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

■ Abstract The literature on effects of habitat fragmentation on biodiversity is huge. It is also very diverse, with different authors measuring fragmentation in different ways and, as a consequence, drawing different conclusions regarding both the magnitude and direction of its effects. Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat. Results of empirical studies of habitat fragmentation are often difficult to interpret because (a) many researchers measure fragmentation at the patch scale, not the landscape scale and (b) most researchers measure fragmentation in ways that do not distinguish between habitat loss and habitat fragmentation per se, i.e., the breaking apart of habitat after controlling for habitat loss. Empirical studies to date suggest that habitat loss has large, consistently negative effects on biodiversity. Habitat fragmentation per se has much weaker effects on biodiversity that are at least as likely to be positive as negative. Therefore, to correctly interpret the influence of habitat fragmentation on biodiversity, the effects of these two components of fragmentation must be measured independently. More studies of the independent effects of habitat loss and fragmentation per se are needed to determine the factors that lead to positive versus negative effects of fragmentation per se. I suggest that the term “fragmentation” should be reserved for the breaking apart of habitat, independent of habitat loss.

/pdf/effects-of-habitat-fragmentation-on-biodiversity-4qxfu95ock.pdf

Effects of Habitat Fragmentation on Biodiversity

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

/pdf/species-distribution-models-ecological-explanation-and-1szux2yl31.pdf

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

Cause, conseguenze e strategie di mitigazione Proponiamo il primo di una serie di articoli in cui affronteremo l’attuale problema dei mutamenti climatici. Presentiamo il documento redatto, votato e pubblicato dall’Ipcc - Comitato intergovernativo sui cambiamenti climatici - che illustra la sintesi delle ricerche svolte su questo tema rilevante.

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Climate Change 2007: The Physical Science Basis.

Climate change 2014 - Synthesis Report

1 Introduction and Overview.- 1.1 Objectives.- 1.2 Multivariate Statistics: An Ecological Perspective.- 1.3 Multivariate Description and Inference.- 1.4 Multivariate Confusion!.- 1.5 Types of Multivariate Techniques.- 1.5.1 Ordination.- 1.5.2 Cluster Analysis.- 1.5.3 Discriminant Analysis.- 1.5.4 Canonical Correlation Analysis.- 2 Ordination: Principal Components Analysis.- 2.1 Objectives.- 2.2 Conceptual Overview.- 2.2.1 Ordination.- 2.2.2 Principal Components Analysis (PCA).- 2.3 Geometric Overview.- 2.4 The Data Set.- 2.5 Assumptions.- 2.5.1 Multivariate Normality.- 2.5.2 Independent Random Sample and the Effects of Outliers.- 2.5.3 Linearity.- 2.6 Sample Size Requirements.- 2.6.1 General Rules.- 2.6.2 Specific Rules.- 2.7 Deriving the Principal Components.- 2.7.1 The Use of Correlation and Covariance Matrices.- 2.7.2 Eigenvalues and Associated Statistics.- 2.7.3 Eigenvectors and Scoring Coefficients.- 2.8 Assessing the Importance of the Principal Components.- 2.8.1 Latent Root Criterion.- 2.8.2 Scree Plot Criterion.- 2.8.3 Broken Stick Criterion.- 2.8.4 Relative Percent Variance Criterion.- 2.8.5 Significance Tests.- 2.9 Interpreting the Principal Components.- 2.9.1 Principal Component Structure.- 2.9.2 Significance of Principal Component Loadings.- 2.9.3 Interpreting the Principal Component Structure.- 2.9.4 Communality.- 2.9.5 Principal Component Scores and Associated Plots.- 2.10 Rotating the Principal Components.- 2.11 Limitations of Principal Components Analysis.- 2.12 R-Factor Versus Q-Factor Ordination.- 2.13 Other Ordination Techniques.- 2.13.1 Polar Ordination.- 2.13.2 Factor Analysis.- 2.13.3 Nonmetric Multidimensional Scaling.- 2.13.4 Reciprocal Averaging.- 2.13.5 Detrended Correspondence Analysis.- 2.13.6 Canonical Correspondence Analysis.- Appendix 2.1.- 3 Cluster Analysis.- 3.1 Objectives.- 3.2 Conceptual Overview.- 3.3 The Definition of Cluster.- 3.4 The Data Set.- 3.5 Clustering Techniques.- 3.6 Nonhierarchical Clustering.- 3.6.1 Polythetic Agglomerative Nonhierarchical Clustering.- 3.6.2 Polythetic Divisive Nonhierarchical Clustering.- 3.7 Hierarchical Clustering.- 3.7.1 Polythetic Agglomerative Hierarchical Clustering.- 3.7.2 Polythetic Divisive Hierarchical Clustering.- 3.8 Evaluating the Stability of the Cluster Solution.- 3.9 Complementary Use of Ordination and Cluster Analysis.- 3.10 Limitations of Cluster Analysis.- Appendix 3.1.- 4 Discriminant Analysis.- 4.1 Objectives.- 4.2 Conceptual Overview.- 4.2.1 Overview of Canonical Analysis of Discriminance.- 4.2.2 Overview of Classification.- 4.2.3 Analogy with Multiple Regression Analysis and Multivariate Analysis of Variance.- 4.3 Geometric Overview.- 4.4 The Data Set.- 4.5 Assumptions.- 4.5.1 Equality of Variance-Covariance Matrices.- 4.5.2 Multivariate Normality.- 4.5.3 Singularities and Multicollinearity.- 4.5.4 Independent Random Sample and the Effects of Outliers.- 4.5.5 Prior Probabilities Are Identifiable.- 4.5.6 Linearity 153.- 4.6 Sample Size Requirements.- 4.6.1 General Rules.- 4.6.2 Specific Rules.- 4.7 Deriving the Canonical Functions.- 4.7.1 Stepwise Selection of Variables.- 4.7.2 Eigenvalues and Associated Statistics.- 4.7.3 Eigenvectors and Canonical Coefficients.- 4.8 Assessing the Importance of the Canonical Functions.- 4.8.1 Relative Percent Variance Criterion.- 4.8.2 Canonical Correlation Criterion.- 4.8.3 Classification Accuracy.- 4.8.4 Significance Tests.- 4.8.5 Canonical Scores and Associated Plots.- 4.9 Interpreting the Canonical Functions.- 4.9.1 Standardized Canonical Coefficients.- 4.9.2 Total Structure Coefficients.- 4.9.3 Covariance-Controlled Partial F-Ratios.- 4.9.4 Significance Tests Based on Resampling Procedures.- 4.9.5 Potency Index.- 4.10 Validating the Canonical Functions.- 4.10.1 Split-Sample Validation.- 4.10.2 Validation Using Resampling Procedures.- 4.11 Limitations of Discriminant Analysis.- Appendix 4.1.- 5 Canonical Correlation Analysis.- 5.1 Objectives.- 5.2 Conceptual Overview.- 5.3 Geometric Overview.- 5.4 The Data Set.- 5.5 Assumptions.- 5.5.1 Multivariate Normality.- 5.5.2 Singularities and Multicollinearity.- 5.5.3 Independent Random Sample and the Effects of Outliers.- 5.5.4 Linearity.- 5.6 Sample Size Requirements.- 5.6.1 General Rules.- 5.6.2 Specific Rules.- 5.7 Deriving the Canonical Variates.- 5.7.1 The Use of Covariance and Correlation Matrices.- 5.7.2 Eigenvalues and Associated Statistics.- 5.7.3 Eigenvectors and Canonical Coefficients.- 5.8 Assessing the Importance of the Canonical Variates.- 5.8.1 Canonical Correlation Criterion.- 5.8.2 Canonical Redundancy Criterion.- 5.8.3 Significance Tests.- 5.8.4 Canonical Scores and Associated Plots.- 5.9 Interpreting the Canonical Variates.- 5.9.1 Standardized Canonical Coefficients.- 5.9.2 Structure Coefficients.- 5.9.3 Canonical Cross-Loadings.- 5.9.4 Significance Tests Based on Resampling Procedures.- 5.10 Validating the Canonical Variates.- 5.10.1 Split-Sample Validation.- 5.10.2 Validation Using Resampling Procedures.- 5.11 Limitations of Canonical Correlation Analysis.- Appendix 5.1.- 6 Summary and Comparison.- 6.1 Objectives.- 6.2 Relationship Among Techniques.- 6.2.1 Purpose and Source of Variation Emphasized.- 6.2.2 Statistical Procedure.- 6.2.3 Type of Statistical Technique and Variable Set Characteristics.- 6.2.4 Data Structure.- 6.2.5 Sampling Design.- 6.3 Complementary Use of Techniques.- Appendix: Acronyms Used in This Book.

