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

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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

Genetics and analysis of quantitative traits

Developmental Plasticity and Evolution. In: Mary Jane West-Eberhard, Editor, Oxford University Press (2003) Pp. xi+794. Price $50.00 paper.

Urbanization is an increasingly important dimension of global change, and urban areas likely impose significant natural selection on the species that reside within them. Although many species of plants and animals can survive in urban areas, so far relatively little research has investigated whether such populations have adapted (in an evolutionary sense) to their newfound milieu. Even less of this work has taken place in tropical regions, many of which have experienced dramatic growth and intensification of urbanization in recent decades. In the present study, we focus on the neotropical lizard, Anolis cristatellus. We tested whether lizard ecology and morphology differ between urban and natural areas in three of the most populous municipalities on the island of Puerto Rico. We found that environmental conditions including temperature, humidity, and substrate availability differ dramatically between neighboring urban and natural areas. We also found that lizards in urban areas use artificial substrates a large proportion of the time, and that these substrates tend to be broader than substrates in natural forest. Finally, our morphological data showed that lizards in urban areas have longer limbs relative to their body size, as well as more subdigital scales called lamellae, when compared to lizards from nearby forested habitats. This shift in phenotype is exactly in the direction predicted based on habitat differences between our urban and natural study sites, combined with our results on how substrates are being used by lizards in these areas. Findings from a common-garden rearing experiment using individuals from one of our three pairs of populations provide evidence that trait differences between urban and natural sites may be genetically based. Taken together, our data suggest that anoles in urban areas are under significant differential natural selection and may be evolutionarily adapting to their human-modified environments.

Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus

It is often hoped that population genetics can answer questions about the demographic and geographic dynamics of recent biological invasions. Conversely, invasions with well-known histories are sometimes billed as opportunities to test methods of population genetic inference. In both cases, underappreciated limitations constrain the usefulness of genetic methods. The most significant is that human-caused invasions have occurred on historical timescales that are orders of magnitude smaller than the timescales of mutation and genetic drift for most multicellular organisms. Analyses based on the neutral theory of molecular evolution cannot resolve such rapid dynamics. Invasion histories cannot be reconstructed in the same way as biogeographic changes occurring over millenia. Analyses assuming equilibrium between mutation, drift, gene flow, and selection will rarely be applicable, and even methods designed for explicitly non-equilibrium questions often require longer timescales than the few generations of most invasions of current concern. We identified only a few population genetic questions that are tractable over such short timescales. These include comparison of alternative hypotheses for the geographic origin of an invasion, testing for bottlenecks, and hybridization between native and invasive species. When proposing population genetic analysis of a biological invasion, we recommend that biologists ask (i) whether the questions to be addressed will materially affect management practice or policy, and (ii) whether the proposed analyses can really be expected to address important population genetic questions. Despite our own enthusiasm for population genetic research, we conclude that genetic analysis of biological invasions is justified only under exceptional circumstances.

http://www.speleobiology.com/niemiller/wp-content/uploads/bsk-pdf-manager/Fitzpatrick_etal_2012_31.pdf

What can DNA tell us about biological invasions

The origin of new species can be influenced by both deterministic and stochastic factors. Mate choice and natural selection may be important deterministic causes of speciation (as opposed to the essentially stochastic factors of geographic isolation and genetic drift). Theoretical models predict that speciation is more likely when mate choice depends on an ecologically important trait that is subject to divergent natural selection, although many authors have considered such mating/ecology pleiotropy, or “magictraits” to be unlikely. However, phenotypic signals are important in both mate choice and ecological processes such as avoiding predation. In chemically defended species, it may be that the phenotypic characteristics influencing mate choice are the same signals being used to transmit a warning to potential predators, although few studies have demonstrated this in wild populations. We tested for assortative mating between two color morphs of the Strawberry Poison-Dart Frog, Dendrobates pumilio ,ag roup with striking geographic variation in aposematic color patterns. We found that females significantly prefer individuals of their own morph under two different light treatments, indicating strong assortative mating based on multiple coloration cues that are also important ecological signals. This study provides a rare example of one phenotypic trait affecting both ecological viability and nonrandom mating, indicating that mating/ecology pleiotropy is plausible in wild populations, particularly for organisms that are aposematically colored and visually orienting.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.2007.00174.x

Assortative mating in poison-dart frogs based on an ecologically important trait.

http://faculty.umb.edu/liam.revell/pdfs/Reynolds_etal_2014.MPE.pdf

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

Phylogenetic comparative methods that incorporate intraspecific variability are relatively new and, so far, not especially widely used in empirical studies. In the present short article we will describe a new Bayesian method for fitting evolutionary models to comparative data that incorporates intraspecific variability. This method differs from an existing likelihood-based approach in that it requires no a priori inference about species means and variances; rather it takes phenotypic values from individuals and a phylogenetic tree as input, and then samples species means and variances, along with the parameters of the evolutionary model, from their joint posterior probability distribution. One of the most novel and intriguing attributes of this approach is that jointly sampling the species means with the evolutionary model parameters means that the model and tree can influence our estimates of species mean trait values, not just the reverse. In the present implementation, we first apply this method to the most widely used evolutionary model for continuously valued phenotypic trait data (Brownian motion). However, the general approach has broad applicability, which we illustrate by also fitting the λ model, another simple model for quantitative trait evolution on a phylogeny. We test our approach via simulation and by analyzing two empirical datasets obtained from the literature. Finally, we have implemented the methods described herein in a new function for the R statistical computing environment, and this function will be distributed as part of the 'phytools' R library.

/pdf/a-new-bayesian-method-for-fitting-evolutionary-models-to-3lp3zzo4jg.pdf

R. Graham Reynolds

Papers

Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus

What can DNA tell us about biological invasions

Assortative mating in poison-dart frogs based on an ecologically important trait.

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation.