordination and oversight at the regional level is provided by a full-time Regional 

Inventory and Monitoring Coordinator who reports to the region's senior natural resource staff 

member or other regional staff person designated by the Regional Director. Regional I&M 

Coordinators are responsible for providing technical support along with day-to-day coordination 

among networks, the regional office, and the National Inventory and Monitoring Program. 

8.7 Integration with Other Divisions 

Each vital sign requires different levels of coordination with other divisions, such as resource 

protection, maintenance and interpretation. The members of the TSC, park I&M project leaders, 

and Network staff coordinate with resource management staff at the parks to ensure monitoring 

goals are being met and to keep parks informed of monitoring activities. Division Chiefs pass on 

information about monitoring events and results to senior park management staff at regular 

weekly briefing meetings. Regular updates support interdivisional relationships by letting other 

park staff know what the monitoring staff is doing, and by encouraging other staff to assist with 

the monitoring effort. 

8.8 Existing and Potential Monitoring Partnerships 

The potential for conducting collaborative monitoring programs in the San Francisco Bay region 

is high. It is incumbent upon the Network to establish partnerships and to find additional grants 

to implement vital signs monitoring since NPS I&M funding will not cover all monitoring needs. 

Partnerships assist the SFAN in implementing more vital vigns monitoring projects than would 

be possible without assistance. Organizations, agencies, and institutions ranging from watershed 

management councils to state and federal agencies have existing monitoring programs in the 

area. In fact, many of the SFAN’s existing monitoring efforts have been ongoing for decades and 

are the result of partnerships. These partnerships provide the NPS the opportunity to play a key 

role in the development of region-wide natural resources assessment and monitoring programs. 

The network has formal agreements, such as interagency agreements and cooperative 

agreements, as well as informal partnerships with groups that share common goals with the NPS. 

A few of the partners are: 

Interagency Agreements: 

• The U.S. National Marine Fisheries Service (NMFS) has large scale, long-term monitoring 

studies of marine mammals, sea turtle and fish in the region. The parks currently participate 

in studies of pinnipeds, including harbor seals and northern elephant seals, which contribute 

to the rangewide analyses completed by NMFS. 
124

• USGS Biological Research Division (BRD) has had Research Scientists located at both 

PORE and GOGA since BRD was established. USGS Research Scientists have assisted with 

vertebrate inventories and planning the monitoring program. 

• The U.S. Fish and Wildlife Service has large scale, long-term monitoring studies focused on 

water birds and seabirds at Golden Gate and Point Reyes. Both parks benefit from over 

twenty years of data developed and analyzed by this agency. The Service is involved in the 

re-introduction and monitoring of California condors at PINN. 

• The U.S. National Oceanographic and Atmospheric Administration (NOAA) manages three 

large National Marine Sanctuaries (NMS) off central California, which abut or are near 

PORE and GOGA. The Gulf of the Farallones includes nurseries and spawning grounds for 

commercially valuable species of fish, at least 26 species of marine mammals, and the largest 

concentration of breeding seabirds in the continental United States. Monterey Bay Marine 

Refuge, the nation’s largest NMS, spans 5,300 square miles with an array of habitats from 

rugged rocky shores and lush kelp forests. Cordell Bank NMS is located 40 miles west of 

PORE and is a significant seamount where many marine species forage. The refuges are a 

focal point for research. Each of these sanctuaries is presently conducting inventories and 

identifying elements to monitor. PORE and GOGA already cooperatively monitor several 

marine species with NOAA including seabirds, pinnipeds and intertidal communities. 

Cooperative Agreements: 

• PRBO Conservation Science (PRBO), an ecosystem research group located near PORE, has 

several broad-scale bird monitoring efforts. For example, PRBO has assisted the SFAN with 

monitoring and protocol development of the Northern spotted owl, Western snowy plover, 

and landbird vital signs. 

• The Golden Gate Raptor Observatory located at the Marin Headlands at GOGA has been 

monitoring raptors for over 20 years. 

• SFAN parks have had a long-term relationship with local universities including University of 

California (UC) and California State University. Researchers helped develop and implement 

the coastal biophysical inventory, the subtidal and deep water inventory, and Phases I, II, and 

III of this Monitoring Plan. They participated in workshops, reviewed previous versions of 

this monitoring plan, and peer-reviewed protocols for individual vital signs. 

• The Point Reyes National Seashore Association is a non-profit partner and assists the SFAN 

in raising and managing donations for monitoring projects, such as Northern spotted owl, 

Western snowy plover, stream fish assemblage, pinniped, and rare plant monitoring. 

• Golden Gate National Parks Conservancy is also a non-profit partner and assists SFAN in 

raising and managing donations for monitoring project such as Mission blue butterfly, rare 

plant, invasive plant, stream fish assemblage, Western snowy plover, and landbird 

monitoring. 

• Ventana Wilderness Society is involved in the reintroduction of condors with the USFWS at 

PINN. 
125

• The Nature Conservancy borders several parks and existing collaboration occurs to monitor 

resources. 

Additional Partners: 

• Tomales Bay Watershed Council, Marin County Environmental Health Services, and the 

Regional Water Quality Control Boards are all integral partners in the water quality 

monitoring programs at the SFAN parks. 

• California Native Plant Society volunteers have conducted rare plant inventory surveys at all 

the SFAN parks, assisted with plant community mapping and will likely be partners in the 

monitoring program for rare, threatened and endangered plant species. 

• SFAN cooperatively monitors Northern spotted owls with the Marin County Open Space 

District and Marin Municipal Water District (MMWD), both of which are adjacent to PORE, 

GOGA and MUWO forested lands. SFAN also works with MMWD to monitor stream fish 

assemblages. 

• Six California State Parks are adjacent to or encompassed by the SFAN and have a similar 

conservation and educational mission. SFAN currently coordinates with State Parks for 

monitoring Northern spotted owls, stream fish assemblages, and landbirds. 

• Los Padres National Forest encompasses nearly two million acres in the coastal mountains of 

central California. The north division around Monterey and Santa Lucia is directly east of 

Pinnacles. 

• The Mid-peninsula Regional Open Space District currently manages nearly 50,000 acres of 

land in 26 open space preserves. Their purpose is to permanently protect and restore acquired 

lands forming a regional open space greenbelt. 

• The Peninsula Open Space Trust is a nonprofit group dedicated to preserving the beauty, 

character and diversity of the coastal areas of the San Francisco Peninsula. Since its founding 

twenty years ago, it has protected more than 40,000 acres of San Francisco Bay open space. 

