Designing Monitoring Programs 

in an Adaptive Management 

Context for Regional Multiple 

Species Conservation Plans 

 

 

 

 

 

 

 

U.S. DEPARTMENT OF THE INTERIOR CALFORNIA DEPARTMENT U. S. FISH AND 

U.S. GEOLOGICAL SURVEY OF FISH AND GAME WILDLIFE SERVICE 

WESTERN ECOLOGICAL RESEARCH CENTER 
 ii 

Designing Monitoring Programs in an 

Adaptive Management Context for Regional 

Multiple Species Conservation Plans 

By Andrea J. Atkinson1, Peter C. Trenham1, Robert N. Fisher1, 

Stacie A. Hathaway1, Brenda S. Johnson2, Steven G. Torres3, 

and Yvonne C. Moore4 

U.S. GEOLOGICAL SURVEY 

WESTERN ECOLOGICAL RESEARCH CENTER 

In partnership with 

CALIFORNIA DEPARTMENT OF FISH AND GAME and U. S. FISH AND WILDLIFE SERVICE 

HABITAT CONSERVATION DIVISION CARLSBAD, CA 

1

San Diego Field Station 

U. S. Geological Survey, Western Ecological Research Center 

5745 Kearny Villa Road, Suite M 

San Diego, CA 92123 

2

California Department of Fish and Game 

Habitat Conservation Planning Branch 

1416 Ninth Street, 12th Floor 

Sacramento, CA 95814 

3

California Department of Fish and Game 

Resource Assessment Program 

1416 Ninth Street, RM 1342-C 

Sacramento, CA 95814 

4

California Department of Fish and Game 

Resource Assessment Program 

4500 Glenwood Drive, Bldg. C 

Riverside, CA 92501 

Sacramento, California 

2004 
 iii 

U.S. DEPARTMENT OF THE INTERIOR 

GALE A. NORTON, SECRETARY

U.S. GEOLOGICAL SURVEY 

Charles G. Groat, Director 

Front Cover Photographs (clockwise from upper left): 

Otay Tarplant, Hemizonia conjugens (© 2001 Coralie Cobb) 

Mountain lion, Felis concolor (courtesy of Adam Backlin, U.S. Geological Survey; used with permission from The 

Nature Conservancy; photograph has been retouched to remove a branch in foreground) 

Pallid Bat, Antrozous pallidus (courtesy of Drew Stokes, U.S. Geological Survey) 

Coachella Valley sand dunes (© Gary Nafis) 

Coast horned lizard, Phrynosoma coronatum, (courtesy of Chris Brown, U.S. Geological Survey) 

Least Bell’s vireo, Vireo bellii pusillus (courtesy of Paul Zedler, University of Wisconsin) 

The use of firm, trade, or brand names in this report is for identification purposes only and 

does not constitute endorsement by the U.S. Geological Survey. 

For additional information, contact: 

Center Director 

Western Ecological Research Center 

3020 State University Dr., East 

Modoc Hall, Room 3006 

Sacramento, CA 95819 
 iv 

TABLE OF CONTENTS 

SUMMARY ............................................................................................. 1 

1.0 INTRODUCTION ................................................................................. 2 

2.0 MONITORING IN AN ADAPTIVE MANAGEMENT CONTEXT..................... 3 

3.0 CHALLENGES IN CREATING REGIONAL CONSERVATION PLAN 

 MONITORING PROGRAMS .................................................................. 7 

 3.1 Addressing both covered species and ecosystem integrity ...................... 7 

 3.2 Coordinating and integrating monitoring from local to ecoregional scales ... 7 

 3.3 Acknowledging a high degree of uncertainty ........................................ 8 

 3.4 Phasing-in monitoring program development ...................................... 8 

 3.5 Accommodating staged development of a reserve system network ............. 9 

4.0 STEPWISE APPROACH TO CREATING A MONITORING PROGRAM ........ 10 

4.1 Step 1. Identify the goals and objectives of the regional conservation plan ... 11 

4.2 Step 2. Identify the scope of monitoring program ................................. 11 

4.3 Step 3. Compile information relevant to monitoring program design .......... 12 

4.4 Step 4. Strategically divide the system and set priorities .......................... 13 

4.5 Step 5. Develop simple management-oriented conceptual models ............... 18 

4.6 Step 6. Determine what to monitor and identify critical uncertainties ....... 28 

4.7 Step 7. Determine strategy for implementing monitoring ......................... 34 

4.8 Step 8. Develop data quality assurance, data management, analysis, and 

reporting strategies ........................................................................ 39 

4.9 Step 9. Complete the adaptive management loop by ensuring effective 

 feedback to decision-making ............................................................ 40 

5.0 ADDITIONAL CONSIDERATIONS FOR DESIGNING THE MONITORING 

PROGRAM ............................................................................................41 

6.0 CONCLUSIONS .................................................................................... 42

7.0 ACKNOWLEDGEMENTS ..................................................................... 42 

8.0 ACRONYMS ..................................................................................... 43 

9.0 GLOSSARY ......................................................................................... 44 

APPENDIX A. Suggested components of natural community assemblage conceptual 

models ............................................................................................ 49 

APPENDIX B. Suggested components of landscape-level conceptual models .............. 50 

APPENDIX C. A strategy for linking monitoring of NCCP/HCP covered species with 

ecosystem monitoring ........................................................................... 51 

APPENDIX D. Habitat monitoring as a surrogate for species monitoring ................. 53
 v 

APPENDIX E. Characteristics of good monitoring variables ................................. 54 

APPENDIX F. Species-level monitoring variables ............................................... 55 

APPENDIX G. Natural community assemblage monitoring variables ..................... 56 

APPENDIX H. Landscape-level monitoring variables ......................................... 58 

APPENDIX I. Sampling design approaches that are receiving increased attention ........ 59 

APPENDIX J. Quality assurance plan ............................................................. 60 

REFERENCES .......................................................................................... 61 

LIST OF FIGURES 

Figure 1. NCCP/HCP adaptive management feedback loop .................................... 6 

Figure 2. Monitor at the appropriate geographic scale ........................................ 8 

Figure 3. Key components of management-oriented conceptual models ..................... 21 

Figure 4. Hypothetical hierarchy of nested conceptual models ............................... 23 

Figure 5. Species-focused conceptual model for southwestern arroyo toad (Bufo 

californicus) ...................................................................................... 24 

Figure 6. Aeolian sand natural community assemblage conceptual model of pressures 

on covered species .............................................................................. 25 

Figure 7. Aeolian community sand process model ............................................... 26 

Figure 8. Tasks to occur in planning phase and early implementation of an NCCP/HCP 35 

LIST OF BOXES 

Box 1. Comparison of two covered species requiring different levels of initial focus in an 

NCCP/HCP monitoring program .......................................................... 15 

Box 2. Dividing system into natural community assemblages ............................... 17 

Box 3. Typical landscape-level issues that involve multiple natural community 

assemblages or otherwise require special attention ..................................... 18 

Box 4. Suggested components of covered species conceptual models ........................ 22 

Box 5. Conservation strategy and management activities portion of the aeolian sands 

natural community assemblage conceptual model ....................................... 27 

Box 6. Description of monitoring variables ....................................................... 31

This report should be cited as: 

Atkinson, A. J., P. C. Trenham, R. N. Fisher, S. A. Hathaway, B. S. Johnson, S. G. Torres, and 

Y. C. Moore. 2004. Designing monitoring programs in an adaptive management context for 

regional multiple species conservation plans. U.S. Geological Survey Technical Report. USGS 

Western Ecological Research Center, Sacramento, CA. 69 pages. 
 1 

SUMMARY 

Increasing numbers of regional, multiple species conservation plans have been developed in 

California since the early 1990s. However, building effective monitoring and adaptive 

management programs to support these plans has remained a challenge. In addition to collecting 

data on the status of resources and the results of management actions, monitoring programs for 

these plans need to resolve critical uncertainties and channel information into effective decisionmaking. Because of the broad goals of many regional conservation plans, monitoring programs 

need to address ecosystem integrity and biodiversity while also tracking species “covered” by 

plan permits. 

In this document we provide a step-by-step procedure for developing effective monitoring 

programs in an adaptive management context. The guidance provided here has been gleaned 

from experience with large multiple species plans in southern California. The process begins 

with clearly defining program objectives, partitioning the program into manageable but 

meaningful pieces, and developing management-oriented conceptual models of system function. 

Then, based on the objectives and conceptual models, monitoring recommendations and critical 

uncertainties can be identified and a coordinated program designed. We include practical 

examples and insights from programs in southern California and discuss the evolution of 

monitoring and adaptive management programs through three successive stages: 1) inventorying 

resources and identifying relationships; 2) pilot testing of long-term monitoring and resolving 

critical management uncertainties; and 3) implementing long-term monitoring and adaptive 

management. Ultimately, the success of regional conservation planning depends on the ability of 

monitoring programs to confront the challenges of adaptively managing and monitoring complex 

ecosystems and diverse arrays of sensitive species. 
 2 

1.0 INTRODUCTION 

Landscape-scale conservation planning is increasingly being used as a tool for resolving conflicts 

between urbanization and threatened and endangered species, particularly in biologically rich 

regions that are experiencing unprecedented human population growth. To address these 

challenges, wildlife agencies in California have been focusing on creating regional multiple 

species conservation plans that meet the requirements of both federal Habitat Conservation Plans 

(HCPs) (Endangered Species Act Section 10(a)(1)(B)) and state Natural Community 

Conservation Plans (NCCPs) (California Fish and Game Code Section 2800 et. seq.). These 

plans establish landscape-scale reserve networks and long-term programs designed to conserve 

and manage the species legally “covered” by the plan, allowing development to proceed in less 

ecologically sensitive areas. Unlike typical HCPs, these joint NCCP/HCPs go beyond the 

protection of federal and state listed species to also “cover” species that could become listed if 

not protected (O’Connell and Johnson, 1997; Pollak, 2001). NCCPs also include goals for 

maintaining native biodiversity, rare habitat types, and ecological processes. For such large plans 

to be successful, they need to integrate species conservation with ecosystem management. 

Several joint NCCP/HCPs have been approved in southern California, and more are being 

planned throughout the State. These plans each include large numbers of species and hundreds of 

square miles of land. For example, the San Diego Multiple Species Conservation Program 

(MSCP), one of 11 sub-regional plans intended to conserve the remaining coastal sage scrub 

ecosystem in southern California, encompasses 582,000 acres and seeks to establish a system of 

reserve lands that will protect viable populations of 85 different plant and animal species and 

dozens of habitat types. Some of the species covered under this plan are specialists in specific 

habitats, including marsh (light-footed clapper rail, Rallus longirostris levipes), riparian 

(southwestern arroyo toad, Bufo californicus) and coastal sage scrub (California gnatcatcher, 

Polioptila californica californica), while others range widely over large, contiguous landmasses 

(mountain lion, Felis concolor). The large number of covered species and habitats conserved by 

efforts such as the San Diego MSCP presents unique challenges to management, requiring an 

even more thoughtful and adaptive approach than typical single species HCPs. 

Like other ecosystem management programs, regional NCCP/HCPs are developed despite many 

uncertainties about the behavior of the extremely complex and ever-changing ecological systems 

that the plans are intended to conserve and manage (Christensen et al., 1996; Noss et al., 1997). 

In particular, it is uncertain how ecosystems will respond to perturbations, such as fire, floods, 

and even management actions, some of which are spatially extensive and more intense or 

frequent than the natural range of disturbance. In addition, uncertainties exist due to lack of 

ecological information, including knowledge about rare species life histories, upon which 

dependable models of ecological functioning can be built. Sampling bias, analytical errors, and 

questionable quality of data can all contribute to uncertainty about the conservation strategy and 

management decisions. 

In the face of limited knowledge and ability to make predictions, NCCP/HCPs should be 

designed to improve our understanding of the ecological systems the plans are designed to 

protect, by adjusting management and even the conservation strategy as necessary in an 

“adaptive management” framework. To be effective NCCP/HCPs should develop robust 
 3 

monitoring programs to track progress toward their conservation and management objectives, 

and maximize their ability to meet those objectives in a scientifically defensible and costeffective way while minimizing the risks to the ecosystem. 

The intent of this document is to provide background and recommendations for designing 

monitoring programs in an adaptive management context, based upon lessons learned from 

southern California NCCP/HCPs and other ecosystem monitoring programs around the world. 

This document should not be interpreted as an official agency directive, but rather as advice that 

can help new monitoring programs take advantage of and improve upon previous efforts. Section 

2.0 in this document describes the role of monitoring in an adaptive management context. 

Section 3.0 presents five unique challenges of which designers of NCCP/HCP monitoring 

programs should be aware. In Section 4.0, we recommend nine steps that can be used 

sequentially to create an NCCP/HCP monitoring program. Section 5.0 summarizes the 

characteristics of good monitoring programs and gives some suggestions on how to achieve 

them, and Section 6.0 gives larger context to NCCP/HCP monitoring. Explanations, examples, 

and references can be found in the supplementary boxes, glossary, and appendices. 

2.0 MONITORING IN AN ADAPTIVE MANAGEMENT 

CONTEXT 

Strictly defined, “monitoring” is the systematic and usually repetitive collection of information, 

typically used to track the status of a variable or system. NCCP/HCPs use monitoring to track 

and evaluate many different variables, ranging from the number of acres purchased, to the 

number of species present in an area. NCCP/HCP monitoring programs include three main 

components: implementation (compliance) monitoring, effectiveness monitoring, and targeted 

studies. Definitions and some examples are provided below: 

• Implementation (compliance) monitoring tracks the status of plan implementation, 

ensuring that planned actions are executed. Typical compliance monitoring documents: 

- Reserve land acquisition (e.g., tracking number of acres preserved versus lost, by 

habitat types) 

- Management activities reporting (e.g., proportion of reserves fenced, status of 

invasive species removal activities) 

- Monitoring activities reporting (e.g., what monitoring activities were implemented 

and resulting reports received) 

• Effectiveness monitoring evaluates the success of the plan in meeting its stated biological 

objectives (Noss and Cooperrider, 1994). Typical effectiveness monitoring measures: 

- Status and trends of resources (e.g., quantitative data on covered species, 

biodiversity, vegetative structure) 

- Status and trends of known pressures (e.g., invasive species, contaminants, 

disturbance) 

- Effects of management actions on resources and known pressures (e.g., density of 

invasive plants measured before and then 1 to 5 years after herbicide treatment) 
 4 

• Targeted studies is a special subset of effectiveness monitoring. Targeted studies increase 

the effectiveness of monitoring and management by improving knowledge about the 

ecological system and about management techniques. Targeted studies may be 

implemented as short-term studies rather than as long-term monitoring and typically 

include: 

- Resolving critical uncertainties and improving knowledge of natural systems under 

management (e.g., plant succession and weed dynamics in response to fire; top-down 

predator effects on food webs; identification of stress-sensitive and stress-tolerant 

species) 

- Applying experimental management treatments (e.g., does gradually increasing and 

decreasing flow releases from dams increase arroyo toad tadpole survivorship 

compared with sudden flow releases and stoppages? (Madden-Smith et al., 2003) 

We focus the guidance in this document on effectiveness monitoring and targeted studies 

designed to remove critical uncertainties. While implementation (compliance) monitoring is a 

critical and legally-mandated part of NCCP/HCP implementation, it is not covered here. 

Monitoring and targeted studies for NCCP/HCPs should be designed in an adaptive management 

context if they are to assist decision-making. Adaptive management is an emerging approach to 

natural resource management that openly acknowledges our uncertainty about how ecological 

systems function and how they respond to management actions. Under this model, management 

moves forward in a scientifically-based way that involves monitoring, conducting targeted 

studies, and applying management activities as experimental treatments. The results feed back 

into decision-making, reducing uncertainty and improving the effectiveness of the program 

through time (Walters 1986; Noss et al., 1997; Nyberg, 1998; Wilhere, 2002). Adaptive 

management implies an ongoing scientific commitment to the plan in perpetuity (Noss et al., 

1997). Under adaptive management, managers use the best available information to make 

decisions, but should always be questioning and seeking opportunities to learn how best to 

accomplish the goals of the plan. 

In recognition of a general concurrence among scientists that management of ecosystems should 

be adaptive, the federal Five-Point Policy addendum (USFWS, 2000) to the Endangered Species 

Act recommends that large HCPs be managed adaptively and the California NCCP Act (2003) 

mandates that all NCCPs take an adaptive management approach. Each set of NCCP/HCP 

documents is required to include a description of the plan’s comprehensive adaptive management 

program and monitoring program. As we use the term here, adaptive management includes all of 

the steps that may be involved in a long-term adaptive implementation program, including 

opportunistic learning, hypothesis testing, management, monitoring, and directing the results of 

analysis and assessment back into the program through decision makers. 

Figure 1 provides a flowchart of relationships among components of the NCCP/HCP adaptive 

management feedback loop. In the NCCP/HCP planning stage, foundational scientific principles 

and the best available empirical information are expected to inform both the conservation goals 

and the strategy for implementing them. Ideally, this process includes the following steps: 

identify the goals of the NCCP/HCP, create a simple conceptual model of how the ecosystem 

functions or of a species life history (models can also help to define goals), and use the 
 5 

conceptual model(s) to identify a conservation strategy (including reserve design), followed by 

an implementation approach involving management activities and monitoring. 

Conceptual models summarize our current understanding of ecosystem or community function, 

or species life history, clarifying likely responses to management actions and pressures (i.e., 

stressors, causes of change). An important point is that the same goals and conceptual models 

that inform the conservation strategy should also drive development of the management and 

monitoring programs. Problem-focused conceptual models that link program objectives to causes 

of change and to management activities are particularly helpful to adaptive management and 

provide a key bridge from the conservation strategy to management and monitoring. 

