Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of "Analyse des Donnees" and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy.

/pdf/the-ade4-package-implementing-the-duality-diagram-for-r095ij3wwz.pdf

The ade4 Package: Implementing the Duality Diagram for Ecologists

▪ Abstract Local habitat and biological diversity of streams and rivers are strongly influenced by landform and land use within the surrounding valley at multiple scales. However, empirical associations between land use and stream response only varyingly succeed in implicating pathways of influence. This is the case for a number of reasons, including (a) covariation of anthropogenic and natural gradients in the landscape; (b) the existence of multiple, scale-dependent mechanisms; (c) nonlinear responses; and (d) the difficulties of separating present-day from historical influences. Further research is needed that examines responses to land use under different management strategies and that employs response variables that have greater diagnostic value than many of the aggregated measures in current use. In every respect, the valley rules the stream.      H.B.N. Hynes (1975)

http://deq.idaho.gov/media/525804-Landscapes_Riverscapes_Influence_landuse_stream_ecosystems_Allan_2004.pdf

Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems

Terrestrial net primary production (NPP) quantifies the amount of atmospheric carbon fixed by plants and accumulated as biomass. Previous studies have shown that climate constraints were relaxing with increasing temperature and solar radiation, allowing an upward trend in NPP from 1982 through 1999. The past decade (2000 to 2009) has been the warmest since instrumental measurements began, which could imply continued increases in NPP; however, our estimates suggest a reduction in the global NPP of 0.55 petagrams of carbon. Large-scale droughts have reduced regional NPP, and a drying trend in the Southern Hemisphere has decreased NPP in that area, counteracting the increased NPP over the Northern Hemisphere. A continued decline in NPP would not only weaken the terrestrial carbon sink, but it would also intensify future competition between food demand and proposed biofuel production.

Drought-Induced Reduction in Global Terrestrial Net Primary Production from 2000 Through 2009

We describe an approach for estimating occupancy rate or the proportion of area occupied when heterogeneity in detection probability exists as a result of variation in abundance of the organism under study. The key feature of such problems, which we exploit, is that variation in abundance induces variation in detection probability. Thus, heterogeneity in abundance can be modeled as heterogeneity in detection probability. Moreover, this linkage between heterogeneity in abundance and heterogeneity in detection probability allows one to exploit a heterogeneous detection probability model to estimate the underlying distribution of abundances. Therefore, our method allows estimation of abundance from repeated observations of the presence or absence of animals without having to uniquely mark individuals in the population.

Estimating abundance from repeated presence–absence data or point counts

Failure to estimate capture efficiency, defined as the probability of capturing individual fish, can introduce a systematic error or bias into estimates of fish abundance. We evaluated the efficacy of multipass electrofishing removal methods for estimating fish abundance by comparing estimates of capture efficiency from multipass removal estimates to capture efficiencies measured by the recapture of known numbers of marked individuals for bull trout Salvelinus confluentus and westslope cutthroat trout Oncorhynchus clarki lewisi. Electrofishing capture efficiency measured by the recapture of marked fish was greatest for westslope cutthroat trout and for the largest size-classes of both species. Capture efficiency measured by the recapture of marked fish also was low for the first electrofishing pass (mean, 28%) and decreased considerably (mean, 1.71 times lower) with successive passes, which suggested that fish were responding to the electrofishing procedures. On average, the removal methods overe...

https://www.fs.fed.us/rm/pubs_other/rmrs_2004_peterson_j001.pdf

An evaluation of multipass electrofishing for estimating the abundance of stream-dwelling salmonids