• The Muir Heritage Land Trust preserves undeveloped land to provide a buffer between cities 

and suburbs of Contra Costa County. They are interested in establishing wildlife migratory 

corridors by connecting protected lands. One current campaign is to protect 1,500 acres of 

land linking ridge lands from the Carquinez Strait, extending south to Briones Regional Park, 

and continuing to areas near Las Trampas Regional Wilderness. This may help provide some 

connectivity for EUON and JOMU. 

• Marin Municipal Water District monitors several species in common with GOGA and PORE, 

including stream fish assemblages and Northern Spotted Owls. 

8.9 Program Integration 

SFAN has made a commitment to implement long-term monitoring, analyze data, and report 

findings to various audiences in the parks including resource management, park administration, 

and interpretation. Integrating science into park management, however, is more complex than 

simply reporting results. The SFAN will be working closely with each park through the Board of 
126

Directors, the Technical Steering Committee, and with other senior management staff to make 

sure all SFAN products are fully integrated and used by park management. Regular meetings 

between SFAN staff and park staff including senior management, planners, interpreters, 

maintenance, and park rangers will ensure that final products will meet park needs and 

appropriate deadlines. As part of the program review (see section 8.10), SFAN will analyze how 

well SFAN is integrated into park operations. 

8.10 Program Reviews 

The SFAN Charter (SFAN 2001a) established a schedule program reviews starting in 2007 and 

every 5-10 years thereafter. The purpose of this review will be to evaluate the overall vital signs 

monitoring program accomplishments,staffing and products, data management, fiscal 

management, cost-effectiveness of each vital sign. The program review shall provide the 

principal basis for any significant changes in program direction as well as reassignment of 

resources to any park or office. Participants in the review could include the TSC, BOD, and 

additional personnel to be determined later. The SFAN Charter will be revised following a 

programmatic review to serve as the document of record for the program’s administration and 

management structure. 

A group of three technical peers will review individual vital sign protocols every five years or 

three cycles, depending on the cycling schedule and history of the vital sign. Annually monitored 

vital signs will be reviewed every five years. A cycled vital sign such as plant community change 

may only be monitored every five to ten years. Therefore, the initial review will likely occur 

after three cycles of the monitoring activities. 

The review of vital sign protocols will examine whether the vital sign is measuring the defined 

monitoring goals. The review will include a statistical analysis of the results. In addition, the 

vital sign report will contain a list of the information used for the review, an evaluation of 

program costs, monitoring schedule, data management protocols, and management benefits from 

the monitoring program. 
127

Chapter 9 Schedule 

9.1 Timing and Frequency 

This chapter explains the schedule that the Network will follow during the next five years to 

develop vital signs monitoring protocols and to implement the Monitoring Plan. The following 

schedule (Table 9.1) lists the eighteen top priority vital signs scheduled for monitoring and 

describes when protocol development and peer review will be completed. Table 9.1 also 

describes key issues that must be addressed in establishing protocols for each for the 18 vital 

signs. 

Table 0.1 Schedule of vital signs protocol development. 

Vital Sign Name 

Target Year for 

Protocol 

Completion and 

Implementation Key Issue to be Addressed Before Implementation 

Air Quality TBD 

Data collection for air quality monitoring is ongoing. Protocols 

outlining data management, analysis, and reporting are being 

developed and implemented by the NPS Air Resource Division 

(ARD). Data are already being collected by partnering agencies. 

Weather and Climate FY 06 

Data collection for weather and climate monitoring is ongoing. A 

draft protocol outlining data management, analysis, and reporting has 

been developed by I&M Staff and will be peer reviewed in FY06. 

Protocols will be revised upon receiving review comments. 

Freshwater Dynamics FY 06 

A draft protocol outlining data management, analysis, and reporting 

has been developed by I&M Staff and will be peer reviewed in FY06. 

Data collection will continue and protocols will be revised upon 

receiving review comments. 

Water Quality FY 06 

A draft protocol outlining data management, analysis, and reporting 

has been developed by I&M Staff and will be peer reviewed in FY06. 

Data collection will continue and protocols will be revised upon 

receiving review comments. 

Invasive Plant 

Species FY 06 

A draft protocol using a volunteer based methodology has been 

developed by I&M staff in FY05. The protocol will be field tested in 

FY06 and submitted for peer review. 

Wetlants TBD 

A strategy including a timeline and budget for developing and 

implementing monitoring protocols will be initiated in FY06. 

Riparian Habitat TBD 

A strategy including a timeline and budget for developing and 

implementing monitoring protocols will be initiated in FY06. 

Stream Fish 

Assemblages FY 06 

Data collection for stream fish assemblage monitoring is ongoing. A 

draft protocol outlining data management, analysis, and reporting has 

been developed by I&M Staff and will be peer reviewed in FY06. 

Protocols will be revised upon receiving review comments. 

Amphibians and 

Reptiles TBD 

A strategy including a timeline and budget for developing and 

implementing monitoring protocols will be initiated in FY06. The first 

workshop of this planning process is scheduled for end of FY05. 

Landbird Dynamics FY06 Data collection for landbird monitoring is ongoing. A draft protocol 
128

Vital Sign Name 

Target Year for 

Protocol 

Completion and 

Implementation Key Issue to be Addressed Before Implementation 

outlining data management, analysis, and reporting has been 

developed by I&M Staff and will be peer reviewed in FY06. Protocols 

will be revised upon receiving review comments. 

Raptors and Condors FY06 

Data collection for raptor and condor monitoring is ongoing. A draft 

protocol outlining data management, analysis, and reporting has been 

developed by I&M Staff and will be peer reviewed in FY06. Protocols 

will be revised upon receiving review comments. 

Pinnipeds FY06 

A protocol outlining data management, analysis, and reporting has 

been developed by I&M Staff and was reviewed in FY04 and will be 

finalized in FY06. 

Plant Community 

Change TBD 

Protocols will be initiated by I&M staff in FY06 and FY07. Funding 

for completion and implementation of the protocol must also be 

established. 

Rare Plant Species FY 07 

A draft protocol outlining data management, analysis, and reporting 

has been developed by I&M Staff and will be peer reviewed in FY06. 

Protocols will be revised upon receiving review comments. Standard 

Operating Procedures will be added for priority rare plants over a 

multi year period. 

Northern Spotted 

Owl FY 04 

A protocol outlining data management, analysis, and reporting has 

been developed by I&M Staff and was peer reviewed in FY05 and 

will be finalized in FY06 

Western Snowy 

Plover FY 06 

Data collection for snowy plover monitoring is ongoing. A draft 

protocol outlining data management, analysis, and reporting has been 

developed by I&M Staff and will be peer reviewed in FY06. Protocols 

will be revised upon receiving review comments. 