Assumptions upon which the proposed conservation strategy and management program are 

based can be tested through 1) monitoring and 2) targeted studies and experimental management. 

Monitoring, which measures ecosystem condition and responses of the ecosystem to both 

intentional (management actions) and natural perturbations, is a critical piece of the adaptive 

management feedback loop. Ideally, monitoring can identify problems early so that corrective 

management action can be taken as soon as it is needed. In contrast, targeted studies (at small 

spatial scales or in pilot studies) may be more appropriately used to resolve critical questions 

regarding ecosystem functioning or management applications. While some management 

activities may have little uncertainty regarding application or outcomes (e.g., trash removal or 

sign posting), other management activities have much greater uncertainty (e.g., habitat 

restoration). Such activities should be designed as experiments to increase our understanding of 

the system and the effectiveness of management (e.g., determining the most effective way to 

control non-indigenous species or to restore river flows below a dam). 

The results from monitoring and targeted studies are evaluated and used to update goals and 

conceptual models, revise the conservation strategy and implementation (management) program, 

as well as the monitoring methodology and even foundational scientific knowledge. The 

remainder of this document will focus on the challenges and steps of designing monitoring 

programs in an adaptive management context. More detailed guidance on designing the 

management portion of adaptive management programs, including administrative structure, will 

be provided in a separate document. 
 6 

Figure 1. NCCP/HCP adaptive management feedback loop. 

NCCP/HCP Goals 

Implement Management Plan 

and Reserve Network 

Analyze

 and 

Evaluate

Scientific Principles and 

Best Existing Information 

Conceptual 

Models 

Conservation Strategy, 

including Reserve Design 

Management Plan and 

Monitoring Approach 

Adapt Models 

and 

Components 

Monitoring and Targeted 

Studies of Ecosystem 

Response 
 7 

3.0 CHALLENGES IN CREATING REGIONAL 

CONSERVATION PLAN MONITORING PROGRAMS 

Due to the multiple scales involved and the legal requirements of NCCP/HCPs, monitoring 

programs for regional conservation plans face special challenges, some of which are discussed 

below. These issues include monitoring both covered species and ecosystem integrity, 

coordinating and integrating monitoring at multiple scales, developing programs while 

acknowledging high degrees of uncertainty, developing programs in phases, and accommodating 

gradual increases in the sizes of reserves. 

3.1 Addressing both covered species and ecosystem integrity 

Although designing intensive monitoring for each covered species would technically satisfy 

USFWS assurance requirements, this approach would not satisfy the principles of California’s 

Natural Community Conservation Planning Act. Conversely, a monitoring program that tracks 

changes in general biological communities and processes, without specific attention to covered 

species, might not have sufficient power to assess individual species status and trends. This could 

limit the effectiveness of management for covered species. Thus, a significant challenge for 

NCCP/HCP monitoring programs is integrating monitoring of covered species with monitoring 

of ecosystem integrity in an effective and cost-efficient way. 

 

3.2 Coordinating and integrating monitoring from local to ecoregional scales 

The monitoring program will need to measure and evaluate change in resources and threats 

across different scales, ranging from individual reserves, NCCP/HCP planning areas, and the 

ecoregion (see Figure 2). To be effective, monitoring should be designed at a scale that is 

relevant to the species and to the types of management responses required. This may necessitate 

coordination across several reserves or across an entire ecoregion. Otherwise, it will be difficult 

to interpret whether a species decline in an individual NCCP/HCP is a local phenomenon or is 

part of a regional trend—dictating different types and scales of management response. For wideranging species such as mountain lions and deer, data collection and evaluation should be 

coordinated across large scales. Data from any single reserve will tell us little about their 

regional status or trends, and less about potential causes of any observed change (Beier, 1993; 

Ernest et al., 2003). Some covered species, such as neotropical migratory birds, may not even be 

appropriately addressed within the confines of the entire coastal southern California ecoregion, 

while others, such as the status of annual plants, small mammals, and reptiles,may be 

appropriately assessed within single reserves. 

To assess trends across the ecoregion, monitoring design should be coordinated across the 

ecoregion. This requires standardizing of protocols, sampling design and training of personnel, 

and integrative data analyses. If monitoring data are to be used to assess change at multiple 

scales, e.g., individual reserves and the ecoregion, then the program will need to be designed to 

be scaleable, providing useful information at multiple scales. Creating such coordinated and 

scaleable programs requires identifying and planning for such needs early. 
 8 

Figure 2. Monitor at the appropriate geographic scale. Progress toward meeting the 

objectives of regional conservation plans should be monitored at the appropriate geographic 

scale. The status of essentially immobile species can be addressed at the scale of a single 

reserve. Large-scale issues and wide-ranging species can only be appropriately assessed at 

larger scales, requiring coordinated sampling across multiple reserves and possibly non-reserve 

lands. In addition, if information needs to be interpreted at multiple scales, then the sampling 

design will need to be appropriately scaleable to address these needs. 

3.3 Acknowledging a high degree of uncertainty 

Prior to implementation of a NCCP/HCP, documents describing the management and monitoring 

programs must be completed. Rarely at this point will there be sufficient information to 

confidently design a long-term management and monitoring program that encompasses all covered 

species and ecological systems. As a result, the documents produced should acknowledge the 

underlying uncertainty and include mechanisms to reduce critical knowledge gaps while still 

fulfilling monitoring requirements. These documents describing the monitoring and management 

programs are a starting point in the mission to understand and appropriately manage the underlying 

ecosystems. Thus, it is essential that the personnel ultimately responsible for managing and 

monitoring regional conservation plans have sufficient scientific capacity and resources to adapt 

the programs appropriately. The NCCP/HCP efforts in southern California provide several 

examples of how an initial monitoring program might be created. It is our hope that future 

monitoring programs will utilize the lessons learned in these efforts and improve upon them as 

appropriate.

3.4 Phasing-in monitoring program development 

Due to the large amount of uncertainty in managing and monitoring the ecosystem and covered 

species, monitoring program development and implementation typically proceeds in three phases: 

1) inventorying resources and identifying relationships; 2) pilot testing of long-term monitoring 

and resolving critical management uncertainties; 3) implementing long-term monitoring and 

adaptive management. Different components of a monitoring program may be in different phases. 

Very little may be known about some covered species, whereas long-term monitoring programs 

may have already been established for other species and biological communities. The progression 

USFS NPS 

Reserve 

Ecoregion 

NCCP/HCP NCCP/HCP NCCP/HCP 

Coordination

Scaleable 

Sub-area Sub-area

Reserve Reserve Reserve Reserve Reserve Reserve Reserve Reserve
 9 

from Phase 1 to Phase 2 to Phase 3 is driven by data collection, hypothesis testing, and the 

resulting increase in understanding of the system. 

• Phase 1 – Inventorying resources and identifying relationships: The main goal of phase 

one is to determine the baseline condition of the system as a prelude to long-term 

monitoring program design. This generally involves an inventory of what species, 

habitats, and other resources are present, their locations and general conditions. Some 

management can be applied during this phase, but in general, this should be limited to 

actions of known-impact, such as hand-removal of weeds or fence construction to prevent 

vehicular access or maintaining existing habitat management, such as water distribution or 

grazing, until such management can be appropriately evaluated. This phase can also be 

used to develop or test hypothesized relationships between species, habitats, processes and 

other causes of variation, such as roads or invasive species. For example, inventories for 

reptiles in coastal sage scrub across San Diego, Orange, and Riverside Counties were used 

to assess relationships between species and vegetation, soils, habitat fragmentation, and 

presence of invasive Argentine ants (Case and Fisher, 2001; Fisher et al., 2002). 

• Phase 2 - Pilot testing of long-term monitoring and resolving critical management 

uncertainties: Phase two is characterized by pilot testing of long-term monitoring 

protocols and sampling designs to select cost-effective designs with sufficient statistical 

power to detect biologically-relevant and management-relevant changes. The pilot phase 

often progresses through an iterative process, including revisions to protocols and 

comparisons of multiple methods. For example, USGS is currently pilot testing a 

monitoring protocol for arroyo toads (Bufo californicus). Because prior work showed 

estimates of adult population size to be insufficiently precise, a new protocol is being 

tested which tracks changes in the amount and quality of habitat and the proportion of 

available habitat with tadpoles present (Brehme et al., 2004). In addition, the pilot phase 

is an opportunity to conduct targeted studies to resolve critical management uncertainties 

and refine conceptual models based on emerging information. 

• Phase 3 – Implementing long-term monitoring and adaptive management: Activities 

include implementation of long-term monitoring protocols and periodic evaluation and 

refinement of the monitoring program. The program continues to address uncertainties, 

principally by evaluating responses to management and extreme events. Emerging 

uncertainties are also addressed and prioritized, such as a new invasive species or 

pollution source. As an example, California least terns (Sterna antillarum browni ) have 

been monitored for decades by counting nesting pairs and measures of reproductive 

success, but attempts at refinement of the protocol continue (Keane, 1999). 

3.5 Accommodating staged development of a reserve network 

The assembly of an NCCP/HCP reserve network may proceed in stages, with land gradually 

dedicated to the reserve system over a decade or longer. Because sampling private lands is 

usually not feasible, monitoring programs should allow for staged implementation as lands are 

acquired. Following acquisition and initial inventory, these lands can then be incorporated into 

the long-term monitoring program. The program can even use such staged implementation to its 

advantage by using these new lands to critically evaluate hypotheses regarding species-habitat 

relationships and regional distributions. 
 10 

4.0 STEPWISE APPROACH TO CREATING A MONITORING 

PROGRAM 

Up to this point, we have addressed monitoring broadly, considering some general philosophical 

guidelines, potential challenges and the need for an adaptive management approach. We now lay 

out more specific guidelines and recommendations for constructing a functional and 

scientifically-defensible monitoring program. There is no one best approach for managing and 

monitoring any system, however, following these steps will lead to the production of a 

monitoring program based on the best available science. Although we tailor this guidance to 

monitoring programs that fulfill specific requirements of NCCP/HCP regional conservation 

plans, the approach should be applicable to monitoring design for other programs. The approach 

we take integrates monitoring species “covered” by the plan with monitoring ecological integrity 

and incorporates an adaptive management approach. We have divided the design and creation of 

a monitoring program into a nine-step process. 

Step 1. Identify the goals and objectives of the regional conservation plan 

Step 2. Identify scope of monitoring program 

Step 3. Compile information relevant to monitoring program design 

Step 4. Strategically divide the system and prioritize for monitoring program development 

Step 5. Develop simple management-oriented conceptual models 

Step 6. Identify monitoring recommendations and critical uncertainties 

Step 7. Determine strategy for implementing monitoring 

Step 8. Develop data quality assurance, data management, analysis, and reporting 

strategies 

Step 9. Complete the adaptive management loop by ensuring effective feedback to 

decision-making 

In practical application, the steps in this process may overlap. At each step it is likely that 

information or insights will surface that can inform and improve the products of earlier steps. In 

addition, Steps 1-5 could be coordinated and developed to simultaneously meet the needs of the 

conservation strategy, management program design and monitoring program design (e.g., 

Coachella Valley Multiple Species habitat Conservation Plan (CVMSHCP, 2004 draft)). 

However, if these three development efforts are occurring on different schedules, the monitoring 

program may have to complete Steps 1-5 independently. 

The program should clearly document its decisions and seek input and review from scientists, 

managers and stakeholders throughout the process. Developing high quality monitoring programs 

requires creativity as well as sufficient information on which to build a sound foundation. To 

keep the process as transparent as possible and for future reference, we recommend keeping 

detailed records of important decisions and the rationale behind them. Because science benefits 

from peer-review and an open and unbiased process, review should be sought early and regularly, 

and should include some scientists completely independent of the local program. 

For those seeking additional assistance, some excellent general references for designing 

monitoring in an adaptive management context have been published (National Research Council, 

1990; Margoluis et al., 1998; Gibbs et al., 1999; Mulder et al., 1999; Elzinga et al., 2001; 

Morrison et al., 2001; Busch and Trexler, 2003; Fourqurean and Rutten, 2003; Noon, 2003). 
 11 

4.1 Step 1. Identify the goals and objectives of the regional conservation plan 

To evaluate the success of any plan, clearly stated goals and objectives are essential. List the 

goals and objectives of the regional conservation plan. These should be defined in the plan 

documents; however, if explicit goals and objectives have not yet been established, this is the 

time to get them nailed down. For every item that the monitoring program needs to evaluate, 

there should be a specific stated goal and/or objective. There should be a stated goal for each 

covered species or habitat (USFWS, 2000). To assist monitoring program development, goals 

and objectives should ideally be:

• Easily understandable 

• Biologically meaningful 

• Measurable 

• Feasible, both financially and scientifically 

• Written with level of detail consistent with level of current knowledge 

• Compatible with goals and objectives for all covered species and habitats 

• Compatible with goals and objectives for neighboring conservation lands (e.g., other 

NCCP/HCPs, state parks, ecological reserves, etc.) 

Specific goals and objectives make the design and implementation of the monitoring program 

easier. Vague goals and objectives consume staff time because monitoring program designers 

have to interpret the initial intention. Where program designers must interpret plan goals, the 

process followed and rationale used should be well documented. An example might be “we 

interpreted ‘maintain natural processes’ as ‘maintenance of natural processes such as sediment 

deposition, hydroperiod, and fire frequency within the natural range of variability as defined by 

data collected over the past 50 years.’” Another example could be “we interpreted ‘provide for 

conservation of the species in the plan area’ as ‘the extent and quality of habitat for this species 

will be maintained, species abundance will be maintained compared to abundance at initiation of 

the plan, or reproductive success rate will be sufficient to sustain the local population or cause it 

to increase.’ ” 

Because plan goals and objectives guide plan implementation, defining clear, measurable goals 

and objectives at this point is critical to assembling a monitoring program that can evaluate plan 

success over time. 

4.2 Step 2. Identify the scope of the monitoring program 

The purpose of this step is to identify the scope and boundaries of what the monitoring program 

will be evaluating and identify any requirements, constraints, and opportunities that should be 

accommodated in the program’s design. Identification of the following will facilitate the program 

design in subsequent steps: geographic scope, land ownership and constraints, audiences/users of 

monitoring information, spatial scales of focus, relevant time scales, and available resources. For 

regional conservation plans, many of these issues are defined in the plan documents. 

• Geographic scope: Monitoring generally seeks to draw inferences from sampled areas to 

unsampled areas. The way we do this is by randomly distributing monitoring across the 

area from which we seek to draw inferences. The geographic boundaries of the desired 

area of inference should be spatially defined, preferably via maps in a Geographic 
 12 

Information System (GIS). Areas excluded from consideration should also be mapped 

and the reasons for exclusion articulated. 

• Land ownership and constraints: The various jurisdictions and land management entities 

who own or manage the lands identified in the geographic scope, such as cities, counties, 

state lands, federal lands, non-profit organizations, and others, need to be identified. Any 

legal and programmatic constraints involved with such entities’ participation in the 

program should also be identified. For example, a park may be mandated to manage for 

recreational use or some federal lands may have existing monitoring programs that are 

being developed in coordination with a national program, e.g. NPS Vital Signs program.. 

• Audiences/users of monitoring program information: The program should identify the 

various audiences who need to receive and utilize monitoring and adaptive management 

information. Reserve managers, government agencies, stakeholders, lawmakers, scientists, 

and program reviewers are potential audiences. Each audience has different needs regarding 

the timing, frequency, level of technical detail, and preferred mode of communication. 

• Spatial scales of focus: The program should identify the scale or scales of focus for data 

analysis and reporting. Likely scales of interest include an individual reserve, one 

NCCP/HCP program area, a watershed, or an entire ecoregion that spans multiple 

planning entities. 

• Relevant time scales – biological and programmatic: Relevant time scales for reporting 

and decision-making should be identified. These will be determined by the expected 

duration of the program, the expected time scale for responses to management treatments, 

and any mandated reporting schedules. 

• Available resources and opportunities: At least in a general sense, the availability of 

resources, such as funding, personnel and equipment, should be identified and coupled 

with any constraints on their use. For example, some monitoring partners may only be 

able to supply vehicles, equipment, or people during specific months of the year when 

their other duties are less demanding. 

4.3 Step 3. Compile information relevant to monitoring program design 

Using the NCCP/HCP goals as a guideline, the next step is to assemble the information needed 

to guide the design of the monitoring program. In particular, the monitoring program designers 

should assemble information for developing conceptual models (see Step 5), information on 

existing monitoring programs in or near the plan area, and existing data on species, habitats, and 

other environmental factors. Relevant information may come from a wide variety of sources. In 

evaluating the usefulness of information sources, potential biases and limitations should be 

noted. For example, museum records provide some information on regional distribution and 

habitat associations, but sampling is usually biased towards the most accessible sites and large 

areas may have been completely unsampled. Listed below are examples of common existing 

information sources that are often useful, most of which should have been identified in the 

regional conservation plan. 

• Programmatic documents: If an approved regional conservation plan exists, that 

document should be reviewed first. Other resources that may hold additional useful 

information include USFWS biological opinions, USFS plans, Department of Defense 

Integrated Resource Management Plans (IRMP), California State Parks management 

plans, reserve management plans, and environmental impact studies focused on species 
 13 

and systems within the plan area. 

• Spatial data: Vast amounts of information can be extracted from maps. Map resources are 

increasingly available as GIS datasets, making them even more useful. Valuable, if not 

essential, spatial data include topography, vegetation, land use, reserve boundaries, 

projected urban boundaries, species ranges, geology, and distributions of factors 

influencing native systems (e.g., weeds, rainfall). 

• Technical information: Relevant technical information sources include books, scientific 

articles, technical reports, and museum records. Because rarely is sufficient technical 

information available for any given species or system, information from outside the plan 

area should also be considered. 

