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

There is now ample evidence of the ecological impacts of recent climate change, from polar terrestrial to tropical marine environments. The responses of both flora and fauna span an array of ecosystems and organizational hierarchies, from the species to the community levels. Despite continued uncertainty as to community and ecosystem trajectories under global change, our review exposes a coherent pattern of ecological change across systems. Although we are only at an early stage in the projected trends of global warming, ecological responses to recent climate change are already clearly visible.

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Ecological responses to recent climate change.

How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.

/pdf/generalized-linear-mixed-models-a-practical-guide-for-3gh61pkir0.pdf

Generalized linear mixed models: a practical guide for ecology and evolution

Biotic invaders are species that establish a new range in which they proliferate, spread, and persist to the detriment of the environment. They are the most important ecological outcomes from the unprecedented alterations in the distribution of the earth's biota brought about largely through human transport and commerce. In a world without borders, few if any areas remain sheltered from these im- migrations. The fate of immigrants is decidedly mixed. Few survive the hazards of chronic and stochastic forces, and only a small fraction become naturalized. In turn, some naturalized species do become invasive. There are several potential reasons why some immigrant species prosper: some escape from the constraints of their native predators or parasites; others are aided by human-caused disturbance that disrupts native communities. Ironically, many biotic invasions are apparently facilitated by cultivation and husbandry, unintentional actions that foster immigrant populations until they are self-perpetuating and uncontrollable. Whatever the cause, biotic invaders can in many cases inflict enormous environmental damage: (1) Animal invaders can cause extinctions of vulnerable native species through predation, grazing, competition, and habitat alteration. (2) Plant invaders can completely alter the fire regime, nutrient cycling, hydrology, and energy budgets in a native ecosystem and can greatly diminish the abundance or survival of native species. (3) In agriculture, the principal pests of temperate crops are nonindigenous, and the combined expenses of pest control and crop losses constitute an onerous "tax" on food, fiber, and forage production. (4) The global cost of virulent plant and animal diseases caused by parasites transported to new ranges and presented with susceptible new hosts is currently incalculable. Identifying future invaders and taking effective steps to prevent their dispersal and establishment con- stitutes an enormous challenge to both conservation and international commerce. Detection and management when exclusion fails have proved daunting for varied reasons: (1) Efforts to identify general attributes of future invaders have often been inconclusive. (2) Predicting susceptible locales for future invasions seems even more problematic, given the enormous differences in the rates of arrival among potential invaders. (3) Eradication of an established invader is rare, and control efforts vary enormously in their efficacy. Successful control, however, depends more on commitment and continuing diligence than on the efficacy of specific tools themselves. (4) Control of biotic invasions is most effective when it employs a long-term, ecosystem- wide strategy rather than a tactical approach focused on battling individual invaders. (5) Prevention of invasions is much less costly than post-entry control. Revamping national and international quarantine laws by adopting a "guilty until proven innocent" approach would be a productive first step. Failure to address the issue of biotic invasions could effectively result in severe global consequences, including wholesale loss of agricultural, forestry, and fishery resources in some regions, disruption of the ecological processes that supply natural services on which human enterprise depends, and the creation of homogeneous, impoverished ecosystems composed of cosmopolitan species. Given their current scale, biotic invasions have taken their place alongside human-driven atmospheric and oceanic alterations as major agents of global change. Left unchecked, they will influence these other forces in profound but still unpredictable ways.

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Biotic invasions: causes, epidemiology, global consequences, and control

▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...

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Mechanisms of Maintenance of Species Diversity

The high-level language of R is recognized as one of the most powerful and flexible statistical software environments, and is rapidly becoming the standard setting for quantitative analysis, statistics and graphics. R provides free access to unrivalled coverage and cutting-edge applications, enabling the user to apply numerous statistical methods ranging from simple regression to time series or multivariate analysis. Building on the success of the authors bestselling Statistics: An Introduction using R, The R Book is packed with worked examples, providing an all inclusive guide to R, ideal for novice and more accomplished users alike. The book assumes no background in statistics or computing and introduces the advantages of the R environment, detailing its applications in a wide range of disciplines. Provides the first comprehensive reference manual for the R language, including practical guidance and full coverage of the graphics facilities. Introduces all the statistical models covered by R, beginning with simple classical tests such as chi-square and t-test. Proceeds to examine more advance methods, from regression and analysis of variance, through to generalized linear models, generalized mixed models, time series, spatial statistics, multivariate statistics and much more. The R Book is aimed at undergraduates, postgraduates and professionals in science, engineering and medicine. It is also ideal for students and professionals in statistics, economics, geography and the social sciences.

The R book

To curb the future economic and environmental impacts of invasive exotic species, we need to understand the mechanisms behind exotic invasions. One commonly accepted mechanism for exotic plant invasions is the enemy release hypothesis (ERH), which states that plant species, on introduction to an exotic region, experience a decrease in regulation by herbivores and other natural enemies, resulting in a rapid increase in distribution and abundance. The success of classical biological control has been used as support for ERH, but this observational evidence does not directly test ERH, and the more experimental evidence is equivocal. Competitive release through greater generalist enemy impact on natives seems to be an important but understudied mechanism of enemy release, but there is a serious need for experiments involving exclusion of natural enemies in invaded plant communities. With a clearer understanding of the role of enemy release in exotic plant invasions, we can begin to build a comprehensive predictive model of exotic plant invasions.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(02)02499-0.pdf

Exotic plant invasions and the enemy release hypothesis

Preface An Ecological Example The GLIM Language Introduction to Experimental Design Understanding Data: Graphical Analysis Understanding Data: Basic Statistics Regression and GLIM Anova and GLIM Analysis of Covariance in GLIM Linear Models Model Simplification Model Criticism Analysing Count Data: Poisson Errors Analysing Proportion Data: Binomial Errors Binary Response Variables Data with Gamma Errors Survival Data Ecological Techniques What GLIM Doesn't Do Programming in GLIM Technical Appendices Statistical Tables Library of GLIM Programmes and Macros (on disk)

GLIM for ecologists

Preface.Statistical methods. Introduction to S Plus. Experimental design Central tendency. Probability. Variance. The Normal Distribution. Power calculations. Understanding data: graphical analysis. Understanding data: tabular analysis. Classical tests. Bootstrap and jackknife. Statistical models in S Plus. Regression. Analysis of variance. Analysis of covariance. Model criticism. Contrasts. Split plot Anova. Nested designs and variance components analysis. Graphs, functions and transformations. Curve fitting and piecewise regression. Non linear regression. Multiple regression. Model simplification. Probability distributions. Generalised linear models. Proportion data: binomial errors. Count data: Poisson errors. Binary response variables. Tree models. Non parametric smoothing. Survival analysis. Time series analysis. Mixed effects models. Spatial statistics. Bibliography. Index.

Michael J. Crawley

Papers

The R book

Exotic plant invasions and the enemy release hypothesis

GLIM for ecologists

Statistical Computing: An Introduction to Data Analysis using S-Plus

Herbivory: The Dynamics of Animal-Plant Interactions.