Multivariate statistics for wildlife and ecology research

https://www.fs.fed.us/rm/pubs_other/rmrs_2006_cushman_s001.pdf

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Ecologists have used a variety of comparative mensurative and manipulative experimental approaches to study the biological consequences of habitat fragmentation. In this paper, we evaluate the merits of the two major approaches and offer guidelines for selecting a design. Manipulative experiments rigorously assess fragmentation effects by comparing pre- and post-treatment conditions. Yet they are often constrained by a number of practical limitations, such as the difficulty in implementing large-scale treatments and the impracticality of measuring the long-term (decades to centuries) responses to the imposed treatments. Comparative mensurative studies generally involve substituting space for time, and without pre-treatment control, can be constrained by variability in ecological characteristics among different landscapes. These confounding effects can seriously limit the strength of inferences. Depending on the scale of the study system and how “landscape” is defined, both approaches may be limited by the difficulty of replicating at the landscape scale. Overall, both mensurative and manipulative approaches have merit and can contribute to the body of knowledge on fragmentation. However, from our review of 134 fragmentation studies published recently in three major ecological journals, it is evident that most manipulative and mensurative fragmentation experiments have not provided clear insights into the ecological mechanisms and effects of habitat fragmentation. We discuss the reasons for this and conclude with recommendations for improving the design and implementation of fragmentation experiments.

https://www.umass.edu/landeco/pubs/mcgarigal.cushman.2002.pdf

Comparative evaluation of experimental approaches to the study of habitat fragmentation effects

Predicting population‐level effects of landscape change depends on identifying factors that influence population connectivity in complex landscapes. However, most putative movement corridors and barriers have not been based on empirical data. In this study, we identify factors that influence connectivity by comparing patterns of genetic similarity among 146 black bears (Ursus americanus), sampled across a 3,000‐km2 study area in northern Idaho, with 110 landscape‐resistance hypotheses. Genetic similarities were based on the pairwise percentage dissimilarity among all individuals based on nine microsatellite loci (average expected \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\en...

/pdf/gene-flow-in-complex-landscapes-testing-multiple-hypotheses-2c1wu3dqli.pdf

Gene Flow in Complex Landscapes: Testing Multiple Hypotheses with Causal Modeling.

https://www.fs.fed.us/rm/pubs_other/rmrs_2008_cushman_s002.pdf

Samuel A. Cushman

Papers

Multivariate statistics for wildlife and ecology research

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Comparative evaluation of experimental approaches to the study of habitat fragmentation effects

Gene Flow in Complex Landscapes: Testing Multiple Hypotheses with Causal Modeling.

Parsimony in landscape metrics: Strength, universality, and consistency