• Existing monitoring programs and data sources: Descriptions of existing monitoring 

programs and data sources within and near the plan area should be compiled. Some 

existing monitoring programs for covered species may already meet the regional 

conservation plan’s needs with little or no adjustment. Monitoring programs in 

neighboring areas may provide monitoring protocols and assistance with sampling design. 

Historical data sets can sometimes provide baseline information and help resolve 

uncertainties. Useful information that can be compiled from existing programs includes: 

program objectives, geographic scope, protocols used, funding sources, duration of 

program, constraints on data use, as well as the actual data. 

Although existing information should be used to the extent possible, in some cases new data will 

need to be collected. After existing information has been gathered, data gaps will be apparent. It 

will be tempting at this point to begin gathering field data to remedy this situation. However, to 

plan new data collection more efficiently, the next four steps should be completed first. 

4.4 Step 4. Strategically divide the system and set priorities 

Designing effective monitoring and adaptive management programs requires a clear strategy for 

identifying the most important elements of the system to monitor and the critical uncertainties to 

address. This strategy should realistically meet the need for tracking individual “covered” 

species while taking a systems approach, as is increasingly recommended by scientists (e.g., Ives 

and Cardinale, 2004). However, no program can afford to monitor everything or to succumb to 

“datakleptomania” – the uncontrolled desire to collect more data (Vos et al., 2000). In this step 

we suggest methods for dividing the system into practical pieces to facilitate program design. 

Whatever strategy the program chooses should be relevant to the management program and to 

the accomplishment of subsequent monitoring steps. 

4.4.1 Divide the system into pieces for monitoring program development.

There is an infinite number of ways to conceptually divide any ecological system into pieces for 

monitoring. Although any attempt to partition a system will not be perfectly satisfactory, the 

following approach has been useful: 

• Group covered species according to intensity level required for model development, 

management, and monitoring 

• Group natural communities into natural community assemblages 

• Identify landscape level issues that involve multiple natural community assemblages or 

for other reasons do not fit neatly into the natural community assemblages stratification 
 14 

Below we provide examples and suggestions for completing these steps. Once the program has 

identified its overall strategy for dividing the system into manageable pieces and prioritizing 

them, it can proceed with developing conceptual models in Step 5. 

4.4.2 Group covered species according to intensity level required for model development, 

management, and monitoring 

Regional NCCP/HCPs in California typically cover large numbers of species. Covered species 

are listed in the planning documents and typically include federally listed species, state listed 

species, and species of local concern. The Coachella Valley Multiple Species Habitat 

Conservation Plan (CVMSHCP, 2004 draft ) covers 27 species, the San Diego Multiple Habitat 

Conservation Program (MHCP, 2003) covers 59 species, and the Western Riverside Multiple 

Species Habitat Conservation Program covers 146 species (MSHCP, 2003). 

Dividing these long species lists into groups with similar types and intensity levels of expected 

management and monitoring can be useful during the development phase of a monitoring 

program. All covered species do not need to be monitored with the same intensity. However, the 

approach for tracking the status of each species and the corresponding underlying assumptions 

should be well-reasoned and clearly documented. Some covered species will require intensive 

conceptual model development that goes well beyond the information provided in the 

NCCP/HCP documents, for example, those species already suspected to be in decline or for 

which management is challenging. On the other hand, it may be possible to lump species that use 

similar habitats, require similar management, or are detectable using a single method (such as 

reptiles or neotropical riparian migratory birds). Some basic criteria that can be used to group 

and rank species include: 

• Goals and objectives for the species, e.g., “maintain” versus “increase” 

• Range, distribution, and rarity of the species, i.e., rare species existing in a few 

populations may need a different approach from widely distributed populations 

• Degree of threat to the species, i.e., whether a decline is occurring or is anticipated to 

occur in the future; the potential for extinction, plus potential for recovery 

• Degree of management conflict or challenge, e.g., species status or uncertainty affects 

decision-making such as dam operations, reserve design, land use, or management for 

other species 

• Added informational value, i.e., whether intensively monitoring a covered species also 

provides added value as an indicator of ecosystem quality, as a measure of the level of 

biodiversity present in a specific taxonomic group, or as an early warning indicator of 

change in the system 

Other methods of grouping are possible such as grouping by habitat or functional group (Elzinga 

et al., 2001). Lambeck (1997) presents a process in which species at risk are grouped by threats, 

such as fragmentation, and those species which are most sensitive to the threat are used to guide 

conservation planning. Theoretically this method could also be applied to identifying which 

species are most sensitive to pressures in the system for investigation as early warning indicators 

of stress. 

 
 15 

NCCP/HCP species assessments, coupled with input from area scientists, can be used to 

categorize species according to the intensity of management and monitoring required. Once the 

species have been grouped, a strategy for addressing each group should be devised. Examples of 

potential groupings include species requiring intensive conceptual model development and focus, 

species that can be grouped into biological communities for monitoring program design, and 

species for which an inventory is needed to determine whether any populations exist in the 

planning area. 

Although the categorization of covered species will likely evolve as conceptual models are 

refined, strategic grouping allows the program to make rapid progress on species that appear to 

be under the greatest threat or are constraining decision-making. An example of two species 

requiring differing intensities of initial focus is given in Box 1. 

4.4.3 Group natural communities into natural community assemblages 

In addition to protecting the species covered by the plans, NCCP/HCPs seek to maintain system 

integrity and biodiversity. Regional NCCP/HCPs typically identify large numbers of “natural 

communities” that will be conserved (e.g., 23 in the MHCP (2003) and 27 in the draft 

Box 1. Comparison of two covered species requiring different levels of initial focus in an 

NCCP/HCP monitoring program. 

Higher initial priority

The southwestern arroyo toad (Bufo californicus) is listed as an endangered species under 

the Federal Endangered Species Act (USFWS 1994). It has disappeared from 75% of its 

previously occupied habitat (Jennings and Hayes, 1994), 40% of which has been altered by 

dam construction and operation (USFWS 1994, 1999; Madden-Smith et al., 2003). This species 

breeds only in shallow, low velocity riparian habitats with sandy substrate. Maintaining this 

species in areas below dams requires habitat management, appropriate volumes and timing of 

flows, and control of invasive species. This species is covered under NCCP/HCP programs in 

San Diego, Orange and Western Riverside counties, including the Joint Water Agencies 

NCCP/HCP. Because potential impacts on the endangered toad constrain the operation of 

Loveland Dam on the Sweetwater River in San Diego County, detailed conceptual models were 

assembled to illustrate the toad’s life cycle, water management operations, and the interaction 

of the two. The conceptual models were then used to conduct a risk assessment that evaluated 

the effects of Loveland dam operation on arroyo toads and made initial management, 

monitoring, and research recommendations for the Joint Water Agencies NCCP/HCP planning 

effort (Madden-Smith et al., 2003). 

Lower initial priority

The Torrey pine (Pinus torreyana ssp . torreyana) is a federal species of concern and a 

covered species under the San Diego MSCP. The primary threats to this species are urban 

development and fire suppression. One hundred percent of the single naturally occurring 

mainland population is conserved under the MSCP (MSCP, 1998). Because Torrey pine is a 

long-lived tree species that occurs in an ecological reserve, developing a detailed conceptual 

model for this species is less urgent than for the arroyo toad. However, some monitoring and 

adaptive management of Torrey pine will eventually be required because this species appears 

to require fire to break open seed cones and establish new seedlings (Wells, 2001). 
 16 

CVMSHCP (2004)). These can often be combined into a smaller number of “natural community 

assemblages.” Examples include “floodplain and riparian habitat”, “chaparral/coastal sage 

scrub/grassland community”, and “lagoons and tidal wetlands.” Communities grouped together 

in an assemblage are assumed to be affected by the same physical and biological processes and 

the same general set of pressures. These assemblages partition the landscape into fewer 

categories than natural communities, yet are relevant biologically, practical to management, and 

facilitate subsequent design steps. Box 2 lists the complete sets of natural community 

assemblages chosen for the MHCP and the draft CVMSHCP. 

Two instructive examples of how multiple natural communities can be combined into natural 

community assemblages are given by: 1) the chaparral/coastal sage scrub/grassland natural 

community assemblage specified in the MHCP and 2) the aeolian sands natural community 

assemblage identified in the draft CVMSHCP. First, coastal sage scrub, chaparral, and grassland 

are each classified as separate natural communities in the MHCP (2003). However, these three 

natural communities sometimes occur in mixed stands, and fire, land management, invasive 

grasses, aerial deposition of nitrogen and natural plant succession all contribute to transitions 

among these three natural community types at a given site. While some covered species are 

specific to one natural community or another, others may be found throughout all three natural 

communities. Because many of the processes and pressures affecting these communities are 

common to all three and because one of the main management challenges will be to maintain an 

appropriate balance of these community types, identifying a “chaparral/coastal sage 

scrub/grassland” natural community assemblage was appropriate for the MHCP (2003). 

Similarly the draft CVMSHCP (2004) identified the “aeolian sand” natural community 

assemblage. This natural community assemblage combines “active desert dunes,” “active desert 

sand fields,” “ephemeral desert sand fields,” “stabilized shielded desert sand,” and “mesquite 

hummocks.” Again, the processes and pressures that affect these natural communities are similar 

and the communities are dynamically linked. For example, unstabilized sand can transition 

through time to stabilized dunes. The aeolian sand natural community assemblage will need to be 

managed to maintain a balance of the component natural communities due to different habitat 

requirements of the covered species. 

Also influencing decisions about grouping into natural community assemblages is the number 

and types of covered species found in each natural community. For example, in the draft 

CVMSHCP (2004) only two covered species, gray vireo (Vireo vicinior) and Peninsular bighorn 

sheep (Ovis canadensis), inhabit the “desert scrub, chaparral, woodland, and forest communities 

in mountainous areas.” This large, diverse array of natural communities was lumped into a single 

natural community assemblage in the draft CVMSHCP due to the small number of covered 

species present, the similar nature and low intensity of the pressures affecting these natural 

communities, and the similarity of the management challenges across these areas (i.e., managing 

recreation, fire, and invasive species). 

Because the natural communities in an assemblage are affected by the same suite of processes, 

pressures and management actions, this method of partitioning resources provides a natural 

transition to the subsequent steps of conceptual model development and specification of 

monitoring and adaptive management actions.
 17 

Box 2. Dividing system into natural community assemblages. Below are examples of 

how two NCCP/HCP multiple species conservation plans in California divided their planning 

areas into natural community assemblages. This step precedes and facilitates the 

development of conceptual models and monitoring and research recommendations. At this 

stage each plan also identified landscape-scale issues which involved multiple natural 

community assemblages or otherwise required special attention. 

San Diego Multiple Habitat Conservation Program (for Cities of Carlsbad, Encinitas, 

Escondido, Oceanside, San Marcos, Solana Beach, and Vista, California) (MHCP, 2003): 

Natural Community Assemblages:

Coastal sage scrub, chaparral, and grassland 

Riparian vegetation communities 

Lagoons 

Oak woodlands 

Vernal pools 

Landscape-level issues (affecting multiple natural community assemblages)

 Wildlife corridors 

 Exotic species 

 Weather and climate 

Coachella Valley Multiple Species Habitat Conservation Program (CVMSHCP, 2004 draft) 

Natural Community Assemblages: 

Aeolian sand communities: Sand dunes and sand fields 

Alluvial fan and wash communities 

Riparian and desert fan palm communities 

Saltbush scrub and alkali flats communities 

Marsh communities 

Desert scrub, chaparral, woodland and forest communities in mountainous areas 

Landscape-level issues (affecting multiple natural community assemblages)

Effects of recreation on Peninsular bighorn sheep 

 Biological corridors and linkages 

 Impacts to covered species from overhead power lines 

Public Access and Use 
 18 

4.4.4 Identify landscape-level issues that affect multiple natural community assemblages

Some issues that need to be addressed by the monitoring program are not encompassed under the 

covered species or any single natural community assemblage (see Box 3). Often these are issues 

that simultaneously impact multiple natural community assemblages, and thus are most 

appropriately addressed at larger spatial scales. These may benefit from an overarching 

conceptual model that ties all the natural community assemblages together or may only need to 

be addressed as a few additional issues, such as biological corridors and recreational use (see 

Boxes 2 and 3).

4.4.5 Set Priorities

The end product of Step 4 should be a prioritized list of the natural community assemblages, 

covered species, and landscape scale issues that the monitoring program will be designed to 

address. 

4.5 Step 5. Develop simple management-oriented conceptual models 

Once the vast array of plan components has been organized into a smaller number of covered 

species groups, natural community assemblages, and landscape-level issues, the next step is 

conceptual model development. Monitoring and adaptive management program design is greatly 

assisted by conceptual models (National Research Council, 1990; Margoluis et al, 1998; 

CALFED Bay-Delta Program, 2000a, 2000b; Elzinga et al., 2001; Stevens and Gold, 2003; 

Noon, 2003, Ogden et al., 2003; RECOVER, 2004). In this section we describe the purposes and 

characteristics of management-oriented conceptual models, provide procedures and examples 

illustrating how conceptual models are constructed, and discuss how information compiled for 

covered species assessments can be used to draft conceptual models at the natural community 

assemblage level. 

Box 3. Typical landscape-level issues that involve multiple natural community 

assemblages or otherwise require special attention. 

• Maintaining dispersal corridors and habitat connectivity. 

• Managing regional processes such as river hydrology and groundwater levels, which 

affect multiple natural community assemblages. 

• Managing keystone ecosystems in a landscape context, such as floodplain and 

riparian areas or desert springs, whose role in the landscape is greater than their 

area (deMaynadier and Hunter, 1997) 

• Ensuring the persistence of species requiring multiple habitats such as carnivores 

(Beier, 1993; Ernest et al., 2003), bats (Ball, 2002), raptors, and waterfowl. 

• Controlling the establishment, distribution, and abundance of invasive species. 

• Reducing aquatic and airborne contaminants, especially those that travel long 

distances from source of pollution to point of impact. 

• Managing public access and the effects of recreation.
 19 

4.5.1 Purposes of conceptual models

Although conceptual models are not an official requirement of NCCP/HCPs, programs that do 

not use management-oriented conceptual models frequently experience difficulty in the steps that 

follow. Conceptual models are qualitative or quantitative models used to clearly describe a 

system. In developing monitoring programs in an adaptive management context, conceptual 

models help program designers: 

• summarize existing knowledge and hypotheses about a system 

• select and prioritize important components of the system to monitor 

• identify and prioritize critical uncertainties that require research 

In addition, conceptual models: 

• communicate understanding of the system to all program participants and encourage 

interdisciplinary dialog 

• facilitate review of the program by outside experts by summarizing system complexities 

in a digestible form 

There are many different types of conceptual models in use. Sometimes confusion results 

because the term “conceptual model” means different things to different people. Model form and 

details differ depending on the purposes, scales of focus, and system complexity. An important 

point is that a conceptual model is usually designed for a specific purpose; the level of detail 

and complexity of the model should reflect that purpose. The program may choose to create 

very basic conceptual models for some parts of the system, while creating very specific and 

detailed conceptual models for other aspects of the system. The level of focus and detail depends 

on which aspects of the program have the greatest uncertainty and anticipated difficulty in 

meeting program objectives. 

Models can be narrative (e.g., MHCP, 2003) or can be diagrams supplemented by narratives 

(e.g., CVMSHCP, 2004 draft). Diagrams can summarize the “big picture” by showing the 

hypothesized relationships between the key components of the model. Narrative models explain

the hypothesized relationships in detail, provide an estimate of their level of certainty, and 

identify alternative hypotheses and gaps in knowledge. Based on the outcomes of monitoring and 

research, conceptual models should evolve through time, a consideration discussed in more detail 

below. 

4.5.2 Characteristics of management-oriented conceptual models

NCCP/HCP conceptual models should be management–oriented tools that assist the design of 

the conservation strategy and adaptive management. This is achieved by linking the 

conservation plan objectives to causes of change and to management activities. Managementoriented conceptual models make identifying and prioritizing monitoring variables and critical 

uncertainties much easier (Step 6) and greatly assist sampling design (Step 7). 

In our discussion of conceptual models, we use the term “pressure” to refer to agents that either 

promote or inhibit change in the state of the environment. These are called stressors, threats, or 

drivers in other programs. Because such agents may have a negative effect on some species 

while having a positive effect on others, we use pressure as a more neutral term. Pressures can be 
 20 

anthropogenic (e.g., barriers to movement, disturbance, contaminants) or natural (e.g., climate 

variability, 100-year flood events). Pressures can also include natural constraints such as limited 

seed dispersal. 

A management-oriented conceptual model links pressures on the state of the environment to 

hypothesized effects of those pressures. This requires a sufficient understanding of the interrelationships among species, habitats and ecological processes, to speculate on how pressures 

are affecting the state of the environment, and to make hypotheses about appropriate program 

actions (conservation strategy and management activities) that should be implemented in 

response (see Figure 3, page 21). More detailed models of food webs or ecological processes are 

developed as needed to assist understanding of the effects of pressures and program actions on 

system dynamics. 

Both the San Diego Multiple Habitat Conservation Plan (MHCP, 2003) and the Coachella Valley 

Multiple Species Habitat Conservation Plan (CVMSHCP, 2004 draft) used this general 

management-oriented approach. Similar approaches have been applied in other ecosystem 

management programs, although the terminology varies (New Zealand Ministry for the 

Environment, 1997; Bertram and Stadler-Salt, 2000; Atkinson et al., 2002; California Resources 

Agency, 2002; Noon, 2003; RECOVER, 2004). A similar method uses web envirograms 

(Andrewartha and Birch, 1986; Longcore et al., 2003). 

4.5.3 Details and examples of conceptual models

Models can be created in different formats to best meet the planning needs of the program. 

