Andrew B. Cooper

Optimal Size and Number of Propagules: Allowance for Discrete Stages and Effects of Maternal Size on Reproductive Output and Offspring Fitness

Existing optimality models of propagule size and number are not appropriate for many organisms. First, existing models assume a monotonically increasing offspring fitness/propagule size relationship. However, offspring survival during certain stages may decrease with increasing propagule size, generating a peaked offspring fitness/propagule size function (e.g., egg size in oxygen‐limited aquatic environments). Second, existing models typically do not consider maternal effects on total reproductive output and the expression of offspring survival/propagule size relationships. However, larger females often have greater total egg production and may provide better habitats for their offspring. We develop a specific optimality model that incorporates these effects and test its predictions using data from salmonid fishes. We then outline a general model without assuming specific functional forms and test its predictions using data from freshwater fishes. Our theoretical and empirical results illustrate that, when offspring survival is negatively correlated with propagule size, optimal propagule size is larger in better habitats. When larger females provide better habitats, their optimal propagule size is larger. Nevertheless, propagule number should increase more rapidly than propagule size for a given increase in maternal size. In the absence of density dependence, females with greater relative reproductive output (i.e., for a given body size) should produce more but not larger propagules.

THE APPLICATION OF DISCRETE CHOICE MODELS TO WILDLIFE RESOURCE SELECTION STUDIES

This paper introduces the theory and application of discrete choice models to resource selection studies. Discrete choice models calculate the probability of an individual selecting a resource as a function of the attributes of that resource and all other available resources. The data for these attributes may be continuous or categorical. When availability is the same for all individuals and only two resources are available, the multinomial logit discrete choice model reduces to the logistic model. Discrete choice models and advances in GIS technology give the researcher flexibility in defining resource availability separately for each individual over time and space. The output of the discrete choice approach also provides managers with a tool to explore the effects of potential management actions and provides researchers with new hypotheses deserving of further investigation. To illustrate the application of discrete choice models to resource selection studies, we present a case study of summer diurnal bed site selection by elk (Cervus elaphus) in Custer State Park, South Dakota, United States. The results demonstrate the importance of factors relating to thermal regulation, hiding cover, and potentially forage, in elk bed site selection in this region.

Design and analysis of long-term ecological monitoring studies

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.

Accounting for Variation in Resource Availability and Animal Behavior in Resource Selection Studies

Publisher Summary There are two important assumptions contained in the techniques developed for analyzing resource selection data: the availability of resources is constant over time and each individual has equal access to those resources deemed available to that individual. Violations of these assumptions are discussed in the area of habitat selection. Habitat selection studies assume that all habitats in the study site are available to all individuals or that some spatially or temporally defined subsets of the area are available to different individuals. With the complications of defining resource availability, there is also often an unexplored aspect of resource selection relating to animal behavior. In the case of habitat selection, animals choose different habitat patches for different behaviors. Discrete choice models are derived from economic utility theory, where “utility” is synonymous with satisfaction. These models assume that an individual gains satisfaction from selecting a given resource. Discrete choice models give an insight into how the characteristics of the resources in question and of the individuals selecting those resources affect the probability of a particular resource being chosen. Such resources are a patch of habitat or a type of prey or forage item. The data required for these models is similar to that necessary for logistic regression, and the characteristics of the resources and individuals may be either continuous or categorical variables.

An approach for population assessment in the absence of abundance indices

Population assessment models give managers insight into both the current status of a given population and how that population may respond to management measures. Nearly all of the techniques in both terrestrial and aquatic wildlife management require either an independent estimate of absolute abundance or an index that is consistently proportional to abundance. When neither of these exists, some information can still be mined from the changes in the sex and age ratios within the population over time. When harvesting is highly skewed toward a single sex or age class, the change in these ratios provides information about the exploitation rate and, when combined with absolute numbers removed, also provides information on absolute abundance. Traditional change-in-ratio techniques require independent estimates of other variables in order to be used in a predictive sense for open populations. This paper proposes a new method that combines the synthetic approach of fisheries stock assessment with the information contained in sex and age ratios to allow for the assessment of populations when no estimate of absolute abundance or reliable index of abundance exists. Although estimates of population parameters such as survival rates and fecundity are produced, the primary output of the estimation routine is the current population size and structure and the potential population sizes and structures that may result from future management options. The approach is validated using simulated data and is then applied to data for an elk population in north-central Idaho. n nCorresponding Editor: B. A. Maurer

Design and Analysis of Long-term Ecological Monitoring Studies: Acknowledgments

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.

Design and Analysis of Long-term Ecological Monitoring Studies: List of contributors

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.

Design and Analysis of Long-term Ecological Monitoring Studies: Contents

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.

Design and Analysis of Long-term Ecological Monitoring Studies: Index

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.

Design and Analysis of Long-term Ecological Monitoring Studies: Abbreviations

List of contributors Foreword Preface Acknowledgements Part I. Overview: 1. Ecological monitoring: the heart of the matter Robert A. Gitzen and Joshua J. Millspaugh 2. An overview of statistical considerations in long-term monitoring Joel H. Reynolds 3. Monitoring (that) matters Douglas H. Johnson 4. Maximizing the utility of monitoring to the adaptive management of natural resources William L. Kendall and Clinton T. Moore Part II. Survey Design: 5. Spatial sampling designs for long-term ecological monitoring Trent McDonald 6. Spatially balanced survey designs for natural resources Anthony R. Olsen, Thomas M. Kincaid and Quinn Payton 7. The role of monitoring design in detecting trend in long-term ecological monitoring studies N. Scott Urquhart 8. Estimating variance components and related parameters when planning long-term monitoring programs John R. Skalski 9. Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs Brian R. Gray 10. Simulating future uncertainty to guide the selection of survey designs for long-term monitoring Steven L. Garman, E. William Schweiger and Daniel J. Manier Part III. Data Analysis: 11. Analysis options for estimating status and trends in long-term monitoring Jonathan Bart and Hawthorne L. Beyer 12. Analytical options for estimating ecological thresholds - statistical considerations Song S. Qian 13. The treatment of missing data in long-term monitoring programs Douglas H. Johnson and Michael B. Soma 14. Survey analysis in natural resource monitoring programs with a focus on cumulative distribution functions Thomas M. Kincaid and Anthony R. Olsen 15. Structural equation modeling and the analysis of long-term monitoring data James B. Grace, Jon E. Keeley, Darren J. Johnson and Kenneth A. Bollen Part IV. Advanced Issues and Applications: 16. GRTS and graphs: monitoring natural resources in urban landscapes Todd R. Lookingbill, John Paul Schmit and Shawn L. Carter 17. Incorporating predicted species distribution in adaptive and conventional sampling designs David R. Smith, Lei Yuancai, Christopher A. Walter and John A. Young 18. Study design and analysis options for demographic and species occurrence dynamics Darryl I. MacKenzie 19. Dealing with incomplete and variable detectability in multi-year, multi-site monitoring of ecological populations Sarah J. Converse and J. Andrew Royle 20. Optimal spatio-temporal monitoring designs for characterizing population trends Mevin B. Hooten, Beth E. Ross and Christopher K. Wikle 21. Use of citizen-science monitoring for pattern discovery and biological inference Wesley M. Hochachka, Daniel Fink and Benjamin Zuckerberg Part V. Conclusion: 22. Institutionalizing an effective long-term monitoring program in the US National Park Service Steven G. Fancy and Robert E. Bennetts 23. Choosing among long-term ecological monitoring programs and knowing when to stop Hugh P. Possingham, Richard A. Fuller and Liana N. Joseph References Index.