Threatened and 

Endangered 

Butterflies TBD 

Protocols will be developed by I&M staff in FY06 and FY07. Once 

peer review is completed, long-term monitoring will be implemented. 

Landscape Dynamics TBD 

A strategy including a timeline and budget for developing and 

implementing monitoring protocols will be initiated in FY06. 

Table 9.2 depicts the frequency and timing of sampling. While some data will be collected 

continuously (e.g., climate data), other data will be collected for several weeks at one time of 

year (e.g., snowy plovers surveys). It can also be seen from this table that our field efforts are not 

entirely weighted to one season but are distributed throughout the calendar year. 
129

Table 0.2 Annual schedule of vital signs data collection. 

Vital Sign Name Sampling frequency 

January 

February 

March 

April 

May 

June 

July 

August 

September 

October 

Air Quality Continuous X X X X X X X X X X Weather Daily X X X X X X X X X X Freshwater Dynamics Monthly & storm based X X X X X X X X X X Freshwater Quality* Monthly X X X X X X X X X X Invasive Plant Species Annually X X X X X X Wetlands TBD Riparian Habitat TBD Stream Fish Assemblages Monthly X X X X X X X X X X Amphibians and Reptiles TBD Landbirds Weekly X X X X X Raptors and Condors Weekly X X X X X X X Pinnipeds 

Weekly during breeding seasons/Bi-weekly year round 

X X X X X X X X X X 

Plant Community Change TBD Rare Plants Spring/Summer X X X X X X X X Northern Spotted Owl Spring/Summer X X X X X Western Snowy Plover Summer/Winter X X X X X X X X X X Threatened and Endangered Butterflies Spring X X X X X Landscape Dynamics TBD 

* = See Table 9.3 for a monitoring schedule for specific streams within SFAN. 
130

9.2 Water Quality Schedule 

As with other vital signs, the monitoring schedule for the water quality is dependent on the 

sampling design. The monitoring protocol will identify when each stream is monitored, the 

number of sample sites, and the sampling frequency. Refer to the monitoring protocol in for 

specifics (Cooprider 2005). 

Opportunities for phasing-in additional water bodies (e.g., Presidio streams) or eliminating the 

rotating basin approach will continue to be considered. Due to the Pathogen TMDL program 

monitoring on Olema Creek, it will continue to be monitored annually for the foreseeable future. 

Ideally, Lagunitas Creek tributaries would also be monitored annually since this stream is an 

impaired water body. However, nutrient and sediment TMDL monitoring programs are not yet in 

place for this creek (they should be in place by 2008). 

Table 0.3 Water quality monitoring schedule. Note that the table displays on monitoring cycle; 

therefore FY10 will mirror FY06. 

Stream Park Unit FY06 FY07 FY08 FY09 

Olema Creek PORE M, S, W M, S, W M,S, W M,S,W 

Lagunitas Creek PORE/GOGA M M 

Pine Gulch PORE M M 

Lower Redwood Creek GOGA/MUWO M ,S M, S 

Upper Redwood Creek GOGA/MUWO M M 

Rodeo Creek GOGA M, S M, S 

Tennessee Creek GOGA M, S M, S 

Nyhan Creek GOGA M, S M, S 

Oakwood Creek GOGA M, S M, S 

West Union Creek GOGA M M 

Franklin Creek JOMU M M 

Strentzel Creek JOMU S S 

Chalone Creek PINN M, S M, S 

M monthly monitoring (Winter and Spring only for Chalone Creek and West Union Creek) 

S monitoring during at least one storm event 

W weekly monitoring for five weeks in winter and summer
131

Chapter 10 Budget 

10.1 Annual Funding Sources 

Every year, the SFAN receives $751,600 to fund its staff and projects (table 10.1). 

Table 0.1 Annual funding sources. 

Funding Source Amount 

I&M Program - allocation for SFAN $747,200 

WRD - allocation for SFAN $69,000 

Total $816,200 

In addition, the Water Resources Division provides $69,000 to support the Network Water 

Quality Specialist position. A detailed budget is provided in the Freshwater Quality Monitoring 

Protocol. 

10.2 Annual Program Budget 

The proposed budget for the SFAN Monitoring Program is separated into the budget categories 

of personnel, cooperative agreements, contracts, operations and equipment, travel and other costs 

(table 10.2). Most of the program costs (76%) are committed to the network staff (table 10.2). 

Seventeen percent of the budget in FY06 goes to agreements and seven percent to travel, 

equipment and supplies, training, and uniforms. Because many positions are subject to furlough, 

the annual budget can be flexible to accommodate additional expenses which may vary from 

year to year. These additional expenses may include the need to get additional statistical support, 

to complete the development of protocols, awards, or repay pcs move obligation to region. 

10.3 Annual Vital Signs Allocation 

Another way of showing budget costs is to estimate the annual cost of monitoring for each vital 

sign (Table 10.3). The costs are shown in more detail in each protocol development summary in 

Appendix 4. Budget costs in this table show expenditures for each of the vital signs projects. The 

cost estimates include personnel dedicated to each vital sign. The table also shows estimated 

costs allocated toward project management, administration, statistical support and miscellaneous 

costs which include travel, training, and peer review. It should be noted that table 10.3 also 

indicates that 26% of the budget is dedicated to salaries for data managers. The amount dedicated 

to data management, however, is closer to 30 % because at least 20% of the time from all of the 

technicians who support the program is also dedicated to data management activities. 
132

10.4 Protocol Development and Implementation Costs 

It is expected that the annual average budget (tables 10.2 and 10.3) will change slightly over the 

next few years as the program moves from protocol development towards implementation. The 

Table 0.2 Annual monitoring budget. 