However, the components of the conceptual models will be the same regardless of format. Box 4 

(page 22) lists the suggested components of a covered species conceptual model. Appendices A 

and B list the components of natural community assemblage models and landscape-level issue 

models, respectively. The program will likely develop a series of nested conceptual models (see 

Figure 4, page 23). The number and complexity of the models depend on the needs of the 

program. 

Three conceptual model examples are discussed below: 1) an arroyo toad species-focused 

conceptual model (Figure 5, page 24), 2) an aeolian sand natural community assemblage model 

that links pressures to covered species (Figure 6, page 25), and 3) a more detailed sub-model of 

the aeolian sand natural community assemblage detailing relationships among geomorphic 

processes and species (Figure 7, page 26). Only brief descriptions are provided here. More 

details for each of these models are provided in the source documents (Atkinson et al., 2003b; 

CVMSHCP, 2004 draft). All three of these examples highlight the pressures that affect the 

systems and possible program actions in response. 

The arroyo toad is very sensitive to a diverse array of pressures affecting its different life stages, 

including lack of connectivity between upland areas and breeding habitat, degradation of 

breeding habitat quality due to altered river hydrology and geomorphology, and invasive 

predators such as bullfrogs. The conceptual model in Figure 5 (page 24) is designed to 

emphasize life stage-specific pressures on the toad. The model also highlights important 

relationships while omitting many details already summarized in the species recovery plan 

(USFWS, 1999). 
 21 

Program 

Actions

Conservation 

Strategy & 

Management 

Activities 

State of Environment

Processes Habitats Species 

MANAGEMENT-ORIENTED CONCEPTUAL MODEL 

Effects

Pressures 

Figure 3. Key components of management-oriented conceptual models. Conceptual 

models facilitate adaptive management by showing how pressures and program actions are 

hypothesized to affect key components of the environment and their interactions. The 

components of conceptual models include: 

• State of Environment: the condition of ecological processes, habitats, and species (and 

their inter-relationships), which are directly or indirectly addressed by program 

objectives. 

• Pressures: these are agents that either promote or inhibit change, also called stressors, 

threats, or drivers. Because such agents may have opposite effects for two species, we 

use pressure as a more neutral term. Pressures can be anthropogenic (e.g., barriers to 

movement, disturbance, contaminants) or natural (e.g., climate variability, 100-year 

flood events). Pressures can also include natural constraints such as limited seed 

dispersal. 

• Program Actions: these include the conservation strategy of the NCCP/HCP and 

ongoing management activities expected to impact the State of Environment or

Pressures. 

• Effects: these are changes resulting from either Pressures or Program Actions. 
 22 

Box 4. Suggested components of covered species conceptual models. Each covered 

species should be represented by one or more conceptual models. Often key model 

components can be derived from the initial species assessments for the NCCP/HCP, but gaps 

in knowledge will undoubtedly exist. For each species, an attempt should be made to assemble 

the information below. 

Program objectives 

• List program objectives for the covered species. 

Species background and description 

• Life history: 

- For plants, describe life history, life expectancy (annual-biennial-perennial), 

reproductive ecology (pollinators, flowering period, annual variability in flowering, 

seed production, seed viability), seedling ecology (regularity of establishment, 

germination requirements, establishment requirements), dispersal patterns (Elzinga 

et al., 2001). 

- For animals, describe life history, life expectancy, food habits, predators, competitors, 

breeding season, age at maturity, number of offspring produced annually, frequency 

of breeding, home range, migratory patterns (Elzinga et al., 2001). 

• Describe current and historical species distribution; provide maps of known or 

hypothesized distribution and species occurrences. 

• Describe species-habitat associations including vegetation community associations, 

characteristics of good and poor quality habitat, and any other factors such as soil type, 

climate, slope, aspect, and moisture that are known to or hypothesized to influence the 

distribution of species across the landscape. 

• Describe species relationships to ecological processes (e.g., post-fire colonizing species).

Species status and trend 

• Identify relevant existing monitoring programs and historical data repositories. 

• Describe current known or hypothesized status and trends: estimate current population 

sizes, annual variation, number and distribution of populations, productivity of different 

populations, and condition of different populations. 

Pressures, program actions and their anticipated effects 

• Describe anthropogenic and natural pressures (i.e., threats, causes of change) and their 

hypothesized effects on the species, plus constraints such as limited seed dispersal or 

limited seed longevity. The hypothesized relationships between the pressures, the state 

of the species or habitat, and management actions should be explained. Some pressures 

may occur extremely rarely, such as extreme flood events that may be responsible for 

current species distributions. 

• Identify planned or potential management actions and their hypothesized effects on 

covered species. 

Special issues and critical assumptions 

• Describe any special issues and critical assumptions that should be included in the 

model. Examples might include: issues of scale, special assumptions made during 

reserve planning that require early testing, alternative hypotheses and alternative 

models, tradeoffs between managing habitat for different species, and public recreation 

access requirements. For example, the MHCP (2003) assumes that California 

gnatcatchers will use the small reserves in the MHCP as “stepping stones” to move 

between lands in southern San Diego County and Marine Corps Base Camp Pendleton 

in northern San Diego County. 

Diagram 

• Provide a simplified diagram of the conceptual model showing relationships between the 

covered species’ status and pressures and management actions. 
Coastal sage 

scrub/chaparral/ 

grassland model 

Hydrological/ 

geomorphic/ 

vegetation interaction 

Neotropical 

migratory bird 

model 

Fire & 

vegetation 

succession 

model 

Southwestern 

 pond turtle 

model 

Round-tailed 

ground 

squirrel model

Jerusalem 

cricket 

model

Least Bell’s 

vireo model 

Food web 

model 

Resident 

birds model 

California 

gnatcatcher 

model 

Reptile & 

small 

mammal 

community 

 model 

Coastal 

horned lizard 

model 

Figure 4. Hypothetical hierarchy of nested conceptual models. This hierarchy includes overarching multipnatural community assemblages models, various sub-models such as processes-vegetation models and food-specific covered species models. Examples of three of these conceptual models are given in Figures 5 throug

Riparian & 

associated floodplain 

model 

 Geomorphic 

model of dune mobilization & 

stabilization 

(Figure 7) 

Aeolian sands: 

 sand dunes and fields 

 (Figure 6) 

Arroyo toad 

model 

(Figure 5) 

Multiple natural community 

assemblages model 

& special issues 

23 
ADULTS 

Uplands 

BREEDING 

Jan – Early July** 

JUVENILES 

Uplands 

EGGS 

Feb-Early July** 

TADPOLES 

March-July** 

METAMORPHS 

(10-17mm) 

May-August** 

Breeding Adult Stage Characteristics

Breeding is nocturnal in spring after water temperatures reach at least 14 oC and water levels (<30 cm 

appropriate for breeding • Females assumed to lay only one egg mass • Males may mate with multiple Habitat Conditions

Clear still to slow-moving water with shallow, exposed clean, sandy bottom and open canopy [see influPressures (Stressors/Risk Factors)

Breeding habitat loss due to urbanization • Lack of flushing flows and sediment supply causes habitat 

Breeding habitat quality degradation and loss due to exotic plants (arundo, tamarisk) or to native plant

due to low annual rainfall, excessive water diversions and/or groundwater pumping • Roadkill / crushinPredation by raccoons, crows, bullfrogs, bass, crayfish, fire ants, Argentine ants? • Light pollution • Nocalling males but may have an effect on female response • Aquatic contaminants (sewage effluent, peretardant? • Disease? Influencing Factors

Episodic flushing flows and floods are needed to naturally disturb riparian habitat, clear vegetation on Variability in climate, amount of rainfall, and timing of rainfall strongly affect available habitat and bree

at all in drier years • Water diversions, and groundwater pumping can reduce flows • Dams alter the a

sediment supply • Beaver dams block sediment supply and alter river and stream hydrology • Excessiand contain contaminants • Weeds like arundo can slow flows and increase siltation • Ephemeral watelower concentrations of non-native fish and bullfrogs and perennial habitats have higher concentration breeding habitat 

Adult Life Stage Characteristics (limited knowledge)

Lifespan about 5 years (???) • Favor nights for activity, burrow in sand during day • Typically do not go more than 0.5-0.75 miles from breeding pools but may travel over 1 mile, distance influenced by topography and microclimate • Very dispersed • Feed on native ants and other invertebrates Habitat Conditions

Coastal sage scrub, chaparral, oak woodland, but not grasslands (may travel thru grasslands). Require friable soils and permeable plant understory for burrowing. Pressures (Stressors/Risk Factors)

Habitat loss • Lack of connectivity between breeding habitat and uplands • Roadkill / crushing by vehicles • Non-native ants (Argentine & fire ants) • Predation-native and house cats • Fire • Pesticides • Drought (starvation) 

Juvenile Life Stage Characteristics (limited

knowledge)

Assume moving into upland but may remain by pools for up to 6 months • More dispersed than metamorphs • Nocturnal • Assume eat native ants and beetles • Upland movement is close and parallel to stream and influenced by topography and availability of suitable microhabitatHabitat Conditions & Pressures 

Similar to adults 

Metamorph Life Stage Characteristics

Active during day on sandy benches • Still fairly clustered together • Feed on native ants and possibly other invertebratesHabitat Conditions

Soft, exposed, sand and moist sandy benches with partial shading adjacent to pools Pressures (Stressors/Risk Factors)

Crushing from vehicles and humans (when still clustered they are especially vulnerable) • Fire ants and Argentina ants displacing native ants • Predation from garter snakes, bullfrogs, birds (killdeer, herons) • Contaminants: pesticides, heavy metals, urban runoff, etc. • Habitat loss (arundo) • Compaction of sand prevents metamorph burrowing 

Tadpole Lif

Active durindownstreamHabitat Con

Similar to brperiphyton Pressures 

Predation: eetc. • Crushvehicles, livcan wash taDesiccation pumping, anContaminanurban runof

Egg Life St

Strings of 2mud along Habitat Co

Same as brsediment/tuPressures 

Desiccation pumping, adue to humUnseasonaPredation: eDisease? • treated efflu

Females mature: 2-3 years Males: 1-2 years 

* For details see arroyo toad recovery plan (USFWS, 1999) ** These dates may shift in some years depending on rainfall. Dates also shift in montane or inland desert areas. 

Possible Management Actions

• Protect and maintain breeding habitat and connectivity with upland 

habitats. Maintain sandy soil next to rivers. 

• Manage natural hydrology and sediment supply to extent possible to 

allow natural creation and maintenance of toad habitat. Maintain flushing flows during winter and avoid unseasonal floods during spring 

• Control invasive predators such as bullfrogs, African clawed frogs, 

non-native fish in and around breeding areas. Control invasive plants in and around breeding areas (arundo, tamarisk, watercress). Control beavers. 

• Avoid disturbance, crushing, and siltation of breeding areas by 

vehicles/humans/livestock during breeding season 

• Minimize contaminants 

12-20 days 

65-85 days 

Figure 5. Species-focused 

conceptual model for southwestern 

arroyo toad (Bufo californicus) * 

(taken from Atkinson et al., 2003b) 

24 
 25 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 6. Aeolian sand natural community assemblage conceptual model of pressures on 

covered species. This example comes from the draft Coachella Valley Multiple Species Habitat 

Conservation Plan (Figure 8-7, CVMSHCP, 2004). The figure summarizes the main pressures, 

their relationships and their hypothesized effects on covered species in the aeolian sand natural 

community assemblage. In any management-oriented conceptual model, making the link to 

potential management activities is critical. Box 5 (page 27) shows the related conservation 

strategy and management activities. 

Urbanization 

adjacent to 

conserved areas 

Off-road vehicle 

trespass 

Prolonged drought 

Exotic plant 

infestations 

Blocked 

sand/wind corridor 

Prolonged above 

average rainfall 

Habitat 

fragmentation - 

roads 

Increased feral 

animal predation 

Exotic ant 

infestation 

Collapsed burrows

Reduction in 

native plant 

abundance

Stabilization of 

aeolian sand 

habitat 

Road mortality – 

edge effects 

Reduced roundtailed ground 

squirrels 

Reduced Palm 

Springs pocket 

mice

Reduced CV 

Jerusalem crickets

Reduced flattailed horned 

lizards 

Reduced CV 

fringe-toed lizards

Reduced CV giant 

sand-treader 

crickets 

Reduced CV milkvetch 

The 

shaded 

part of this 

model is 

expanded 

upon in 

the sand 

process 

sub-model 

in Figure 7 

Human-induced 

and natural pressures 

Effects on 

covered species
 26 

 

Figure 7. Aeolian community sand process model. This sub-model of Figure 6 summarizes 

the geomorphic processes of sand dune stabilization and destabilization and their relationships 

to weather, non-indigenous plants, and sand movement blockage. The figure is from the draft 

Coachella Valley Multiple Species Habitat Conservation Plan (Figure 8-6, CVMSHCP, 2004; 

See also Barrows, 1996) and is explained in greater detail in the text of that document. 

Rare, 

intense 

storm event 

(ranging in 

periodicity 

from 

decades to 

centuries) 

delivering 

sand to the 

valley floor 

Tree rows 

and buildings 

block 

downwind 

sand 

movement 

Strong winds 

sort sands, 

with those 

particles from 

1.0 to 0.1 

mm accreting 

downwind 

into dunes 

and 

hummocks 

Reduced 

water table 

reduces 

mesquite & 

other shrubs 

that promote 

dune 

development 

Aeolian sand 

dune animals 

expand 

distribution 

with 

increased 

sand mobility. 

Food web 

depends on 

perennial 

plants, 

detritus 

Dunes and 

hummocks 

increase 

mobility and 

expand 

coverage of 

Aeolian 

habitat 

downwind 

“Average” 

Rainfall 

Dunes and 

hummocks 

reduce 

mobility; 

high number 

of annual 

plants on 

dunes 

Higher organic content of dunes favors 

exotic weed establishment, increasing 

stabilization and favoring exotic plant 

establishment 

Multi-year 

drought 

Weather 

Multi-year 

above 

average 

rainfall 

Mortality and 

reproduction 

roughly equal 

for stabilized 

and destabilized dune 

lizards, and 

other species 

Increased 

dune 

stabilization 

favors 

stabilized dune 

species. 

Species 

favoring active 

dunes reduced.

Flood control 

and alluvial fan 

development 

eliminates sand 

transport onto 

the valley floor 

[aeolian 

transport zone] 
 27 

Box 5. Conservation strategy and management activities portion of the aeolian 

sand natural community assemblage conceptual model (see Figure 6). The activities 

are rated by the degree of knowledge about results: *** = high, ** = moderate, * = low. 

Conservation Strategy

Maintain natural communities and covered species by protecting sufficient connected 

habitat and maintaining ecological processes (**) 

Protect wind and sand deposition corridors (**) 

Management activities within reserves

Eliminate OHV trespass through fencing, signage, and enforcement (***) 

Restrict human access to most sensitive habitats (***) 

Remove structures and exotic trees blocking wind and sand deposition corridors (**) 

Control exotic plants (*) 

Restore active dunes and structural complexity, if necessary, by hauling sand lost from the 

downwind side of reserves back into upwind sand corridor, using sand fencing, and/or 

destabilizing stabilized sand dunes (*) 

Other habitat enhancement and restoration (*) 

If determined necessary, experiment with dog-proof fencing to exclude feral dogs—but 

evaluate unintended impacts of excluding coyotes (*) 

If necessary to reduce road mortality, place low, fine-mesh fencing near roads on 

Thousand Palms reserve (*) 

If unable to prevent local extinction, reintroduce lizard species from other reserves in 

CVMSHCP (assumes prior evaluation of local population genetics) (*) 
 28 

The conceptual model for the CVMSHCP aeolian sand natural community assemblage is shown 

in Figures 6 and 7 and in Box 5 (pages 25-27). Figure 6 summarizes hypothesized relationships 

between pressures and the effects on covered species. Figure 7 is a sub-model of Figure 6 that 

shows in greater detail the relationships between sand deposition, stabilization, and 

destabilization processes, annual rainfall, exotic plants, and stabilized and destabilized sand 

species. Box 5 summarizes the conservation strategy and proposed management activities that 

were determined by analyzing of the aeolian sand natural community assemblage conceptual 

model. For proposed management activities we have also assigned levels of certainty about how 

to implement them and the expected response; actions involving a high degree of uncertainty 

should be initially designed as experiments. 

4.5.4 Utilizing species assessments to create models of natural community assemblages

Building a conceptual model for a natural community assemblage can be daunting. One way to 

create one is to utilize the large amount of information gathered for the covered species 

assessments. Many covered species are affected by similar pressures, as is shown in Figure 6. 

For plans with large numbers of covered species, draft natural community assemblage models 

can be assembled by summarizing all the pressures identified for the covered species and using 

that list to identify 1) the main pressures on the assemblage components and 2) key management 

issues. Once this initial model is drafted, additional areas of the model that need further 

development can be identified, such as the detailed aeolian sand process sub-model in Figure 7. 

Models developed in this way make clear the link between management at the natural 

community assemblage level and the status of covered species, and take advantage of the 

considerable information assembled in the NCCP/HCP planning process. A step-by-step 

description of building from covered species models to natural community assemblage models 

and landscape-level models is given in Appendix C. 

4.6 Step 6. Determine what to monitor and identify critical uncertainties 

Once draft conceptual models have been assembled, the program can select which attributes of 

the system to monitor, determine the specific monitoring objectives and appropriate monitoring 

variables for each attribute, and identify critical uncertainties requiring targeted study. The 

program should also assess the suite of monitoring and research opportunities from a programwide viewpoint, identifying any remaining gaps and eliminating unnecessary redundancies. 

Although outside review of the conceptual models is helpful, the program need not wait to 

receive such review before moving forward with Step 6. 

