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

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

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.

Count data can be analyzed using generalized linear mixed models when observations are correlated in ways that require random effects However, count data are often zero-inflated, containing more zeros than would be expected from the typical error distributions We present a new package, glmmTMB, and compare it to other R packages that fit zero-inflated mixed models The glmmTMB package fits many types of GLMMs and extensions, including models with continuously distributed responses, but here we focus on count responses glmmTMB is faster than glmmADMB, MCMCglmm, and brms, and more flexible than INLA and mgcv for zero-inflated modeling One unique feature of glmmTMB (among packages that fit zero-inflated mixed models) is its ability to estimate the Conway-Maxwell-Poisson distribution parameterized by the mean Overall, its most appealing features for new users may be the combination of speed, flexibility, and its interface’s similarity to lme4

/pdf/glmmtmb-balances-speed-and-flexibility-among-packages-for-efr2bq6jaw.pdf

glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling

Emerging infectious diseases (EIDs) of free-living wild animals can be classified into three major groups on the basis of key epizootiological criteria: (i) EIDs associated with “spill-over” from domestic animals to wildlife populations living in proximity; (ii) EIDs related directly to human intervention, via host or parasite translocations; and (iii) EIDs with no overt human or domestic animal involvement. These phenomena have two major biological implications: first, many wildlife species are reservoirs of pathogens that threaten domestic animal and human health; second, wildlife EIDs pose a substantial threat to the conservation of global biodiversity.

/pdf/emerging-infectious-diseases-of-wildlife-threats-to-4s3pc5irzv.pdf

Emerging Infectious Diseases of Wildlife-- Threats to Biodiversity and Human Health

Sexual selection in mammals has resulted in the evolution of sexual size dimorphism (SSD), with males usually being the larger sex. Comparative analyses indicate that the evolution of SSD is associated with the evolution of male-biased mortality, suggesting a possible causal link between the two. Here, we use a comparative approach to investigate the possible role of parasites in generating this relation. We show that there is a robust association between male-biased parasitism and the degree of sexual selection, as measured by mating system (monogamous or polygynous) and by the degree of SSD. There is also a positive correlation, across taxa, between male-biased mortality and male-biased parasitism. These results are consistent with the hypothesis that parasites contribute to the observed association between SSD and male-biased mortality.

https://science.sciencemag.org/content/sci/297/5589/2015.full.pdf

Parasites as a Viability Cost of Sexual Selection in Natural Populations of Mammals.

A major debate in ecology concerns the relative importance of intrinsic factors and extrinsic environmental variations in determining population size fluctuations1,2,3,4,5,6. Spatial correlation of fluctuations in different populations caused by synchronous environmental shocks2,7,8 is a powerful tool for quantifying the impact of environmental variations on population dynamics8,9. However, interpretation of synchrony is often complicated by migration between populations8,10. Here we address this issue by using time series from sheep populations on two islands in the St Kilda archipelago11,12,13. Fluctuations in the sizes of the two populations are remarkably synchronized over a 40-year period. A nonlinear time-series model shows that a high and frequent degree of environmental correlation is required to achieve this level of synchrony. The model indicates that if there were less environmental correlation, population dynamics would be much less synchronous than is observed. This is because of a threshold effect that is dependent on population size; the threshold magnifies random differences between populations. A refined model showsthat part of the required environmental synchronicity can be accounted for by large-scale weather variations. These results underline the importance of understanding the interaction between intrinsic and extrinsic influences on population dynamics14.

/pdf/noise-and-determinism-in-synchronized-sheep-dynamics-1dogqn3oz6.pdf

Noise and determinism in synchronized sheep dynamics

Summary In this chapter we discuss how to make best use of sex ratio data. We identify three basic questions that such data can be used to answer: does the sex ratio differ from some theoretically expected mean value, does it differ from an expected distribution and is variation in sex ratio associated with some measured explanatory terms ? Our main focus is on the latter question. We discuss analytical methods in order of ‘sophistication’, starting with nonparametric methods (which make few assumptions about underlying statistical distributions), then classical parametric methods (which assume that data conform to a normal distribution of deviations from a statistical model) and finally generalized linear models ( GLMs ). GLMs are semi-parametric methods that encompass models assuming a normal distribution but may also assume other distributions. This is an important advantage as sex ratio data are best expressed as proportions (sex ratio = males/(males + females)) and deviations are expected to conform to a binomial distribution. GLMs assuming binomial distributions are often termed logistic regression models . Distributions may not conform to the normal or binomial assumptions of classical parametric analyses or logistic GLMs, and we discuss how these problems can be overcome. The statistical approaches we discuss are illustrated with worked examples and case histories from recent sex ratio literature. We also perform simulations to evaluate the relative performances of nonparametric, classical parametric and logistic GLM analyses: GLMs win.

Statistical analysis of sex ratios : an introduction.

Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high levels of genetic diversity widely observed at the major histocompatibility complex (MHC) of vertebrate hosts are consistent with the hypothesis of parasite-driven balancing selection acting to maintain MHC genetic diversity. To date, however, empirical evidence in support of this hypothesis, especially from natural populations, has been lacking. A large unmanaged population of Soay sheep (Ovis aries L.) is used to investigate associations between MHC variation, juvenile survival, and parasite resistance. We show in an unmanaged, nonhuman population that allelic variation within the MHC is significantly associated with differences in both juvenile survival and resistance to intestinal nematodes. Certain MHC alleles are associated with low survivorship probabilities and high levels of parasitism or vice versa. We conclude that parasites are likely to play a major role in the maintenance of MHC diversity in this population.

/pdf/major-histocompatibility-complex-variation-associated-with-18cld3dirx.pdf

Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population (Ovis aries L.)

Kenneth Wilson

Papers

Parasites as a Viability Cost of Sexual Selection in Natural Populations of Mammals.

Noise and determinism in synchronized sheep dynamics

Statistical analysis of sex ratios : an introduction.

Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population (Ovis aries L.)

Heterogeneities in macroparasite infections : patterns and processes.