Budget Category Item Annual Cost 

Program Development 

I&M Coordinator (GOGA, GS-12, STF perm) $ 95,000 

Data Manager, Lead (GOGA, GS-11 STF perm) $ 79,000 

Program Administration 

Budget Analyst (PORE) $ 15,000 

Administrative Support (PORE) $ 10,000 

Protocol Development and Monitoring 

Natural Resouces Specialist (GOGA 21 PP GS-09 term) $ 65,000 

Biologist, Fisheries* 

 (PORE, 25 PP GS-07 term) $ 53,000 

Data Manager* (PORE, GS-09 term) $ 69,000 

Biotech, Biologist (WQ: PORE , 25 PP GS-07 term) $ 45,000 

Biotech, Wildlife (PORE, 20 PP GS-07 term) $ 40,000 

Biotech, Invasive (PORE, 16 PP GS-07 term) $ 35,000 

Data Manager (PINN, GS-09 term) $ 65,000 

Biotech, Raptors (PINN, 13 PP GS-07 seasonal) $ 21,000 

SCA Volunteer (1) includes housing (12 months) $ 13,000 

Regional Aquatic Hydrologist $14,000 

Personnel 

Subtotal – Personnel (76%) $ 619,000 

PRBO - Landbird Monitoring $ 64,520 

Marin Conservation Corps - Pinniped Monitoring $ 13,000 

Cooperative 

Agreements 

PRBO - Owl Monitoring (partial payment) $ 8,000 

Water Quality Testing Laboratory $ 34,000 

Weather Data Suport $8,000 

Special projects (e.g statistical support, vegetation mapping, etc) $ 22,380 

Contracts 

Subtotal – Cooperative Agreements and Contracts (17%) $ 149,900 

Operations/ Network and Park Vehicles $ 11,000 

Equipment Supplies and Equipment $ 9,200 

Travel Network and Project Travel $ 7,000 

Misc. (uniforms, training) $ 3,300 

Protocol Peer Review $ 4,800 

Network Software Maintenance $ 6,000 

IT Assessments $ 6,000 

Other 

Subtotal – Operations (7%) $ 47,300 

Total Estimated Annual Cost $ 816,200 

* = These positions are funded to the next higher grade level paid for by the host park. 
133

development of long-term monitoring protocols with detailed standard operating procedures 

present high upfront costs that are expected to decrease as each protocol is completed and phased 

into implementation. Implementation costs are expected to reduce especially for protocols that 

have a cyclic sampling design. Some monitoring protocols collect data only during certain years. 

During an off year for a particular program, there may be no associated project cost, which 

liberates funding for other projects during that year. 

Table 0.3 Estimated annual vital signs project costs for FY05-FY09. 

Level 1 

Category Network Vital Sign 

SFAN 

VS Rank Year One 

% of Total 

Budget 

Air and Weather and Climate 1 $ 16,250 2% Climate Air Quality (done by the ARD) 4 $ 0 0% 

Water Freshwater Dynamics 14 $ 21,000 3% 

Freshwater Quality 3 $ 92,000 11% 

Landbird Dynamics 17 $ 44,000 5% 

Raptors and Condors 18 $23,000 3% 

T&E Butterflies 13 TBD TBD 

Pinnipeds 10 $29,000 4% 

Amphibians and Reptiles 8 TBD TBD 

Western Snowy Plover 9 $ 5,000 1% 

Northern Spotted Owl 7 $ 35,000 4% 

Stream Fish Assemblages 5 $ 59,000 7% 

Rare Plant Species 6 $ 13,000 2% 

Invasive Plant Species (early detection) 2 $ 65,000 8% 

Wetlands 15 TBD TBD 

Riparian Habitat 16 TBD TBD 

Biological 

Integrity 

Plant Community Change 11 13,000 TBD 

Ecosystem 

Pattern and 

Processes 

Landscape Dynamics 12 TBD TBD 

Subtotal Vital Signs Monitoring $ 415,250 51 % 

Program Management $ 95,000 12% 

Administration $ 25,000 3% 

Program Data Management $ 213,000 26% 

Operations (travel and training) 

 Misc. Costs (travel, training, special 

projects, etc) $ 67,950 8% 

Subtotal Program Management $ 400,950 49 % 

TOTAL $ 816,200 100 % 

At the time of completion of this monitoring plan, nine protocols will have been largely 

completed or submitted for review. Water quality and streamfish assemblages have been 

completed and will be implemented in FY06. Spotted owl and pinniped protocols have been 

submitted for review and will continue to be monitored in FY06. Draft protocols are nearly 

complete for weather, snowy plovers, freshwater dynamics, raptors and condors, and landbirds. 
134

Costs have been especially high for some of these protocols because the I&M program is 

supporting not only the protocol development but has also been supporting continued monitoring 

for previously existing monitoring efforts (e.g. pinnipeds, snowy plovers, weather, raptors and 

condors). Once the nine protocols are completed, funds will become available to develop 

protocols for the remainig high priority vital signs. The next set of selected protocols for 

development include: invasive species, rare plant species, and community assemblages. The final 

set of protocols that will be developed are amphibians and reptiles, wetlands, riparian habitat, 

and landscape dynamics. 

10.5 Projected Costs 

Personnel expenses for federal employees often increase annually because of cost of living 

adjustments and raises. These raises are not always covered by increases in ONPS base funding 

to parks and Networks. Additionally, permanent and term staff get step (time-in-grade) increases 

over time, another source of inflating fixed operating costs. Since the increase in park funds does 

not total the salary increase, park and Network budgets erode steadily. None of these increases 

are currently covered by the I&M and WRD funding; therefore, the buying power of the funds 

we receive erodes each year. 

As the infrastructure costs increase, the amount of money left for projects decreases. One way to 

deal with budgetary erosion is to seek additional funding. This is a key strategy which the 

network has been and will continue to employ. Through the teamwork of the Board of Directors, 

the TSC, and the Network Coordinator, the SFAN will aggressively pursue additional funding 

and partnerships for its monitoring program, with both the long and short term in mind. 

As the protocols become better defined, the projected operating costs will become clearer. This 

will help forecast program costs. The Network Coordinator and the Board of Directors will lead 

network efforts to provide funding and other resources to fuel the SFAN Vital Signs Monitoring 

Program. SFAN will utilize the existing I&M funding allocation as seed money from which to 

create the most robust, informative, useful and productive network vital signs monitoring 

program possible. SFAN will employ the creative use of partnerships, allegiances, and existing 

internal and external programs to help reach the service-wide monitoring program goals. 
135

Chapter 11 Literature Cited 

Adams, D. 1989. Incidence of pine pitch canker in California 1988-1989. California Department 

of Forestry and Fire Protection. Sacramento, CA. 

Adriano, D.C. and M. Havas. 1990. Acidic precipitation. Springer-Verlag, New York, NY. 

Avise, J. C., and R. L. Crawford. 1981. A matter of lights and death. Nat. Hist. 90: 6-14. 

American Public Health Association. 1998. Standard methods for the examination of water and 

wastewater (18th ed.), American Public Health Association, Washington, D.C. 

Andreasen, J.K., R.V. O’Neill, R. Noss, and N. C. Slosser. 2001. Considerations for the 

development of a terrestrial index of ecological integrity. Ecological Indicators 1:21–35. 