4.6.1 Select the attributes to monitor 

Using the conceptual models developed in Step 5, the appropriate attributes of the system to 

monitor can be selected. An attribute is any component or condition of the system that can be 

quantifiably measured, for example, forest cover, precipitation or arthropod species diversity. 

Different attributes are monitored for different purposes. Some are resources described by 

program goals, such as covered species. Others provide early warnings of subtle changes that 

might be of concern, such as the appearance of exotic ants. Still others function as covariates, 

assisting interpretation of other attributes such as annual precipitation. 
 29 

For example, inspection of the aeolian sand conceptual models (Figs. 6 and 7) might suggest 

monitoring some of the following general attributes in addition to covered species population 

trends and distribution: weather, areal extent of each natural community, off-highway vehicle 

activity, vegetation, reptile community, arthropod community, and feral and domestic animal 

activity. Choosing attributes that show sensitivity to pressures and sources of change can 

increase the effectiveness of the program. In this example, monitoring the extent and distribution 

of the different types of natural communities, especially stabilized and destabilized sand, will 

provide a warning of when the system is trending towards having too little habitat for either 

stabilized sand or destabilized sand species. Similarly, changes in the arthropod community, 

especially detection of invasive argentine ants, could be an early warning of food-web shifts with 

potentially serious consequences for higher trophic levels (CVMSHCP, 2004 draft).

Another example of an early warning attribute is monitoring a benthic invertebrate community to 

detect contaminants effects. This approach allows earlier detection than monitoring higher 

taxonomic groups, such as bird populations, and thus may allow remedial action before 

substantial harm has been done. In addition, sometimes monitoring the direct input of a pressure 

itself, such as the quality of water discharged into rivers, may be more effective in improving 

management than monitoring the endpoint such as cumulative changes in water quality at a 

distant point in a watershed or the effect on a sensitive fish species (MacDonald and Smart, 

1992). 

We pause here to interject a note of caution. Using habitat extent and condition as a surrogate for 

species population monitoring is an appealing but controversial issue. In general, we simply 

know too little about species relationships to habitat to monitor reliably most covered species by 

habitat-only monitoring (e.g., Lawler and Schumaker, 2004). Instead, we recommend monitoring 

both habitat and species at some level. Appendix D discusses this issue further. 

4.6.2 Specify monitoring objectives 

Once the general attributes to monitor have been selected, the specific testable “questions” or 

objectives that the monitoring program will address should be clearly articulated. Then the 

monitoring variables and the exact scope of the monitoring should be specified. Monitoring 

objectives should be directly derived from the overarching goals and objectives of the 

NCCP/HCP conservation strategy. The specific monitoring objectives should be articulated as 

clearly as possible, leading directly to how data will be collected, interpreted and put to practical 

use. The clearer these objectives, the easier it is to design the rest of the monitoring program 

(MacDonald and Smart, 1992; Olsen et al., 1999; Yoccoz et al., 2001). 

For example, the MHCP conservation goals for least Bell’s vireo (Vireo bellii pusillus) are: 

“Ensure species persistence in the plan area and contribute to species recovery. Improve habitat 

quality and increase species abundance to contribute to regional population viability.” (MHCP, 

2003). How the monitoring program will specifically measure progress towards these goals 

needs to be clear when they are restated as monitoring objectives. Objectives can be formatted as 

questions or as statements. 
 30 

In the least Bell’s vireo example above, the MHCP monitoring objectives during Phase 1 

(inventorying resources and identifying relationships) are fairly straightforward: 

• What is the distribution and status of least Bell’s vireo populations in the planning area? 

• With what specific habitats is least Bell’s vireo associated? 

• What are the extent, distribution, and condition (e.g., level of obvious pressures) of those 

habitats? 

• To what pressures is least Bell’s vireo sensitive? 

For monitoring in Phase 2 (pilot testing of long-term monitoring and resolving critical 

management uncertainties) or in Phase 3 (implementing long-term monitoring and adaptive 

management) the questions will be more specific. Long-term monitoring questions (objectives) 

for least Bell’s vireo will likely fall into the following categories: 

• “Status and trends” questions: Is the estimated abundance of least Bell’s vireo in the plan 

area within the bounds of the baseline range of variation? If not, is it increasing or 

decreasing? 

• “Early warning of problem” questions: Is the areal extent of least Bell’s vireo habitat 

changing? What is the abundance or proportion of area occupied by cowbirds (Molothrus 

ater), a nest parasite, in least Bell’s vireo nesting areas? 

• “Targeted study” questions: At what rate does cowbird nest parasitism have a measurable 

impact on reproductive success of least Bell’s vireo? Which habitat restoration techniques 

result in a least Bell’s vireo reproductive success rate at or above a level sufficient to 

sustain populations? 

A monitoring strategy should attempt to accommodate the different scales of analysis identified 

in Step 2. These include individual reserve scale, NCCP/HCP scale, and ecoregional scale. Both 

the goals for an individual reserve plus the reserve’s regional role will influence the approach to 

monitoring at individual reserves. For example, putative breeding habitat for California 

gnatcatchers (Polioptila californica californica) might be surveyed differently than dispersal 

habitat (MHCP, 2003). The monitoring focus might also be different at different scales. For 

example, wide-ranging species like mountain lions (Felis concolor) might be monitored 

throughout an ecoregion, in an individual NCCP/HCP as part of a targeted study to determine 

whether biological corridors are functioning as intended, and in local reserves as part of medium 

and large carnivore inventories. It might be possible to address these different scales 

concurrently with a single monitoring design (e.g., radio-tracking studies), or different 

approaches may be required. Because funding is limited, the monitoring program should focus 

on the level that is most relevant to management of the resources. At this point the program also 

needs to consider how exactly the monitoring data will be analyzed and interpreted so that 

collected data will be applicable to all scales. 

4.6.3 Select monitoring variables

Once the monitoring objectives have been articulated, the monitoring variables can be selected. 

Frequently these variables are fairly obvious based upon the objectives. A good monitoring 

variable should be relevant to management, have strong scientific underpinnings, be measurable 

and feasible, statistically rigorous, and easily understood and interpreted. Appendix E lists and 
 31 

describes characteristics of good monitoring variables in greater detail. Obviously not all 

monitoring variables will meet all criteria, but they should meet as many as possible. 

Based upon the monitoring objectives for least Bell’s vireo, a possible monitoring variable would 

be an estimate of seasonal least Bell’s vireo relative abundance based upon point-distance 

surveys in vireo habitat and using double-observer methods to create confidence intervals that 

account for observer bias. Another alternative is to monitor the proportion of area occupied by 

vireos, dividing potential habitat into sampling units which are visited two or more times for 

presence rather than abundance. Additional monitoring variables based on the objectives could 

include the relative abundance of brown-headed cowbirds seen during transect counts, locations 

of invasive riparian vegetation (e.g., Arundo donax) and other measures that reflect vireo habitat 

quality. 

Once candidate monitoring variables have been identified, a description of each monitoring 

variable and its characteristics should be made (see Box 6). The intensity of monitoring for 

species or biological communities may vary considerably depending on the attribute monitored, 

the ultimate goal, and the priority of the issue or species. In Appendix F we provide examples of 

species-level monitoring variables of increasing intensity of effort. In Appendices G and H, we 

provide examples of variables used to monitor natural community assemblages and landscapelevel issues.

While selecting the monitoring variables, program designers should visualize how the 

monitoring data will be analyzed and interpreted. Sometimes what seems like a good variable to 

monitor becomes less desirable when one actually visualizes using the information. For example, 

trends in bird abundance might seem like useful information to have. However, they might be 

difficult to interpret without other simultaneous monitoring of habitat extent and condition, or 

without comparison with trends in neighboring areas. Realizing these limitations up front allows 

these considerations to be built into the program, or may dictate the selection of different 

monitoring variables. Program designers should imagine a range of possible future scenarios 

Box 6. Description of monitoring variables. Supporting documentation should 

accompany the selection of each monitoring variable, to improve clarity and understanding 

among all program managers in the present as well as in the future. A description of each 

monitoring variable should include the following details: 

• “What” will be monitored 

• “Why” tracking this variable is useful and the specific question the data will be used 

to address 

• The conceptual model that underlies the monitoring variable 

• The geographical area where it will be monitored 

• The specific protocol that will be used to collect data 

• The range of values the data can take and what the values mean 

• The expected response of the monitoring variable to pressures or to management 

(i.e., increase, decrease, or remain stable) and the magnitude of change expected 

• The temporal and spatial scales over which change is expected to be manifested 

• Whether the needed data are already being gathered, and, if so, by whom 

 (Adapted from Gibbs et al., 1999; National Research Council, 2000)
 32 

to determine if the monitoring variables selected will be sensitive to anticipated and unanticipated 

sources of change, and to determine how the data should be analyzed and interpreted. For 

example, a program might initially choose “relative abundance estimated by number of pairs of 

California gnatcatchers observed on reserves” as its monitoring variable. Program designers 

might then visualize the following scenario using this sampling design: 

Observers conduct complete censuses of the numbers of gnatcatcher pairs on each reserve. 

The number of gnatcatcher pairs initially counted across all reserves is 563. In subsequent 

years, counts of 595, 420, and 457 pairs occurred. Observers varied among reserves and 

among years. 

One can anticipate that it will be difficult to interpret these data, because annual changes in the 

number of gnatcatcher pairs observed could be due either to a trend in gnatcatcher abundance or 

to different levels of expertise of the different observers. To reliably estimate the number of 

gnatcatcher pairs, some estimate of observer variability is needed. Correct interpretation of the 

data, in this case, might require a double-observer technique (Nichols et al., 2000). However, 

because the effort involved in implementing this design in a statistically sound manner is very 

high, an alternate monitoring variable such as a proportion of area occupied approach might be 

more desirable. This method is more easily standardizable across observers than counts, allowing 

program-wide estimates of occupancy to be made with statistically robust confidence limits 

(MacKenzie et al., 2002; Winchell, 2004). This design can be linked to management by also 

assessing covariates such as the dominant plant species at sampling points. By making the link to 

the type of habitat gnatcatchers inhabit, and monitoring the extent of this habitat in the reserve 

system, an effective link to vegetation management activities can be made. 

4.6.4 Identify critical uncertainties and targeted study questions 

Resolving critical uncertainties is a key feature of the adaptive management process. Because 

NCCP/HCP monitoring and adaptive management programs start with very little knowledge, 

they should work proactively to learn about the ecosystem before problems arise. Effective 

adaptive management goes beyond simply monitoring an ecosystem until an adverse condition 

occurs and then responding with an appropriate correction. Given the high variability in 

abundance of some species and the high level of uncertainty about causes and appropriate 

management actions, a species could go extinct by the time that 1) a negative trend is statistically 

discernable, 2) the cause of the trend is discovered, 3) an action to correct the problem is 

identified, and 4) the action is implemented. In adaptive management, monitoring is used not 

only to detect changes but also to discern potential causes of change. The program may also 

employ short-term targeted studies or establish adaptive management experiments to more 

effectively resolve critical uncertainties. 

Typical uncertainties that NCCP/HCPs confront include: 

• Critical gaps in knowledge of range and distribution of covered species, their specific 

habitat requirements and the pressures that affect them. 

• Uncertainties about the relationships between the various NCCP vegetation communities 

and the ecological processes and pressures that drive system dynamics. 

• Critical assumptions behind the conservation strategy that are important to the long-term 

success of the program – for example, the San Diego Multiple Habitat Conservation 
 33 

Program (MHCP, 2003) assumes that corridors and linkages between reserves will 

maintain access for top-down predators such as coyotes that control feral cat populations, 

which in turn prey upon covered species. 

• Uncertainties about the most appropriate and cost-effective management strategies to 

employ. 

Conceptual models should be used to identify critical uncertainties and assumptions. These 

uncertainties should be evaluated to determine their likely influence on decision-making and the 

level of effort needed to resolve them. Uncertainties that constrain decision-making should be 

prioritized. Some of these can be resolved quickly while other decision-making is moving 

forward. Others may take longer to answer, but should be clearly identified in program design if 

they potentially impact decision-making. Not all uncertainties must be resolved before the 

program moves forward, but the possible consequences should be understood. Some questions 

that surface during conceptual model development may be more effectively addressed by 

targeted studies than by long-term monitoring. 

For example, the relationships among Coachella Valley ground squirrels (Spermophilus 

tereticaudus chlorus), vegetation and substrate were hypothesized but untested. A subsequent 

study suggested modifications to the conceptual model based on where the squirrel was found 

during surveys (L. Ball and P. Doherty, unpublished data). In a second example, development of 

the Coachella Valley aeolian sand conceptual model highlighted a critical uncertainty about how 

far urban development edge effects extended into the reserves and how this would change as 

urbanization progressed. This uncertainty could affect estimates of how much active core (nonedge) dune habitat remained in the reserves. As a result, the pilot phase of the monitoring 

program was designed in part to resolve uncertainties regarding edge effects (Barrows, 2003). 

Similarly, because the lifespan of the southwestern arroyo toad (Bufo californicus) is not known, 

predictions about how the combination of Loveland Dam water operations and multiple-year 

drought might affect the toad cannot yet be made with confidence (Madden-Smith et al., 2003). 

Monitoring programs should approach conventional wisdom with skepticism. Sometimes, ideas 

are repeated so often that they appear “true.” Conceptual models should be revised and tested by 

investigating critical assumptions and replacing correlations between variables with more 

mechanistic understandings of cause-and-effect relationships. Critical relationships in the model 

that have some degree of uncertainty should be represented as a set of competing hypotheses 

that, once tested, reduce the uncertainty in that relationship (Nichols, 2001). For example, the 

disappearance of southwestern pond turtle populations in San Diego County has been suggested 

to be a response to diseases from introduced pet turtles, competition with introduced pet turtles, 

degradation of water quality, and loss of upland breeding habitat (Meyer et al., 2003). These 

should be viewed as competing but not mutually exclusive hypotheses. Methods such as 

Akaike’s Information Criterion (AIC) can be used to evaluate the relative fit of these different 

hypotheses to the data (Burnham and Anderson, 2002). 

4.6.5 Assess the suite of monitoring variables and any critical uncertainties 

When the program has identified its monitoring variables and critical uncertainties, it is good to 

step back and assess the suite of variables and targeted studies from a “big picture” viewpoint, 

filling in any gaps and eliminating unnecessary redundancies. All program goals should be 
 34 

addressed. Ideally the suite of monitoring and research recommendations should each be clearly 

linked to conceptual models and be necessary, sufficient, and feasible for meeting their 

objectives while avoiding unnecessary redundancy. 

At the conclusion of Step 6, the program should have lists of monitoring variables that will be 

tracked and critical uncertainties that need to be resolved. The rationale for each should be clear, 

based on an inspection of the conceptual models for covered species, natural community 

assemblages, and landscape-level issues. This is a good point to solicit additional review of the 

conceptual models, as well as the monitoring and targeted study recommendations. 

4.7 Step 7. Determine strategy for implementing monitoring 

Once the monitoring variables and critical uncertainties have been identified, they should be 

prioritized and organized into a work plan. Good monitoring protocols will need to be identified 

or developed and statistically robust sampling designs implemented. 

Monitoring and research questions should be at least loosely prioritized (e.g., identified as 

“critical,” “important but not immediately critical,” and “interesting but not high priority” or on 

some similar continuum). Monitoring and research should also be categorized by the level of 

effort required. Some uncertainties can be opportunistically resolved as part of other projects. 

For example, during a species inventory, basic habitat information can also be collected with 

little increase in effort. One way to create a prioritized list is to have the scientists and managers 

involved in developing the recommendations individually rank each monitoring and research 

question according to a priority level between 1 and 5 based upon their opinions. The average 

rankings can then be used to guide development of a workplan. 

4.7.1 Develop a workplan

The workplan creates a blueprint for how the program will progress towards its objectives and 

what the monitoring program will have accomplished at the end of 1, 5, 10 years and beyond. 

The program should decide which program elements to implement immediately versus 5 years 

from now, determine the immediate next steps, and identify costs. Examples of workplan tasks 

include: conducting a basic inventory for various taxa coupled with gathering habitat and 

pressures information; designing long-term monitoring protocols for species whose distribution, 

basic life history, and spatial and temporal variation are already understood; collaborating with 

existing monitoring programs and working to fill gaps in the sampling efforts; and standardizing 

monitoring protocols across multiple agencies. Staged implementation of the program may be 

needed to make the best use of funding. 

Anticipated monitoring and adaptive management tasks and timelines for an NCCP/HCP are 

shown in Figure 8. This example is general and hypothetical, but it shows how the program 

needs to be able to evolve through time and how the emphasis on certain tasks will change. 

4.7.2 Coordinate with existing programs

Once the high priority monitoring variables have been identified, the program should determine 

where already existing monitoring programs might meet its needs. Existing programs should be 

assessed based upon: the monitoring objectives of the existing program; appropriateness and 
 Planning Plan 5 

 Initiated Approved years Identify overarching scientific principles (early Steps 1 & 5) Define NCCP/HCP goals and identify scope (Steps 1 & 2) Compile and assess existing background information and data (Step 3) Partition system, create (and revise) conceptual models (Steps 4 & 5) Design conservation strategy (Steps 1 & 5, further defined) Design (and revise) monitoring program and management program  (Steps 6-9, revisit Steps 1-5 as necessary) Phase 1: Inventorying resources and identifying relationships (Steps 7-9) Phase 2: Pilot testing of long-term monitoring and resolving critical management uncertainties (Steps 7-9) Phase 3: Implementing long-term monitoring and adaptive management (Steps 7-9) Programmatic review of monitoring and management (Step 9) Figure 8. Tasks to occur in planning phase and early implementation of an NCCP/HCP. The steps in this dtask relates to are identified in parentheses. Note that the steps are revisited and increasingly defined as more iavailable and also to meet the specific needs of the monitoring program. Increasing thickness and density of the indicates increasing intensity of work by the program. 