List of boxes xi Preface xiii Acknowledgements xiv Guide to using this book xv Companion website xvii PART I. INTRODUCTION TO DECISION MAKING 1 1 Introduction: Why a Structured Approach in Natural Resources? 3 2 Elements of Structured Decision Making 13 3 Identifying and Quantifying Objectives in Natural Resource Management 24 4 Working with Stakeholders in Natural Resource Management 57 PART II. TOOLS FOR DECISION MAKING AND ANALYSIS 77 5 Statistics and Decision Making 79 6 Modeling the Infl uence of Decisions 147 7 Identifying and Reducing Uncertainty in Decision Making 192 8 Methods for Obtaining Optimal Decisions 232 PART III. APPLICATIONS 261 9 Case Studies 263 10 Summary, Lessons Learned, and Recommendations 294 PART IV. APPENDICES 307 Appendix A Probability and Distributional Relationships 309 Appendix B Common Statistical Distributions 317 Appendix C Methods for Statistical Estimation 339 Appendix D Parsimony, Prediction, and Multi-Model Inference 373 Appendix E Mathematical Approaches to Optimization 384 Appendix F Guide to Software 430 Appendix G Electronic Companion to Book 432 Glossary 433 Index 449

Decision Making in Natural Resource Management: A Structured, Adaptive Approach

Absence of a species when it is not observed from a given area is ensured only when the probability of observation, when present, is 1. This condition is rarely satisfied in surveys of animals in natural environments, particularly with elusive targets such as fish. Detectability (probability of species encounter) is a function of probability of individual capture, which varies widely with sampling method, fish size, physical habitat, and number of individuals present in a given area. An empirical Bayesian approach was developed for estimating probability of presence for zero-catch samples, in which the number of individuals present for a species is predicted from independent samples and used as an empirical prior. The model was illustrated for 16 species of fish sampled in 121 blocked-off stream reaches in which samples were collected using one of five primary gear methods; treatment with an ichthyocide followed. All species present were caught by the primary gear in only 17 (14%) of the samples....

An approach to estimate probability of presence and richness of fish species

Introgressive hybridization threatens the persistence of several species of native salmonids in the western United States, but little is known about the factors influencing the establishment and maintenance of introgressed populations. We examined the occurrence of introgressive hybridization in westslope cutthroat (Oncorhynchus clarki lewisi) and rainbow trout (O. mykiss) populations in relation to physical characteristics of streams, trout density estimates, and the distance from stocking source. Trout were sampled from 80 stream sites in the Clearwater River Basin, Idaho, USA, and tissues from individual trout were analyzed to detect hybridization using noncoding sequences of nuclear DNA. We found a broad zone of hybridization detected at 64% of the sampled sites. The presence and degree of introgression was negatively related to elevation and positively related to stream width in our logistic regression model. Stream elevation and size likely influence hydrologic and thermal regimes. An interaction between the life history characteristics of the native and nonnative trout with these hydrologic and thermal stream gradients could explain the invasion success of rainbow trout and hence, the extent of the hybrid zone. Alternatively, the influence of elevation and stream width could be the result of habitat selection by the parental species, thereby reducing the opportunity for hybridization. Understanding the relationship between abiotic factors and introgressive hybridization will assist fisheries managers when evaluating the potential threat of introgression in different stream habitats and applying the necessary management actions to conserve the native cutthroat trout genotypes across broad landscapes.

Corresponding Editor: K. D. Fausch

https://www.jstor.org/stable/info/3099949

Introgressive hybridization between native cutthroat trout and introduced rainbow trout

Invasions of non-native brook trout (Salvelinus fontinalis) have the potential for upstream displacement or elimination of bull trout (Salvelinus confluentus) and other native species already threa...

https://www.fs.fed.us/rm/pubs_other/rmrs_2006_rieman_b002.pdf

James T. Peterson

Papers

An evaluation of multipass electrofishing for estimating the abundance of stream-dwelling salmonids

Decision Making in Natural Resource Management: A Structured, Adaptive Approach

An approach to estimate probability of presence and richness of fish species

Introgressive hybridization between native cutthroat trout and introduced rainbow trout

Have brook trout (Salvelinus fontinalis) displaced bull trout (Salvelinus confluentus) along longitudinal gradients in central Idaho streams