Association of Bay Area Governments. 2000. City, county, and census tract forecasts 1999- 

2020. Association of Bay Area Governments, San Francisco, California. 

Bakun, A. 1990. Global climate change and intensification of coastal ocean upwelling. Science, 

247:198-201. 

Bailey, R.G. 1995. Description of the ecoregions of the United States. Publication No. 1391. USDA, 

Forest Service. 

Barbour, M.G., J.H. Burk, and W.D. Pitts. 1980. Terrestrial plant ecology. The 

Benjamin/Cummings Publishing Co., Menlo Park, California. 

Barrett, W. G., G. M. VanDyne, and E. P. Odum. 1976. Stress ecology. BioScience 26:192-194. 

Beamish, R.J. and Bouillon, D.R. 1993. Pacific salmon production trends in relation to climate. 

Canadian Journal of Fisheries and Aquatic Sciences 50;1002-1016. 

Bean, M.J., and M.J. Rowland. 1997. Evolution of national wildlife law. Third edition. Paeger 

Publishers, Westport, CT. 

Benson, A.J. and A.W. Trites. 2002. Ecological effects of regime shifts in the Bering Sea and 

eastern North Pacific Ocean. Fish and Fisheries 3:95-113. 

Bloom, A.L. 1998. Geomorphology: a systematic analysis of late cenozoic landforms, 3rd ed. 

Prentice-Hall. 

Blackburn, T.C. & K. Anderson, editors (1993). Before the wilderness: environmental 

management by native Californians. Ballena Press, Menlo Park, CA. 
136

Bondello, M. 1976. The effects of high-intensity motorcycle sounds on the acoustical sensitivity 

of the desert iguana, Dipsosaurus dorsalis. Thesis. California State University, Fullerton. 

Botkin, D. and E. Keller. 1995. Environmental science: earth as a living planet. John Wiley & 

Sons, Inc. Canada. 

Bricker, S.B., Clement, C.G., Pirhalla, D.E., Orlando, S.P., and Farrow, D.G.G. 1999. National 

estuarine eutrophication assessment: effects of nutrient enrichment in the nation’s estuaries. 

Special Projects Office and the National Centers for Coastal Ocean Science. National Ocean 

Service, National Oceanic and Atmospheric Administration, Silver Springs, MD. 

Brooks, K.N. (ed.) 2003. Hydrology and the management of watersheds, 3rd ed. Iowa State 

University Press. 

Brown, A.L. 1990. Measuring the effect of aircraft noise on sea birds. Environment International 

16: 587-592. 

California Department of Water Resources. 1998. Guidelines for preparing quality assurance 

project plans for projects involving physical and chemical measurements of water quality. 

California State Water Resources Control Board. 2001 California ocean plan. California 

Department of Water Resources, Sacramento. 

Carter, R.W.G. 1988. Coastal environments: an introduction to the physical, ecological and 

cultural systems of coastlines. Academic Press, London, UK. 

Carter, R.W.G. and C.D.Woodroffe (eds.) 1994. Coastal evolution: late quaternary shoreline 

morphodynamics. Cambridge University Press, Cambridge, UK. 

Chapin III, F.S., P.A. Matson, H.A. Mooney, and M.C. Chapin. 2002. Principles of terrestrial 

ecosystem ecology. Springer Verlag, New York, NY. 

Chapin III, F.S., B.H. Walker, R.J. Hobbs, D.U. Hooper, J.H. Lawton, O.E. Sala, and D. Tilman. 

1997. Biotic control over the functioning of ecosystems. Science 277: 500-504. 

Chappelka, A., L. Samuelson, J. Skelly, and A. Lefohn. 1996. Effects of ozone on forest trees in 

the Southern Appalachians; an assessment of the current state of knowledge. Report to the 

Southern Appalachian Mountains Initiative. 

Chappelka, A., G. Somers, and J. Renfro. 1999. Visible ozone injury on forest trees in Great 

Smoky Mountains National Park, USA. Water, Air, and Soil Pollution 116: 255-260. 

Cooprider, M. 2005. San Francisco Bay Area Network freshwater quality monitoring protocol: 

version 2.01. National Park Service. Point Reyes National Seashore. Point Reyes Station, 

California. 
137

Cooprider, M. 2004. Preliminary SFAN Water Quality Status Report. National Park Service. 

Unpublished report. 

Croll, D. A., B. B. Marinovic, and M. Mangel. 2000. Climate change and trophic links in coastal 

upwelling centers. Http://nigec.ucdavis.edu/publications/ar/annual2000/westgec/ Croll/

Accessed 2003, 2 July. 

Crossley, Jr., D.A. and D. C. Coleman. 2003. Fundamentals of soil ecology. Academic Press, 

Orlando, FL. 

Dallman, P.R. 1998. Plant life in the world's mediterranean climates. California Native Plant 

Society with University of California Press, Berkeley CA 

Davis, G.E. 2005. National Park stewardship and ‘vital signs’ monitoring: a case study from 

Channel Islands National Park, California. Aquatic Conserv. Mar. Freshw. Ecosyst. 15:71-

89. 

DeBano, L.F., N.G. Neary, and P.F. Ffolliott. 1998. Fire's effect on ecosystems. John Wiley & 

Sons, Inc. New York, NY. 

De Leo, G. A. and S. Levin. 1997. The multifaceted aspects of ecosystem integrity. Conservation 

Ecology [online] 1: 3. Http://www.consecol.org/vol1/iss1/art3. Accessed 2005, 12 

September. 

Drost, Charles A. and Gary M. Fellers. 1995. Non-native animals on public lands. Status and 

Trends Report. Pp. 440 - 442. In: Edward T. LaRoe, Gaye S. Farris, Catherine E. Puckett, 

Peter D. Doran, and Michael J. Mac (eds). Our Living Resources. U.S. Dept. Interior - 

National Biological Service, Wash. D.C. 

Elzinga, Caryl L., D. W. Salzer, and J. W. Willoughby. 1998. Measuring and monitoring plant 

populations. BLM Tech. Reference 1730-1. BLM/RS/ST-98/005+1730. 

Environmental Protection Agency (EPA). 1999. National air quality and emissions trends report. 

EPA report #454/R-00-003. Washington DC. 

Environmental Protection Agency (EPA). 2002. Consolidated assessment and listing 

methodology. Toward a compendium of best practices. Office of wetlands, Oceans, and 

Watersheds. Washington DC. 

Federal Geographic Data Committee. 1998. FDGC-STD-001-1998. Content standard for digital 

geospatial metadata. Federal Geographic Data Committee. Washington DC. 