Plan 

Development 

P

Implem

35 
 36 

statistical rigor of the sampling design and protocols; timing and frequency of sampling; level of 

quality assurance in data collection and data management; reporting cycles and access to the 

data; expected duration of the program; and potential institutional barriers. If no relevant 

monitoring programs intersect the planning area, the program should still investigate neighboring 

areas for monitoring programs. Wherever possible, the NCCP/HCP program should consider 

coordinating with other programs to ensure data compatibility and to allow regional analyses that 

add value to each of the monitoring programs. If existing monitoring programs are not available, 

then the program will need to develop its own protocols and sampling designs. 

4.7.3 Develop good monitoring protocols

A good monitoring protocol should be appropriate for the task and be accurate, reliable, feasible, 

and cost-effective (Margoluis et al., 1998). Monitoring protocols should be well documented, 

easily standardized across observers, and either minimize observer bias or allow estimation of 

bias. A common problem with interpreting monitoring data is uncertainty regarding whether 

changes in the data reflect actual changes in the population or changes in the observer (Sauer et 

al., 1994). The program should plan for the protocol to be applied by multiple people and by 

different people through time. Training to standardize application of the protocol for multiple 

observers is one way to reduce bias. The National Park Service Inventory and Monitoring 

Program provides a good description of the elements of a good monitoring protocol (Oakley et 

al., 2003). 

Because ecosystem elements such as riverine hydrology, water quality and harvested species 

such as waterfowl and fisheries have received a great deal of attention, standardized protocols for 

monitoring them are more widely available. More recently, monitoring protocols for terrestrial 

biota have been developed and tested. Programs seeking to monitor terrestrial biota might 

consult the following documents: Ralph et al. (1993), Heyer et al. (1994), Sutherland (1996), 

Wilson et al. (1996), Elzinga et al. (2001), Krebs (1999), Nur et al. (1999), and Bibby et al. 

(2000). Other sources for protocols include U.S. Geological Survey, Point Reyes Bird 

Observatory (www.prbo.org), California State Parks Inventory Monitoring and Assessment 

Program (http://www.parks.ca.gov/default.asp?page_id=836), National Park Service Inventory 

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

Department of Fish and Game (http://www.dfg.ca.gov). 

4.7.4 Avoid common statistical pitfalls in the development of sampling designs 

Many authors provide excellent detailed advice on sampling design (Thompson and Seber, 1996; 

Margoluis et al., 1998; Thompson et al., 1998; Elzinga et al. 2001; Morrison et al., 2001; 

Thompson, 2002). The following are critical issues and principles: 

Exploratory vs. hypothesis-testing studies 

During Phase 1, when very little is known about a system, correlative investigations assessing 

associations among species, pressures, and habitat characteristics can be very useful. However, it 

is important that the program move on from these exploratory studies to develop and test a priori

hypotheses about the system (Yoccoz et al., 2001). This is because: 1) simple associations and 

correlation are not sufficient to prove causation— independent hypothesis testing through 

experiments is needed to confirm patterns found in exploratory studies and 2) given enough time 

and enough variables, retrospective analyses of a data set may find correlations that are 

statistically significant but have no biological meaning. In addition, monitoring variables that do 
 37 

not add meaningful information should be dropped and the protocol simplified. Thus the 

program should avoid the trap of assuming that retrospective analysis will provide conclusive 

answers – in other words, that the cause of a trend will be discernable from the covariates 

simultaneously measured (Nichols, 2000; Yoccoz et al., 2001). For example, arroyo toad 

tadpoles are negatively associated with pools containing crayfish (Procambarus clarkia) at 

Marine Corps Base Camp Pendleton, but it is unclear if crayfish survive better in pools with 

characteristics avoided by breeding toads, or if the crayfish eat the tadpoles (Brehme et al., 

2004). The answer to this question has very different implications for management and could be 

resolved with an experiment. 

Randomization, stratification, and probability-based sampling 

An approach to data analysis should be determined before a final sampling design is selected and 

data are collected, preferably in consultation with a statistician. This step hopefully ensures 

implementation of a sampling design that will allow the data to be used to the maximum extent 

possible. Non-random selection of sites, use of opportunistic sampling, not accounting for 

imperfect detection, vague questions and hypotheses, and failure to evaluate statistical power can 

all lead to a costly reduction in the information extractable from collected data (Morrison et al., 

2001). Monitoring costs money and consulting with a statistician before entering the field will 

improve the return on monitoring resources invested. 

Balancing a statistically robust sampling design with logistical constraints can be challenging. 

However, as a basic principle, sampling units should be randomly selected from the target 

population such that each member of the target population has a non-zero probability of being 

selected (Olsen et al., 1999; Yoccoz et al., 2001). For example, if the purpose is to measure 

trends in abundance of California gnatcatchers (Polioptila californica californica) throughout 

coastal sage scrub habitat in San Diego County, no suitable habitat should be excluded during the 

sampling unit selection process. If the purpose is instead to measure trends in gnatcatcher 

populations on publicly owned lands within the county, then the sampling units need only be 

selected from this subset of the available habitat. 

Some common biases that occur in sampling unit selection and that should be avoided are: 

• Judgment sampling: If sampling only occurs in what are judged “best sites”, then 

inference can only be made about changes in those “best sites”. This assumes that the 

researcher knows what the “best sites” are, and can define them in such a way that it is 

standardizable and reproducible across observers. 

• Temporary hotspots: Selecting sampling units in what is “good” habitat today is almost 

guaranteed to produce a negative trend in a fluctuating environment as the habitat shifts 

from good to sub-optimal and nearby areas shift from sub-optimal to good. In addition, 

sites selected in this way cannot be used to infer changes in other areas that were not 

included in the random sampling process (Anderson, 2001). 

• Convenience sampling: If lands are excluded from the random selection of sampling 

units, then one can only make (at best) weak inferences about them, e.g., if sampling is 

only done along roads and trails, then one can only draw conclusions about areas along 

roads and trails. The sampling does not allow for inferences about areas that are distant 

from roads and trails. 
 38 

One way to help optimize the sampling design is to stratify the randomization process by habitat 

type or by priority level. For example, if we expect more change and impacts of concern near 

human developments, we might select fewer units in hard to reach areas of a reserve system. 

Using this approach, because each area of the reserve has a non-zero probability of being 

sampled, inferences can be made across the entire reserve system (Olsen et al., 1999). 

Stratification can also be based upon habitat. For example, if Species B only uses a specific type 

of oak woodland, then sampling units for that species need only be placed in that type of habitat. 

Because of their obvious role in sampling design, we recommend that the program develop 

habitat-species relationships and habitat maps before finalizing long-term sampling schemes. 

Sampling designs and techniques for analyzing monitoring are continually being developed. 

Some approaches receiving increased attention are listed in Appendix I. 

Supplement systematic sampling with opportunistic sampling 

Opportunistic sampling can add information about species distributions, but should complement, 

rather than replace, systematic sampling efforts (Gibbs et al., 1999). Examples of opportunistic 

sampling include miscellaneous road-kill data or species observed during hiking or management 

activities. When observations are verified as coming from a reliable source and the location is 

accurately recorded, these data may confirm the continued presence of a species that was not 

detected during more systematic sampling efforts. Opportunistic sampling can also include data 

collected during short-term scientific studies (Gibbs et al., 1999). 

Detection probability of the protocol 

Rarely are species 100% detectable, even when they are known to be present. Thus, most 

protocols and analyses should include some estimate of detection probability and/or observer 

bias (Nichols, 2000; Yoccoz et al., 2001), using methods such as the proportion of area occupied 

(MacKenzie et al., 2002) or double observer methodologies (Nichols et al., 2000). This is 

essential if we hope to differentiate trends in species abundance from changes in the detection 

probability. 

Replication: Use power analysis to optimize sampling design 

Before shifting from Phase 2 (pilot monitoring) to Phase 3 (long-term monitoring), a power 

analysis should be conducted to determine the minimum number of sampling units required to 

detect a specific decline at acceptable levels of power. Sampling designs with insufficient power 

will be unable to distinguish true change from the inherent natural variability of the system and 

thus consume resources without providing useful information. Elzinga et al. (2001) and 

Anderson (1998) provide a good discussion of power analysis. 

Thresholds and trigger points 

Management frequently requests a “threshold” or “trigger” point that will trigger a management 

response if the monitoring variable (e.g., species abundance or distribution) falls below that 

level. Such concepts should be used with extreme caution because 1) a great deal of uncertainty 

exists in establishing appropriate thresholds, 2) managers may assume that no management is 

required unless this threshold is exceeded, 3) managers may over-react if a threshold is exceeded 

in times of drought or other natural variation, and 4) managers may be tempted to manage to the 

threshold, working to maintain abundances at the threshold rather than more biologically-valid 

goals. Terms such as “confidence limits” or “control limits” are slightly less misleading. 
 39 

However, even if 95% confidence limits for variables are calculated from a baseline data set, the 

managers must understand that there is nothing “magical” about these numbers. They only tell 

when current data are different from data collected in the baseline years, not why, or even if this 

is a concern. These control limits or statistical confidence levels are guides to assist management 

but do not replace common sense (Atkinson et al., 2003a). For example if new problems emerge, 

such as the appearance of new non-native plants or predators, managers should not wait until a 

threshold is exceeded before acting. 

Take advantage of extreme events as experiments 

The program should plan to take advantage of extreme circumstances to learn more about system 

function. Opportunities may be presented by extreme fires, extreme droughts, 500-year flood 

events, high contaminant levels during first season rains, and accidental breakdown of water 

pumping facilities. To the extent possible, the program should identify such uncertainties ahead 

of time, as well as any warning indicators for when such an extreme event might occur, to give 

management time to prepare personnel, equipment, permits, and funding in advance. 

4.8 Step 8. Develop data quality assurance, data management, analysis, and reporting 

strategies 

A new monitoring program must not underestimate the importance and cost of data handling, 

analysis and reporting. Monitoring information is “wasted if it is not analyzed correctly, archived 

well, reported timely, or communicated appropriately” (Gibbs et al., 1999). The program should 

invest in a good data management program. The National Park Service Inventory and Monitoring 

Program recommends that at least 30% of monitoring funds go to data management and 

reporting (National Park Service Inventory and Monitoring Program, 2004). 

Good data management maximizes the utility of the data, making it available for queries by 

managers and scientists addressing new issues and research questions, while also providing 

information for the long-term monitoring program. Data generated by regional conservation plan 

monitoring programs has vast potential value beyond its initial intended uses. Maintaining access 

to raw data, coupled with metadata describing data collection methods, greatly increases data 

value and utility. 

A well-designed data management system also improves the level of quality assurance in the 

program and provides strong incentives to all program participants to standardize and coordinate 

protocols. The state of California is developing a multi-taxa, multi-level integrated data 

management system for monitoring data collected throughout the state that will allow powerful 

queries by species, study type, habitat or geography. With increasing sophistication in technology, 

it is possible for data collection entities to maintain a copy of the database and mirror those data in 

near real-time to a state database while maintaining local control over data entry and corrections. 

Quality assurance is a critical feature of a long-term monitoring program, if long-term trends are to 

be reliably assessed. Some elements of quality assurance are listed in Appendix J. 

Transparent and timely reporting is another feature of an effective adaptive management 

program. Results from monitoring, adaptive management experiments, and research all need to 

be reviewed for quality and effectively shared. Information must reach the appropriate audiences 

in a timely fashion and at an appropriate level of detail. Results that alter conceptual models 
 40 

should be made known to all involved parties, especially results that impact management, show 

critical assumptions are incorrect, indicate new problems are developing, or suggest historical 

relationships or correlations are changing. 

Communication of monitoring and adaptive management results may be accomplished by an 

effective web interface including a web-accessible database, a regular newsletter or bulletin, 

technical reports on results of monitoring and targeted studies, progress reports, and scientific 

publications. Communication can also consist of workshops and field days to share new 

management techniques and developments, science conferences to discuss what new information 

has been learned about both the natural resources involved and the success of various 

management and restoration techniques, and regular meetings for monitoring staff and 

management staff within and across NCCP/HCP programs. 

4.9 Step 9. Complete the adaptive management loop by ensuring effective feedback to 

decision-making. 

An efficient decision support system that feeds information efficiently back into decision-making 

requires initial planning and adjustment as time goes on. Ensuring that the monitoring results 

appropriately influence management requires consistent effort from an assigned staff, with 

adequate funding, and a consistent attitude of getting quality information out to be evaluated, 

peer-reviewed, and into the hands of decision-makers in a timely fashion. Such a decision 

support system serves the entire conservation program. 

Major responsibilities of the decision support system include the following. 

• Manage plan implementation including monitoring, management, targeted studies, and 

the conservation strategy 

• Evaluate implementation of monitoring and management projects and targeted studies 

and the quality and scientific rigor of the results and information gained 

• Summarize results into formats useful to decision-makers 

• Assess how well the program is meeting its objectives; if it is not, then determine why not 

and what actions should be taken 

• Identify emerging issues of concern and appropriate responses 

• Revise conceptual models based on new data and make recommendations for changes to 

conservation strategy, management plans and monitoring program design 

• Determine when the program should progress from Phase 1 to 2 to 3 (see glossary for 

definitions) 

• Prioritize actions that need to be taken by the monitoring program 

• Determine when external scientific input will assist the program 

• Coordinate and integrate external scientific review of the program 

• Maintain program momentum and progress 

An effective decision support system not only improves management within and across reserves 

but also can improve public and scientific outreach and increase coordination and potential 

funding opportunities. A well-organized program can attract scientists with external funding as 

well as contributions and bequests from an interested public. 
 41 

5.0 ADDITIONAL CONSIDERATIONS FOR DESIGNING THE 

MONITORING PROGRAM 

The steps in monitoring program design are generally the same for all regional conservation 

plans, but the creation of a complete program for entire suites of natural community 

assemblages, species, and landscape-level issues can occur in several ways. Depending on the 

resources available, all parts of the program could be developed at once, or designers could 

prioritize different parts of the program and proceed with developing different elements piece by 

piece. 

Regardless, a good monitoring program, in addition to being able to assess progress towards 

conservation goals, should be: 

• Committed to scientific quality, incorporating scientific input and peer review at various 

levels (programmatic, conceptual models, selection of monitoring variables, protocols, 

sampling design, analysis, and reports). 

• Responsive to management needs. 

• Inclusive, allowing permittees and stakeholders to have input into the process. 

• Provided sufficient time and funding to develop the program. Scientists should not be 

expected to develop quality monitoring programs in their “spare” time. 

• Committed to communication and creating an effective information feedback loop. 

Some basic suggestions include: 

• Have clear program goals and objectives. 

• Have a specific person (or small group) who is in charge of making the program happen. 

• Incorporate a diversity of perspectives during design of the monitoring program, e.g., from 

scientists in a variety of disciplines, agency personnel, and land managers with applied 

experience. 

• Make sure some “big picture” thinkers are included in the process. 

• Scientists should be involved in every level of the program. 

• People are key. Be willing to pay the right people to get the job done. 

• Dedicated core staff help move the process forward more quickly. 

• Using trained facilitators or providing facilitation training for some staff can expedite 

reaching consensus in workshops and working meetings among technical experts. 

• Clearly document the decision-making and conceptual models. 

• Geographic information systems (GIS) and opportunities for computer modeling are 

essential. 

• Identify early targeted research to assist critical decision-making 

• Rigorous scientific review gives a program credibility and validation. 
 42 

6.0 CONCLUSIONS 

Regional conservation plans endeavor, through strategic land acquisition and management, to 

maintain populations of covered species and certain desired ecological conditions, such as 

biodiversity or natural fire frequency. Well-designed monitoring is needed to assess the success 

of these programs in meeting their objectives and to provide the information needed to 

effectively manage them. However, building effective monitoring and adaptive management 

programs for large-scale multiple species conservation plans is both a science and an art that is 

still in its infancy. The NCCP/HCPs in southern California are all less than a decade old, with 

most parts of their monitoring programs now in Phase 1 and only a relative few in Phase 2. Other 

large-scale resource management programs such as the Comprehensive Everglades Restoration 

Program, Chesapeake Bay Program, National Park Service Inventory and Monitoring Program, 

and the Galapagos Islands monitoring program, are all still early in their development, as well. 

Thus, no one best example exists and monitoring programs should be prepared to learn and 

evolve through time. This requires an institutional structure and process that remains flexible, but 

that is committed to scientific rigor and quality results. 

The success of regional conservation plans depends on their ability to confront the challenges of 

adaptively managing and monitoring complex ecosystems, including diverse arrays of sensitive 

species. Developing monitoring and adaptive management programs takes work, funding, 

dedicated people, and continued scientific input. Although the needs and challenges of each 

NCCP/HCP are unique, the guidance provided in this document, developed from lessons learned 

in southern California, should assist in developing strong and defensible monitoring programs 

that support decision-making. 

7.0 ACKNOWLEDGEMENTS 

We wish to thank Lianne Ball of USFWS, Jerre-Ann Stallcup and Mike White of the 

Conservation Biology Institute and Cameron Barrows of the Center for Natural Lands 

Management for their review and comments on various versions of this document. We also wish 

to thank Clark Winchell, Mark Pavelka, and Will Miller of USFWS, and former USFWS 

personnel Paul Doherty, for their insights regarding the development of multiple species 

NCCP/HCP monitoring programs in southern California, many of which were incorporated into 

the document. We also thank Mary Ann Showers of CDFG for her help with the cover design 

and photos and Carolyn Marn of the U.S. Geological Survey for her assistance in developing 

some of the early ideas upon which this document is based. 
 43 

8.0 ACRONYMS 

BLM U. S. Bureau of Land Management 

CDFG California Department of Fish and Game 

CVAG Coachella Valley Association of Governments 

CVMSHCP Coachella Valley Multiple Species Habitat Conservation Plan 

GIS Geographic Information System 

HCP Habitat Conservation Plan 

MHCP San Diego Multiple Habitat Conservation Program 

MSCP San Diego Multiple Species Conservation Program 

MSHCP Western Riverside Multiple Species Habitat Conservation Plan 

NCCP Natural Community Conservation Plan/Planning 

NPS U. S. National Park Service 

SANDAG San Diego Association of Governments 

USFS U. S. Forest Service 

USFWS U. S. Fish and Wildlife Service 

USGS U. S. Geological Survey 
 44 

9.0 GLOSSARY 

Adaptive management – A scientific approach to resource management that rigorously 

combines management, monitoring and research to effectively manage complex ecosystems in 

the face of uncertainty. Adaptive management tackles uncertainty about the system head-on by 

identifying clear objectives, developing conceptual models of the system, identifying areas of 

uncertainty and alternative hypotheses, testing critical assumptions, monitoring to provide 

feedback about the system and actions, learning from the system as actions are taken to manage 

it, and incorporating what is learned into future actions.

Attribute – A generally-stated biological or physical feature of the ecosystem, e.g., 

precipitation, status of least Bell’s vireo, or extent of least Bell’s vireo habitat.

Baseline – Condition of system or variable of interest that provides a standard against which 

future change of the system is measured. Typically in NCCP/HCP monitoring programs, the 

baseline is defined by the mean and variability in the system during the first several years after 

the plan is implemented. However it could also refer to conditions at some point prior to plan 

implementation. 

Compliance monitoring – see Implementation monitoring 

Conceptual model – (1) "Explicit statements of the hypothesized functional relationships 

underlying management decisions regarding environmental resources." [A Proposal for the 

Development of a Comprehensive Monitoring Assessment and Research Program, April 24, 

1998, page 30]; (2) "A simple non-quantitative model, developed for the purpose of building a 

consensus regarding the most important ecological elements and linkages that characterize a 

stressed ecosystem." [Nick Aumen, Conceptual Modeling Workshop, UC Davis, June 17-18, 

1998]

Conservation strategy – The plan laid out in the NCCP/HCP documents for achieving 

conservation goals. This includes the number and distribution of acres that will be protected, the 

design of the reserves, the species “covered” by the plan, the goals for individual covered 

species, and recommended management activities. 

Covariate – A variable such as precipitation or air temperature that is used in analyses to 

explain some of the variance in a variable of interest. For example, if animal detectability is 

temperature dependent, measuring temperature as a covariate will make it easier to detect 

population trends or experimental treatment effects. 

Covered species – Listed and non-listed species that are being conserved and managed under an 

approved natural community conservation plan and that may be authorized for “take” under the 

provisions of the plan. 

Effectiveness monitoring – The measurement of variables that allow the program to assess the 

success of the HCP/NCCP in meeting its stated biological objectives. This type of monitoring is 

the focus of this document. 
 45 

Habitats – Areas that provide specific conditions (e.g., temperature, moisture, soils, vegetation, 

and cover) necessary to support a community of organisms adapted to life under those 

conditions. 

Implementation (compliance) monitoring – Tracks the status of plan implementation, ensuring 

that planned actions are executed, including reserve creation and design, implementation of 

management activities, and implementation of monitoring activities. 

Invasive species – A species that is non-native to the ecosystem under consideration and whose 

introduction causes or is likely to cause economic or environmental harm or harm to human 

health (Executive Order 13112; http://www.invasivespecies.gov/laws/execorder.shtml). Invasive 

species can be plants, animals, and other organisms (e.g., microbes). Human actions are the 

primary means of invasive species introductions. 

Monitoring – The systematic and usually repetitive collection of information, typically used to 

track the status of a variable or system. 

Monitoring variable – Any living or non-living element of the system or human activity that 

can be measured or estimated that will provide some insight into accomplishment of NCCP/HCP 

goals and objectives, the functioning of the ecosystem, and/or the effectiveness of management 

actions (e.g., relative abundance of least Bell’s vireo in riparian areas on NCCP/HCP lands).

Natural community – Broad habitat categories or biological communities (e.g., anadromous 

fish) that are defined in each NCCP/HCP and are provided some level of protection under the 

plan. These categories typically have some level of acceptance of habitat nomenclature within 

the scientific community, are consistent with existing electronically mapped habitat data, and 

have the potential for being affected by the program’s conservation strategy (CALFED BayDelta Program, 2000c). 

Natural community assemblage – Group of one or more natural communities that can be 

addressed as a unit in the monitoring program design. These communities are typically affected 

by the same physical and biological process and same general set of pressures. Examples include 

“floodplain and riparian habitat,” “chaparral, coastal sage scrub and grassland community,” and 

“lagoons and tidal wetlands.” 

Non-indigenous species – Also called exotic, invasive, introduced, or non-native species. 

Plants and animals that originate from geographic regions other than the ones that they are found 

in and typically from outside of California. They may dominate the local species or have other 

negative impacts on the environment. They are typically spread to new areas through human 

activities, either accidentally (Norway rats (Rattus norvegicus) hitched rides aboard ships) or 

deliberately (Eucalyptus was originally introduced as an ornamental). The principle difference 

between an “invasive” species and a “non-indigenous” species is invasive species are defined as 

causing harm.

Peer review – External scientific review including at least some review that can be considered 

independent of the program. Such review is needed for the program’s conceptual models, 
 46 

monitoring recommendations, protocols, sampling design, analysis and reports. A programmatic 

level of review is also needed that periodically assesses the functioning of the program in 

meeting its objectives and its level of scientific quality. 

Phase 1 – First of three phases of monitoring program design and implementation involving 

inventorying resources and identifying relationships. The main goal of phase one is to determine 

the baseline condition of the ecological system as a prelude to long-term monitoring program 

design. This generally involves an inventory of what species, habitats, and other resources are 

present, their locations and general conditions. Some management can be applied during this 

phase, but in general this should be limited to actions of known-impact, such as hand-removal of 

weeds and fence construction to prevent vehicular access. This phase can also be used to develop 

or test hypothesized relationships between species, habitats, processes and other causes of 

variation, such as roads or invasive species. 

Phase 2 – Second of three phases of monitoring program design and implementation involving 

pilot testing of long-term monitoring and resolving critical management uncertainties. Phase two 

is characterized by pilot testing long-term monitoring protocols and sampling designs to select 

cost-effective designs with sufficient statistical power to detect biologically-relevant and 

management-relevant changes. The pilot phase often progresses through an iterative process, 

including revisions to protocols and comparisons of multiple methods. In addition, the pilot 

phase is an opportunity to conduct targeted studies to resolve critical management uncertainties 

and to refine conceptual models based on emerging information. 

Phase 3 – Third of three phases of monitoring program design and implementation involving 

implementing long-term monitoring and adaptive management. Activities include 

implementation of long-term monitoring protocols and periodic evaluation and refinement of the 

monitoring program. The program continues to address uncertainties, principally by evaluating 

responses to management and extreme events. Emerging uncertainties are also addressed and 

prioritized, such as a new invasive species or identification of a pollution source. 

Power analysis – A power analysis is conducted to determine the minimum number of sampling 

units required to detect a specific degree of change at an acceptable level of power (1- β) and 

significance level (α). “α” is the probability of making a Type I error, i.e., when one concludes 

that a change (e.g., decline) has occurred when in fact the results are nothing more than 

randomly occurring variation and no change has occurred. “β” is the probability of making a 

Type II error, i.e., when one concludes that no change has occurred when in fact a decline is 

actually happening. A sampling design has greater “power” to detect change when the 

probability of making a Type II error is low. An α of 0.05 and β of 4*α =0.20 are often used in 

determining the number of sampling units for environmental studies, but these can be changed 

depending on the objectives of the study. In management of sensitive species, it may be better to 

err on the side of giving a false alert of a problem (Type I error) than to fail to detect a negative 

change (Type II error). Elzinga et al. (2001) and Anderson (1998) provide a good discussion of 

these tradeoffs. Typically one can increase the power of a sampling design by increasing the 

number of replicates, by reducing sources of error in the protocol, and by altering the design to 

better account for known sources of variability in the environment. 
 47 

Pressure – Agents that either promote or inhibit change in the state of the environment. These 

are also called stressors, threats, or drivers in other programs. Because such agents may have a 

negative effect on some species while having a positive effect on others, we use pressure as a 

more neutral term. Pressures can be anthropogenic (e.g., barriers to movement, disturbance, 

contaminants) or natural (e.g., climate variability, disease outbreaks). Pressures can also include 

natural constraints such as limited seed dispersal. 

Regional conservation plan – A large-scale multiple species conservation plan that meets the 

definition of both a Federal Habitat Conservation Plan under the Endangered Species Act and a 

state NCCP under the California Natural Community Conservation Planning Act. Examples 

include the San Diego Multiple Species Conservation Program, the San Diego Multiple Habitat 

Conservation Program, and the Coachella Valley Multiple Species Habitat Conservation Plan. 

Riparian – Strip of woodland vegetation adjacent to a natural water course such as a river or 

stream. 

State of the environment – The integrated manifestation of ecological processes, biological 

composition, ecological function, and rates of change that results in the condition of the system 

at any given time. 

Stressor – Pressure, threat or a negative source of change to a species, community or system.

Targeted study – Also called validation monitoring, cause-and-effect monitoring, and applied 

research, targeted studies increase effectiveness of management by removing or reducing critical 

uncertainties, improving knowledge of natural systems under management and applying 

experimental management treatments. 
 48 

APPENDICES 

A – J 
 49 

Appendix A. Suggested components of natural community assemblage conceptual models. 

The suggested components of natural community assemblage models are listed below. These are similar 

to the components listed for covered species in Box 4, but some of the details differ. The MHCP (2003) 

and draft CVMSHCP (2004) provide practical examples. 

NCCP/HCP Objectives 

• List NCCP/HCP objectives specific to the natural communities in this assemblage. 

Natural community assemblage description and background 

• Describe each component community within the natural community assemblage. 

• List covered species found partially or entirely within the natural community assemblage. 

• Plot the locations of the vegetation communities in this habitat assemblage including other useful 

information, e.g., protected land boundaries and land ownership. 

• Describe vegetation associations and ecological processes specific to this natural community 

assemblage. In addition to basic features, such as soil type, climate, slope, aspect, and moisture, to 

the extent possible describe natural pressures and their return rate. For example, fire and drought 

influence plant succession and thus the relative distribution of coastal sage scrub, grasslands, and 

chaparral dominated communities. 

• For portions of the model needing greater specificity and detail, consider creating sub-models. 

The Coachella Valley aeolian sand community process model (Figure 7) can be considered a submodel of the aeolian sand community model (Figure 6). Other examples of sub-models that might 

be useful are a food-web models describing the impacts of large carnivores, or models that detail 

specific threats. 

Status and trends 

• Identify monitoring programs and historical data relevant to each natural community assemblage. 

• Describe current status of the natural community assemblage and any known or hypothesized 

directional change in the system state, e.g., due to a lack of channel-resetting floods, early 

successional riparian habitat is decreasing in extent, causing a shift in the composition of riparian 

bird and small mammal communities. 

Pressures, program actions, and their anticipated effects (similar to Box 4) 

• Describe anthropogenic and natural pressures (i.e., threats, causes of change) and their 

hypothesized effects on the natural community assemblage. The hypothesized relationships 

between the pressures, the state of the species or habitat, and management actions should be 

explained. Some pressures may occur extremely rarely, such as extreme flood events that may be 

responsible for current natural community distributions. 

• Identify planned or potential management actions and their hypothesized effects. 

Special issues and critical assumptions (see also Box 4) 

• Describe any special issues and critical assumptions that should be included in the model. An 

example of a critical assumption at the natural community assemblage level is the assumption that 

the appropriate sand sources and sand movement corridors have been protected to maintain 

aeolian sands on preserves in Coachella Valley (CVMSHCP, 2004 draft). 

Diagram 

• Provide a simplified diagram of relationships among natural community assemblage elements and 

processes (see Figures 6 and 7). 
 50 

Appendix B. Suggested components of landscape-level conceptual models. 

Models at this level facilitate the consideration of issues that extend beyond any single natural 

community assemblage or species-specific conceptual model. The components for an 

overarching landscape-level model will be similar to the natural community assemblage 

conceptual models. Programs may decide to create separate models for key landscape level 

issues. Examples of large-scale and special issues that extend beyond any single natural 

community include: 

• Biological corridors, linkages, and maintaining connectivity across the landscape 

• Comprehensive planning to control non-indigenous plants and animals 

• Aerial and aquatic contaminants 

• Public access and recreation 

• Species that require multiple natural community assemblages (e.g., raptors, bats, large 

carnivores) 

Models for landscape-level issues will vary considerably. For each landscape-level issue: 

• Identify the relevant program objectives. 

• Describe the landscape level issue and relevant background information. 

• Plot, to the degree possible, the distribution of each special issue on a map that also 

includes the natural communities. 

• Describe the known or hypothesized effect of the issue and estimate the potential 

magnitude of the effect in the plan area and the weight of evidence supporting the 

regional importance of each issue. Because there are so many potential large-scale issues, 

it is critical to focus resources on issues with greater impacts. 

• Estimate the status and trends in these issues. 

• Evaluate how pressures and program actions will likely influence these issues. 

• Describe any special assumptions or considerations. Examples of special issues and 

critical assumptions at this level include: the assumptions regarding the minimum sizes of 

reserves needed to maintain native biodiversity and covered species; the need to provide 

some level of recreational access that precludes removal of all roads and trails; the 

minimum corridor width needed to maintain movement of different types of species. 

• Provide diagrams where helpful. 
 51 

Appendix C. A strategy for linking monitoring of NCCP/HCP covered species with 

ecosystem monitoring. 

Below is one of many possible strategies for building conceptual models that link the monitoring 

of covered species to monitoring of system integrity. The strategy takes advantage of information 

gathered during the NCCP/HCP plan development process. 

This strategy uses the species assessments performed as part of the NCCP/HCP planning 

process, recognizing that some information contained therein is based upon scientific opinion 

rather than scientific studies and the quality of the information is highly variable. The species 

assessments are used here to develop draft conceptual models for covered species. The 

conceptual models for the individual covered species can then be used to develop conceptual 

models and monitoring recommendations at the natural community assemblage level. The 

program is then scaled up further to identify models and recommendations at the landscape level. 

The covered species can then be assessed to determine which are effectively monitored by the 

monitoring variables identified for the natural community assemblages, and which species 

require additional focused attention. 

We assume in using this strategy that covered species assessments collectively provide an initial 

evaluation of the key pressures affecting the system (e.g., see Figure 6). While covered species 

are not necessarily the best “indicator” species or the most sensitive species to pressures in the 

system (Chase et al., 1998, 2000), when programs include large numbers of species, they provide 

a reasonable starting point for designing natural community assemblage conceptual models. This 

approach ties the natural community assemblage conceptual models and resulting monitoring 

and management approach to covered species within that assemblage. 

Steps C.1-C.12 below are a combination of Steps 5 and 6 in the main document. 

Complete the models for the covered species

Step C.1. Complete the conceptual model descriptions for covered species as necessary (see 

Box 4). For some species, the species assessments written as part of the NCCP/HCP 

provide a reasonable initial conceptual model. Examples include slow-growing 

species such as Torrey Pine for which the key management action is hypothesized to 

be protection from development. Species with more complicated relationships with 

hydrological, geomorphological and ecological processes, such as arroyo toads or 

salmonids will require more detailed conceptual models. 

Step C.2 Identify critical uncertainties for covered species that require targeted studies. 

(Wait to develop covered species monitoring recommendations until Step C.10) 

Build up to models of natural community assemblages

Step C.3 Based on habitat affinities identified in Step C.1, group covered species by natural 

community assemblages. 
 52 

Step C.4 Identify pressures for natural community assemblages by 

a) Listing the pressures known or hypothesized to affect covered species in each 

natural community assemblage. 

b) Classifying the pressures as 

i) species-specific pressures (e.g., invasive beetle is eating flower heads), 

ii) general but local pressures (e.g., disturbance, night lighting), and 

iii) large-scale pressures or off-site pressures (e.g., habitat fragmentation, altered 

hydrology, altered fire frequency). 

c) Identifying additional pressures on this natural community that the covered 

species evaluation did not reveal. 

Note: A similar process should be followed for identifying potential management 

activities. 

Step C.5 Develop a basic conceptual model for each natural community assemblage (see list of 

model components in Appendix A). 

Step C.6 Identify where additional detail will assist the program, and develop additional submodels (e.g., vegetation-processes models, food webs, etc.). 

Step C.7 Based on the natural community assemblage conceptual models, select monitoring 

variables, as described in Step 6, and identify and prioritize targeted study 

recommendations. 

Expand to cover landscape-level issues (e.g. affecting multiple natural community assemblages)

Step C.8 Determine if an overarching model that encompasses all the natural community 

assemblages is needed. If so, develop model of program from a landscape viewpoint, 

complete with landscape-level pressures and management activities. If only a few 

additional issues that cut across multiple natural community assemblages exist and a 

larger model is not helpful, then develop models for these issues (See list of model 

components in Appendix B). 

Step C.9 Identify monitoring attributes and variables, etc., and targeted studies for landscapelevel issues. 

Identify additional monitoring needs for covered species

Step C.10 Determine which covered species are encompassed by monitoring proposed in Steps 

C.7 and C.9. 

Step C.11 If appropriate, adjust monitoring identified in Steps C.7 and C.9 to better meet the 

needs of monitoring covered species. 