Fetter, C.W. 2000. Applied hydrogeology, 4th ed. Prentice-Hall Publishers. Englewood Cliffs, 

New Jersey 
138

Fong, D. and L. Canevaro. 1998. Winter 1997-1998 water quality monitoring at Golden Gate 

dairy tributary. U.S. Department of Interior, National Park Service. 

Gordon, N.C., T.A. McMahon, and B. Finlayson. 1992. Stream hydrology: an introduction for 

ecologists. John Wiley and Sons, Inc. 

Grossman, D.H., D. Faber-Langendoen, A.W. Weakley, M. Anderson, P. Bourgeron, R. 

Crawford, K. Goodin, S. Landaal, K. Metzler, K.D. Patterson, M. Pyne, M. Reid, and L. 

Sneddon. 1998. International classification of ecological communities: terrestrial vegetation 

of the United States. Volume I. The National Vegetation Classification System: 

Development, status, and applications. The Nature Conservancy, Arlington, Virginia. 

Holling, C. S. 1986. The resilience of terrestrial ecosystems: local surprise and global change. 

Pp. 292-320 in W. M. and R. E. Munn (eds.). Sustainable Development of the Biosphere. 

Oxford University Press. 

Hyrenback, K.D. and R.C. Dotson. 2001. Post-breeding movements of a male Black-footed 

Albatross Phoebastria nigripes. Marine Ornithology 29: 7-10. 

Jackson, L.E., J. C. Kurtz and W. S. Fisher (eds.) 2000. Evaluation guidelines for ecological 

indicators. EPA/620/R-99/005. U.S. Environmental Protection Agency, Office of Research 

and Development, Research Triangle Park, NC. 

Jenkins, K., A. Woodward, and E. Schreiner. 2002. A Framework for Long-term Ecological 

Monitoring in Olympic National Park: Prototype for the Coniferous Forest Biome. U.S. 

Geological Survey Forest and Rangeland Ecosystem Science Center, Olympic Field Station, 

Port Angeles, WA. 

Jensen, S.P. and P. Honess. 1995. The influence of moonlight on vegetation height preference 

and trappability of small mammals. Mammalia 59: 35-42. 

Karr, J. R. and D. R. Dudley. 1981. Ecological perspective on water quality goals. Environmental 

Management. 5: 55-68. 

Kelly, J.P. and K. Etienne. 1999. Inventory of winter waterbirds and shorebirds on Tomales Bay, 

1998-1999. A report to the Point Reyes National Seashore. Audubon Canyon Ranch 

TechnicalReport #89-12-5, Marshall, CA. 

Ketcham, B. 2001. Point Reyes National Seashore water quality monitoring report. U.S. 

Department of Interior, National Park Service, Point Reyes National Seashore, Point Reyes 

Station, California. 

Lambeck, R.J. 1997. Focal species: a multi-species umbrella for nature conservation. 

Conservation Biology 11: 849-856. 
139

Likens, G. 1992. An ecosystem approach: its use and abuse. Excellence in Ecology, book 3. 

Ecology Institute, Oldendorf/Luhe, Germany. 

Mack, R. N., D. Simberloff, W. M. Lonsdale, H. Evans, M. Clout, and F. A. Bazzaz. 2000. 

Biotic invasions: causes, epidemiology, global consequences, and control. Ecological 

Applications 10: 689-710. 

Mantua, N.J., Hare, S.R., Zhang,Y.,Wallace, J.M. and Francis, R.C. (1997) A Pacific 

interdecadal climate oscillation with impacts on salmon production. Bulletin of the American 

Meteorological Society 78:1069-1079. 

McDonald, L. T. 2003. Environmental trend detection: a review. Environmental Montoring and 

Assesment 85: 277-292. 

Meyer, M.D. and P.M. Schiffman. 1999. Fire season and mulch reduction in a California 

grassland: a comparison of restoration strategies. Madrono 46(1): 25-37. 

Moratto, M. J. 1984. California Archaeology. Academic Press, Orlando, FL. 

Myers, N., R. A. Mittermeier, C. G. Mittermeier, G. A. B. da Gonseca, and J. Kent. 2000. 

Biodiversity hotspots for conservation priorities. Nature 403: 853-858. 

National Academy of Sciences (NAS). 2000. Ecological indicators for the nation. National 

Academy Press. 180. 

National Assessment Synthesis Team (NAST). 2001. Climate change impacts on the United 

States: the potential consequences of climate variability and change overview. U. S. Global 

Change Research Program. Cambridge University Press, Cambridge,UK. 

National Oceanic and Atmospheric Administration (NOAA). 2003. Socioeconomic research and 

monitoring recommendations for marine protected areas in the Channel Islands National 

Marine Sanctuary. NOAA, National Ocean Service, Special Projects: Silver Spring, 

Maryland. July 2003. 

National Park Service. 2001. Director’s order 19: records management. National Park Service. 

Washington DC. http://www.nps.gov/refdesk/DOrders/DOrder19.html. Accessed 2005, 14 

September. 

National Park Service. 1997. The visitor experience and resource protection (VERP) framework: 

a handbook for managers. U.S. Department of Interior, National Park Service, Denver 

Service Center. 

National Park Service. 1995. NPS -75. U.S. Department of Interior, National Park Service. 

http://science.nature.nps.gov/im/monitor/nps75.pdf. Accessed 2005, 2 September. 
140

National Park Service Organic Act, 16 U.S.C. 1 et seq. (1988), Aug. 25, 1916, Ch. 408, 39 Stat. 

535. 

National Park Service Omnibus Management Act, Pub. L. No. 105-391, Nov. 13, 1998, 112 Stat. 

3498. National Park Service Management Policies. 2001. U.S. Department of Interior, 

National Park Service. 

National Weather Service. 2003. Forecast Office, San Francisco Bay Area/Monterey, 

Climatological data. http://www.wrh.noaa.gov/monterey/climate.html. Accessed 2003, 26 

June. 

Noon, B. R., T. A. Spies, and M. G. Raphael. 1999. Conceptual basis for designing an 

effectiveness monitoring program. Chpt. 2 In: The strategy and design of the effectiveness 

monitoring program for the Northwest Forest Plan. USDA Forest Service Gen. Tech. Rept. 

PNW-GTR-437. 

Noss, R. 1990. Indicators for monitoring biodiversity: a hierarchical approach. Conservation Biology 

4: 355-364. 

NPCA (National Parks Conservation Association). 1977. Summary of National Parks Conservation 

Association survey of feral animals in the national park system. National Parks and 

Conservation Magazine 51: 16-20. 

Oakley, K., L. Thomas, and S. Fancy. 2003. Guidelines for long-term monitoring. Wils. Soc. 

Bull. 31: 1000-1003 

Paine, R. T. 1969. A note on trophic complexity and community stability. American Naturalist 

103:91-93. 

Press, D. 2005. SFAN Data Management Plan. San Francisco Bay Area Inventory and 

Monitoring Program, Golden Gate National Recreation Area, San Francisco, California. 

Ralph, C.J., J. R. Sauer, and S. Droege. 1995. Monitoring bird populations by point counts. Gen. 

Tech. Rep. PSDW-GTR-149. Albany, CA: Forest Service, U.S. Dept. Agriculture. 

Regart, J.R. 1991. Physical parameters associated with coho salmon (Oncorhynchus kisutch) 

redds in northwest California. Thesis. Humboldt State University, Arcata, CA. 

Rizzo, D.M. and M. Garbelotto. 2003. Sudden oak death: endangering California and Oregon 

forest ecosystems. Frontiers in Ecology and the Environment 1(5): 197-204. 

Roman, C. T. and N. E. Barrett. 1999. Conceptual framework for the development of long-term 

monitoring protocols at Cape Cod National Seashore. U.S. Geological Survey, Patuxent 

Wildlife Research Center. http://science.nature.nps.gov/im/monitor/networks/caco.pdf . 

Acccessed 2005, 14 September. 
141

Rosenlieb, G., P. Penoyer, B. Jackson, and D. Kimball. 2002. Recommendations for core water 

quality monitoring parameters and other key elements of the NPS vital sings program water 

quality monitoring component. National Park Service, Freshwater Workgroup Subcommittee 

Meeting, August 14, 2002. Fort Collins, CO. 

San Francisco Bay Area Network (SFAN). 2004. SFAN Phase III Vital Signs Monitoring Plan. 

Unpublished. U.S. Department of Interior, National Park Service. 

San Francisco Bay Area Network (SFAN). 2003. SFAN Phase II Vital Signs Monitoring Plan. 

Unpublished. U.S. Department of Interior, National Park Service. 

 

San Francisco Bay Area Network (SFAN). 2001a. Charter of the San Francisco Bay Area 

Network. San Francisco Bay Area Inventory and Monitoring Program, Golden Gate National 

Recreation Area, San Francisco, California. 

San Francisco Bay Area Network (SFAN). 2001b. SFAN Phase I Vital Signs Monitoring Plan. 

Unpublished. U.S. Department of Interior, National Park Service. 

Sawyer, J.O., and T. Keeler-Wolf. 1995. A manual of California vegetation. California Native 

Plant Society. Sacramento. 

Simberloff, D. 1998. Flagships, umbrellas, and keystones: is single-species management passé in 

the landscape era? Biological Conservation 83:247-257. 

Spellerberg, I.F. 1991. Monitoring Ecological Change. Cambridge University Press. 

Stiling, P., Moon, D.C., Hunter, M.D., Colson, J., Rossi, A.M., Hymus, G.J. and Drake, B.G. 

2002. Elevated CO2 lowers relative and absolute herbivore density across all species of a 

scrub-oak forest. Oecologia 134: 82-87. 

Tegler, B., M. Sharp, and M. A. Johnson. 2001. Ecological monitoring and assessment network’s 

proposed core monitoring variables: an early warning of environmental change. 

Environmental Monitoring and Assessment 67: 29-56. 

Tilman, D. 1999. The ecological consequences of changes in biodiversity: a search for general 

principles. Ecology 80: 1455-1474. 

Thurman, H.V. 1988. Introductory Oceanography, 5th ed. Merrill Publishing Co. 

UNESCO. 1995. Biosphere reserves in action: case studies of the american experience . U.S. 

Department of Commerce Department of State Publication 10241, Bureau of Oceans and 

International Environmental and Scientific Affairs. Springfield, Virginia. 

http://www.mabnetamericas.org/publications/case.html#ele1. Accessed 2005, 4 September. 
142

Valentine, J. 1966. Numerical analysis of marine molluscan ranges on the extratropical 

northeastern Pacific Shelf. Limnology and Oceanography 11:198-211. 

Wilcove, D. S., C. H. McLellan, and A. P. Dobson. 1986. Habitat fragmentation in the temperate 

zone. In Michael E. Soule, ed. Conservation Biology: The Science of Scarcity and Diversity, 

pp. 237-256. Sinauer Assoc., Sunderland, MA. 

Woodley, S. 1993. Monitoring and measuring ecosystem integrity in Canadian National Parks. pp. 

155-175 in S. Woodley, J. Kay, and G. Francis, editors. Ecological Integrity and the Management 

of Ecosystems. St. Lucie Press, Delray Beach, FL. 
143

Glossary 

Adaptive Management is a systematic process for continually improving management policies 

and practices by learning from the outcomes of operational programs. In its most effective form–

"active" adaptive management–employs management programs that are designed to 

experimentally compare selected policies or practices by evaluating alternative hypotheses about 

the system being managed. 

Attributes are any living or nonliving feature or process of the environment that can be 

measured or estimated and that provide insights into the state of the ecosystem. The term 

Indicator is reserved for a subset of attributes that is particularly information-rich in the sense 

that their values are somehow indicative of the quality, health, or integrity of the larger 

ecological system to which they belong (Noon et al. 1999). See Indicator. 

Biological integrity has been defined as the capacity to support and maintain a balanced, integrated, 

adaptive community of organisms having a species composition, diversity, and functional 

organization comparable to that of natural habitats of the region (Karr and Dudley 1981). 

Co-location refers to sampling of the same physical units in multiple monitoring protocols 

Conceptual Models are purposeful representations of reality that provide a mental picture of 

how something works to communicate that explanation to others. 

Driver are the major external driving forces that have large-scale influences on natural systems. 

Drivers can be natural forces or anthropogenic. 

Ecological effects are the physical, chemical and biological responses to drivers and stressors. 

Ecological integration involves considering the ecological linkages among system drivers and the 

components, structures, and functions of ecosystems when selecting monitoring indicators. 

Ecological (ecosystem) integrity is a concept that expresses the degree to which the physical, 

chemical, and biological components (including composition, structure, and process) of an 

ecosystem and their relationships are present, functioning, and capable of self-renewal. 

Ecological integrity implies the presence of appropriate species, populations and communities 

and the occurrence of ecological processes at appropriate rates and scales as well as the 

environmental conditions that support these taxa and processes. Indicators of ecosystem integrity 

are aimed at early-warning detection of presently unforeseeable detriments to the sustainability or 

resilience of ecosystems. 