Step C.12 Identify additional species-specific monitoring needs for species that are not 

adequately monitored by the monitoring identified in C.7. and C.8. For example 

reptile community monitoring may be sufficient for species like orange-throated 

whiptails, whereas direct population monitoring is likely needed for rare species like 

the arroyo toad). 
 53 

Appendix D. Habitat monitoring as a surrogate for species monitoring 

Monitoring individual species is expensive, while monitoring habitats is relatively inexpensive. 

Thus, it is tempting for programs to substitute habitat monitoring for species-specific approaches. 

This type of substitution is especially attractive when the primary threat to a species is thought to 

be human conversion of habitat to an unsuitable condition. 

However, using habitat as a surrogate for monitoring a target species requires that: 

• a relationship between the species and measurable habitat characteristics must be 

documented. 

• the limiting habitat requirements must be known with a high degree of certainty, and habitat 

(extent, configuration, structure, and composition) must be the primary factor limiting the 

species distribution and abundance. 

• the target species must be sufficiently abundant and widespread - habitat monitoring is not 

sufficient for highly vulnerable species with small populations and declining numbers. 

• the quantity and condition of its habitat must be quantifiable by mapping or other methods. 

• the habitat-species relationship must be revalidated occasionally, because conditions may 

change and species-habitat relationships are typically based on correlation. 

Recognizing how difficult it is to fulfill the above requirements for any species, extreme caution 

should be exercised when using habitat monitoring as a surrogate. Some papers that discuss the 

challenges of using species-habitat models to predict species presence and population dynamics 

include Gu and Swihart (2003) and Lawler and Schumaker (2004). 

Considerable research is needed to document species-habitat associations and under what 

conditions they are reliably predictable. Because some species are absent from large areas of 

what appears to be suitable habitat, species-habitat relationships should not be applied beyond 

the areas where they were developed. In addition, habitat use by species ranging over large areas 

may be scale-dependent and influenced by landscape characteristics rather than a linear response 

to habitat area. If there is any suspicion that factors other than habitat availability are threatening 

populations, habitat should not be used as the sole surrogate. For example, monitoring habitat as 

a surrogate for the status of western spadefoot toad (Spea hammondii) assumes that factors such 

as invasive species, contaminants, and disease do not strongly influence populations. Such 

assumptions must be supported by data and periodically be reevaluated. 

In urbanizing landscapes where remaining habitats are likely to be subjected to new pressures, 

habitat area will be a less reliable surrogate. Instead, we recommend monitoring that addresses 

both habitat and the target species in concert. 
 54 

Appendix E. Characteristics of good monitoring variables 

(Adapted from Margoluis et al., 1998; Gibbs et al., 1999; Pawley, 2000; Bisbal, 2001; Carolyn 

Marn, personal communication). 

Relevant to Management 

* Relevant to program goals and objectives; can assess program performance 

* Relevant to adaptive management process 

* Appropriate spatial scale 

* Appropriate temporal scale 

Scientifically Defensible

* Biologically pertinent, reflects status and dynamics of system under management 

* Sufficient scientific basis, supported by published scientific findings or conceptual models 

Statistically Powerful and Interpretable

* Directly related to the ecosystem component it is intended to represent or is an acceptable 

surrogate 

* Sensitive to changes in the ecosystem component it represents 

* Indicates cause of change as well as existence of change 

* Timely, relevant to management timeframe 

* Anticipatory, serves as an early warning of change 

* Responsive across necessary range of stress, i.e., provides continuous assessment over wide 

range of stress (does not “level off”) or complements other monitoring variables to achieve 

necessary range 

* Known statistical properties, with baseline data, reference or benchmark available 

Measurable and Feasible

* Technically feasible; measurable using standard methodologies 

* Accurate and precise, with low observer variability and bias 

* Cost effective 

* Low impact to system being monitored 

* Low risk to field personnel 

Coordinated with Existing Programs and Data Sets 

* Compatible with already existing monitoring programs’ data collection, or could be modified 

to be so 

* If data exist, they are obtainable, preferably as long-term data sets 

Easily Understood

* Simple, direct 

* Communicable, easily interpreted and explained 

* Documented; methodology supported by complete standard operating procedures 
 55 

Appendix F. Species-level monitoring variables. Variables are listed in order of increasing 

level of investment and data resolution (adapted from Sierra Nevada Framework (USFS, 2001)). 

Monitoring Variable Definition

Presence in study area Some species may be hypothesized to have been extirpated from part or all of a study 

area. The first priority for these species will be detection. 

Habitat as surrogate Depending on the priority level of a species and the expected pressures, habitat extent 

distribution, and condition may be used as a surrogate for monitoring the species 

directly. However, a great deal of uncertainty exists in doing so and the assumptions 

involved should be clearly documented and reassessed periodically. Typically there 

are insufficient data to allow confident monitoring of populations via habitat (see 

Appendix D). 

Number of populations Number and location of populations can be a useful metric for rare plants and animals, 

especially when the coefficient of variation in the number of individuals per 

population is very high. 

Distribution (Range) Distribution data consist of changes in locations of species occurrence across a region. 

Changes can occur around edges of species range, in association with pressures, or 

with appearance or disappearance of populations. Boundary mapping is sometimes 

used to measure change. 

Occupancy Target value is typically the proportion of sampling units occupied by the species. A 

species may maintain the same distribution, while the proportion of occupied habitat 

changes. When the detection probability of a protocol is less than one, better estimates 

are achieved using proportion of area occupied (PAO) statistics that use repeat visits to 

estimate the detection probability. 

Relative Abundance Relative abundance is an index of abundance derived using a specific protocol. Catch 

per unit effort, timed surveys, timed bird point counts, transect surveys are all different 

indices of relative abundance. Results derived using different protocols are not directly 

comparable. 

Population Size or 

Absolute Abundance

Population size is a direct estimate of the number of individuals. For very rare species, 

an absolute count (census) of the population size is possible. Where a complete census 

is not possible, methods such as mark/recapture and line-distance sampling provide 

estimates of absolute abundance. 

Apparent Recruitment “A qualitative or semi-quantitative measure of key stage classes for plants, often 

including an assessment of the proportion of the population appearing to be composed 

of juveniles.” (USFS, 2001) 

Reproductive Success “Reproductive success can be measured a variety of ways, depending on the species 

and sampling method. Reproductive success is most often pursued for bird species, 

where the number of eggs and fledglings can be readily enumerated to calculate 

number of young produced per adult. It is also described for some taxa in terms of the 

proportion of females reproducing. However, an index of the number of young 

produced per adult or breeding pair can be derived for most species.” (USFS, 2001) 

Population Structure 

and Dynamics

“Many measures of population growth and structure are available for use in 

monitoring. They range from individual attributes of a population (e.g., age ratios, sex 

ratio) to derived rates of change (e.g., mortality rates, fecundity rates, growth rates)” 

(USFS, 2001) to population genetic structure. 

Population condition 

(in association with other 

monitoring) 

A sample of individuals is captured or otherwise inspected and their condition 

determined relative to issues, e.g., tissue contamination index, parasite loads, 

symptoms of disease. The proportion showing signs of impaired condition is then used 

to monitor population condition. 
 56 

Appendix G. Natural community assemblage monitoring variables. 

Below are examples of the types of monitoring variables often suggested as indicators of natural 

community assemblage condition. Such examples are for illustration purposes only and are not 

what would necessarily be chosen to monitor for a specific program. Programs should not skip 

the steps of model development and identifying testable questions. Some monitoring variables 

require research, such as identifying which species are “stress-sensitive species” vs. “stresstolerant species.” In general, prior to adopting any indicator, field verification and fine-tuning in 

the system of interest is required. Definitions are not provided for each suggested measure, but 

key references have been cited where possible. 

Community composition variables : 

Where protection of biological diversity is a goal, community-level monitoring is needed to 

evaluate success. This topic has been addressed in detail in the scientific literature, but ultimately 

the approach taken will depend on the goals of the conservation program. 

• Native species richness – estimate of the number of species in an area (Krebs, 1999). 

• Measures of similarity and association based on species presence or abundance can be 

used to compare community composition with a baseline condition or reference site 

(Krebs, 1999; Morrison et al., 2001). 

• Presence, abundance, biomass, capture rate, or proportional capture rate of 

- guilds or functional groups (e.g., in songbirds: ground gleaners, foliage gleaners, 

aerial hawkers; in planktonic communities: phytoplankton, microzooplankton, 

mesozooplankton). 

- key species, for example focal species (keystone, umbrella, and/or engineer species 

(Noon, 2003)), at-risk species (legally protected species and otherwise sensitive 

species (Noon, 2003)), community indicator species, habitat indicator species, 

economic species, pest species (Goals Project, 1999). 

- stress-sensitive versus tolerant species, e.g., urban-phobic versus urban-philic species, 

disturbance tolerant versus disturbance-sensitive species. 

- native versus non-native species. 

• Index of Biotic Integrity (IBI): Using reference systems of known-condition or integrity, 

a diversity-based index of biotic integrity is developed. This IBI can then used to assess 

the condition of other systems based on a diversity-based score (Noss et al., 1997; 

National Research Council, 2000). 

Vegetation structure and function variables

In many systems wildlife and plants of interest depend critically on local vegetation structure. 

Monitoring vegetation may provide early indication of changes that are known or hypothesized 

to be detrimental, e.g., weeds or community succession. 

• Estimation of absolute and relative abundance (or cover) of native and non-native species 

using standard vegetation survey methods. This is the most time and labor-intensive 

approach to vegetation monitoring. 

• Shrubland vegetation structure metrics (percent cover, canopy height, percent shrub 

cover, percent tree cover, percent grass and forb cover, percent of specific vegetation 

series species, patchiness of vegetation cover, soil type, litter depth). 
 57 

• Forest vegetation structure metrics: frequency distribution of seral stages (age classes) 

for each community type and across all types; woody stem density in various size (dbh) 

classes; average, range and diversity of tree ages or sizes in stand; tree species diversity; 

productivity; canopy density and size and dispersion of canopy openings; foliage-height 

profiles; abundance and density of key structural features, e.g., snags and downed logs; 

crown condition; physical damage to trees (Noss et al., 1997; National Research Council, 

2000). 

• Photo plots: Photos taken from fixed reference points can provide a qualitative and 

sometimes a quantitative assessment of changes in the environment (MacDonald and 

Smart, 1992). Photos should be recorded at the same time of year, in the same direction, 

etc. 

Ecological function 

Although conceptually attractive, monitoring general ecological function is rare unless there is 

an obvious connection to issues of value to humans. 

Terrestrial 

• Energetics/productivity – biomass, carbon storage, net primary production, productivity 

(National Research Council, 2000). Productivity is more clearly of interest in extraction 

systems such as working forests. 

• Fires and other disturbances – frequency, return interval or rotation period of fires or 

other disturbances, location and areal extent, will influence the diversity, abundance and 

distribution of vegetative communities and associated wildlife (Noss et al., 1997). 

• Soil stability and erosive resistance, slumping – early successional species may require 

landslides. 

• Weather (precipitation, high-low-average temperature, humidity, evapotranspiration 

index). 

Aquatic

• Streams/rivers - Stream flow and stage (height), stream flow hydrographs, frequency and 

extent of floodplain inundation 

• Channel migration, bank and channel stability and erosive resistance, stream crosssectional area 

• Water quality – water clarity/turbidity, conductivity, temperature, pH, dissolved oxygen, 

organic carbon, nutrients, contaminants 

• Biological Oxygen Demand (BOD) 

• Sediment quality – composition and grain size, total organic carbon, nitrogen, sulfides, 

pH, contaminants 
 58 

Appendix H. Landscape-level monitoring variables. 

Below are examples of variables that might be used to monitor landscape-level issues that affect 

multiple natural community assemblages or otherwise cross-cutting issues. Such examples are 

for illustration purposes only and are not what would necessarily be chosen to monitor for a 

specific program. Programs should not skip the steps of model development and identifying 

testable questions. 

Extent and distribution of habitats across landscape

• Extent, distribution and location of protected lands and land uses (natural, agricultural, 

disturbed, urban, military, etc.). 

• Extent and distribution of natural communities and natural community assemblages. 

• Extent of core habitat (e.g., >500 m from roads or development), because many species of 

concern do not survive or reproduce well when subject to disturbance or other edge 

effects (Noss et al., 1997; Rutledge, 2003). 

Fragmentation, connectivity, measures of patch characteristics and dispersion 

• Patch characteristics and dispersion measures – inter-patch distance (mean, median, 

range) for various natural community assemblages; patch density; number of patches; 

patch size frequency distribution; nearest neighbor (Noss et al., 1997; Rutledge, 2003). 

• Road density inside reserves and in total planning area (Noss et al., 1997). 

• Studies to assess animal movement across barriers or through hypothesized corridors. Use 

radio-tracking or marked animals, or possibly develop genetic markers to assess gene 

flow indirectly. 

Invasive species

• Range, rate of spread, distribution and size of populations of key non-indigenous plant 

species, (e.g., Arundo donax, Tamarisk spp., perennial pepperweed, purple loosestrife, 

water hyacinth, ice-plant, yellow star-thistle, pampas grass, non-native annual grasses) 

and non-native fauna (e.g. fire ants, Argentine ants, bull-frogs, African clawed frogs, 

crayfish, non-native fish, non-native foxes, non-native turtles, feral cats and dogs ). 

• Detection of new species at common introduction points, e.g., plant nurseries for fire ants, 

trails for yellow-star thistle, international shipyards for aquatic organisms in estuaries. 

• Maintain information clearinghouse to report new invasive species established in region 

and provide information on invasive species status, ecology, and control methods. 

Large-scale or widely-distributed pressures

• Fires and other disturbances – frequency, return interval or rotation period of fires or 

other disturbances, location and areal extent (Noss et al., 1997). 

• Location and severity of potential pressures on system, e.g., dams and impoundments, 

water diversions, sources and distribution of contaminants, etc. 

• Intensity of human recreation use or other land uses, e.g., livestock stocking rates. 
 59 

 

Appendix I. Sampling design approaches that are receiving increased attention 

Sampling designs and analysis techniques for monitoring species are continually being 

developed. Some approaches receiving increased attention include: 

Mark-Recapture: Use of mark-recapture methods allows estimation of true population 

abundance, detection probabilities, mortality rates, and confidence limits on these parameters. 

User-friendly software allowing sophisticated analysis of mark-recapture data is available free of 

charge. Program MARK, available from Colorado State University at 

http://www.cnr.colostate.edu/~gwhite/software.html, is the current industry standard (White and 

Burnham, 1999). Other useful biological analysis statistical software is available at the USGS 

Patuxent website at http://www.mbr-pwrc.usgs.gov/software/. 

Proportion of area occupied (PAO): Useful for species where population size cannot be reliably 

estimated or is highly variable, but detection is possible. For species with detection probability of 

less than one, this method involves repeat visits to sites to estimate the detection probability of 

the protocol and the true proportion of occupied sampling units with estimates of error that can 

be used in statistical calculations. The method is being utilized by the U.S. Geological Survey’s 

Amphibian Research and Monitoring Initiative (http://armi.usgs.gov/monitoring.asp) 

(MacKenzie et al., 2002). 

Adaptive cluster sampling: This method utilizes randomized sampling to locate a population, but 

once a population is located an estimate of population size is made. This technique is especially 

useful for aggregated species such as schooling fish and many rare plants (Thompson and Seber, 

1996). 

Model selection approaches: Multiple competing hypotheses or models are ranked according to 

how well they fit the available data (Anderson et al., 2001; Burnham and Anderson, 2002; 

Johnson and Omland, 2004). 

Adaptive monitoring: When an apparent decline is detected, monitoring intensity increases and 

then intensity decreases when a population returns to the range of naturally occurring variation 

(Smit, 2003). 
 60 

Appendix J. Quality assurance plan 

Maintaining the quality of data collection, data management, and data interpretation is 

challenging, yet essential for the success of a long-term program. 

Some elements of quality assurance include: 

• Develop and use protocols that allow easier standardization across observers and through 

time (i.e., minimize observer bias or provide an estimate of observer bias such as through 

double-observer methods). 

• Standardize units and nomenclature so that everyone uses the same names to mean the 

same thing (for example Point Loma could be recorded as “Point Loma”, “Loma”, Pt. 

Loma, or “Cabrillo National Monument” by different observers). A good database design 

that limits naming options can greatly reduce this problem. 

• Field test protocols, data recording and record-keeping techniques before expanding use 

to a large project. 

• Maintain and distribute current written descriptions of the objectives of the monitoring 

program, protocols, units used, recording and QA/QC procedures, and answers to 

commonly asked questions. Field personnel should understand the “why” of the protocol 

as well as “what” they need to do. 

• When dealing with multiple observers, hold regular training sessions to standardize 

methods across observers and through time. 

• Develop good data recording techniques that minimize errors and forgotten fields. 

• Have field observers double-check their data, preferably the same day. 

• If data are recorded on paper and then entered into a computer, all entries should be 

double-checked. 

• Have a supervisor or data manager check the data regularly for obvious errors (the data 

management system can also be designed to flag obvious outliers for checking, like an 

observation that was entered in centimeters rather than millimeters). Data should be 

reviewed daily when observers are new and regularly after that. Review of data should 

not be left to the end of the field season. 

• Maintain information on who collected the data, entered the data in the database, etc. 

(chain of custody). 

• If data are being maintained in multiple places, e.g., a local database and a regional 

database, steps must be taken to ensure that only one version of the data is kept in 

existence and that updates that are made locally are quickly transferred to the regional 

database. 

• Maintain adequate metadata along with the database. 

• Develop security measures for the database so that the appropriate people have access to 

and the ability to change the appropriate level of data. 

• Track the level of QA/QC associated with a given set of data and make sure that end 

users are aware of the QA/QC status. 

• Maintain connection between those people who analyze and interpret the data and the 

people who collect the data in the field. 

• Regularly backup data and maintain backups at off-site location. 
 61 

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