Ecosystem is defined as, "a spatially explicit unit of the Earth that includes all of the organisms, 

along with all components of the abiotic environment within its boundaries" (Likens 1992). 

Three main ecosystems were identified for the network of parks; terrestrial, wetland and marine. 
144

Ecosystem drivers are major external driving forces such as climate, fire cycles, biological 

invasions, hydrologic cycles, and natural disturbance events (e.g., earthquakes, droughts, floods) that 

have large scale influences on natural systems. Trends in ecosystem drivers will suggest what kind of 

changes to expect and may provide an early warning of presently unforeseen changes to the 

ecosystem. Natural ecosystem processes include both external and internal forces and processes 

(e.g., herbivory, respiration, productivity).

Ecosystem management is the process of land-use decision making and land-management 

practice that takes into account the full suite of organisms and processes that characterize and 

comprise the ecosystem and is based on the best understanding currently available as to how the 

ecosystem works. Ecosystem management includes a primary goal of sustainability of ecosystem 

structure and function, recognition that ecosystems are spatially and temporally dynamic, and 

acceptance of the dictum that ecosystem function depends on ecosystem structure and diversity. 

Coordination of land-use decisions is implied by the whole-system focus of ecosystem 

management. 

Focal resources are park resources that, by virtue of their special protection, public appeal, or other 

management significance, have paramount importance for monitoring regardless of current threats or 

whether they would be monitored as an indication of ecosystem integrity. Focal resources might 

include ecological processes such as deposition rates of nitrates and sulfates in certain parks, or they 

may be a species that is harvested, endemic, alien, or has protected status. 

Forms are sub-categories within each ecosystem. Marine forms include ocean, sandy beach, 

rocky intertidal, bay/estuary; aquatic/wetland forms include running water, standing water, and 

ground water and apply to both freshwater and saltwater wetlands; and terrestrial forms include 

grassland, shrubland, woodland, and distinct landforms (e.g., serpentine). 

Indicators are a subset of monitoring attributes that are particularly information-rich in the sense 

that their values are somehow indicative of the quality, health, or integrity of the larger 

ecological system to which they belong (Noon et al. 1999). Indicators are a selected subset of the 

physical, chemical, and biological elements and processes of natural systems that are selected to 

represent the overall health or condition of the system, known or hypothesized effects of 

stressors, or elements that have important human values. 

Measures are the specific feature(s) used to quantify an indicator, as specified in a sampling 

protocol. 

Metadata: Data about data. Metadata describes the content, quality, condition, and other 

characteristics of data. It's purpose it to help organize and maintain a organization's internal 

investment in spatial data, provide information about an organization's data holdings to data 

catalogues, clearinghouses, and brokerages, and provide information to process and interpret data 

received through a transfer from an external source. 

Monitoring: collection and analysis of repeated observations or measurements to evaluate 

changes in condition and progress toward meeting a management objective (Elzinga et al. 1998). 

Detection of a change or trend may trigger a management action, or it may generate a new line of 
145

inquiry. Monitoring is often done by sampling the same sites over time, and these sites may be a 

subset of the sites sampled for the initial inventory. 

Programmatic integration involves the coordination and communication of monitoring 

activities within and among parks, among divisions of the NPS Natural Resource Program 

Center, and among the NPS and other agencies, to promote broad participation in monitoring and 

use of the resulting data. At the park or network level, for example, the involvement of a park’s 

law enforcement, maintenance, and interpretative staff in routine monitoring activities and 

reporting results in a well-informed park staff, wider support for monitoring, improved potential 

for informing the public, and greater acceptance of monitoring results in the decision-making 

process. 

Protocols are detailed study plans that explain how data are to be collected, managed, analyzed 

and reported and are a key component of quality assurance for natural resource monitoring 

programs (Oakley et al. 2003). 

Resource realms include four major categories— biosphere, hydrosphere, atmosphere, and 

lithosphere. These realms were used to conceptualize broad categories of interrelated ecosystem 

processes and components. 

Socio-political forces are the laws, mandates, economic pressures and environmental 

perceptions influencing political decisions that bear upon anthropogenic stressors, and thereby, 

have a cascading effect on ecosystem function. These can include environmental laws (ESA, 

CWA, etc.), budgets, and changing social values. 

Spatial integration involves establishing linkages of measurements made at different spatial scales 

within a park or network of parks, or between individual park programs and broader regional 

programs (i.e., NPS or other national and regional programs). 

Stressors are physical, chemical, or biological perturbations to a system that are either (a) foreign 

to that system or (b) natural to the system but applied at an excessive [or deficient] level (Barrett 

et al. 1976). Stressors cause significant changes in the ecological components, patterns and 

processes in natural systems. Examples include water withdrawal, pesticide use, timber 

harvesting, traffic emissions, stream acidification, trampling, poaching, land-use change, and air 

pollution. Anthropogenic stressors are those perturbations to a system that directly result from 

human activity. Monitoring of stressors and their effects, where known, will ensure short-term 

relevance of the monitoring program and provide information useful to management of current 

issues. 

Temporal integration involves establishing linkages between measurements made at various 

temporal scales. It requires nesting the more frequent and, often, more intensive sampling within the 

context of less frequent sampling. 

Trend refers to directional change measured in resources by monitoring their condition over 

time. Trends can be measured by examining individual change (change experienced by 
146

individual sample units) or by examining net change (change in mean response of all sample 

units). 

Umbrella species are typically large-bodied, wide-ranging species that require large patches of 

habitat and corridors connecting these patches to maintain viable populations. By protecting 

areas large enough to maintain these species, sufficient habitat 

can also be maintained which ensures the viability of most other species in that area. 

Vital Signs, as used by the National Park Service, are the subset of indicators chosen a by park 

or park network as part of the vital signs monitoring program. They are defined as any 

measurable feature of the environment that provides insights into changes in the state of the 

ecosystem. Vital signs are intended to track changes in a subset of park resources and processes 

that are determined to be the most significant indicators of ecological condition of those specific 

resources that are of the greatest concern to each park. This subset of resources and processes is 

part of the total suite of natural resources that park managers are directed to preserve 

“unimpaired for future generations,” including water, air, geological resources, plants and 

animals, and the various ecological, biological, and physical processes that act on these 

resources. Vital signs may occur at any level of organization including landscape, community, 

population, or genetic levels, and may be compositional (referring to the variety of elements in 

the system), structural (referring to the organization or pattern of the system), or functional 

(referring to ecological processes).