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.

PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate constancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models. These include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Multifurcating trees are supported, as well as trees in which some sequences are ancestral to some others. A heuristic tree search algorithm (star decomposition) is used in the package, but tree making is not a strong point of the current version, although work is under way to implement efficient search algorithms. Major programs in the package, as well as the types of analyses they perform, are listed in Table 1. More details are available in the documentation included in the package, written using Microsoft Word. PAML is distributed free of charge for academic use only. The package, including ANSI C source codes, documentation, example data sets, and control files, can be obtained by anonymous ftp at mw511.biol.berkeley.edu/pub, or from the Indiana molecular biology ftp site at ftp.bio.indiana.edu under the directory Incoming or molbio/evolve . MAC and PowerMac executables are also available, although DOS executables are not prepared yet. Further information about the package is available from the World Wide Web at

PAML: a program package for phylogenetic analysis by maximum likelihood

PAML: a program for package for phylogenetic analysis by maximum likelihood

Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.

/pdf/inference-of-population-structure-using-multilocus-genotype-19wwjas2e3.pdf

Inference of population structure using multilocus genotype data: dominant markers and null alleles

FST describes the processes that lead to genetic differentiation among and within populations and is widely used in population and evolutionary genetics. This article describes the meaning of FST and how it should be estimated and interpreted.

/pdf/genetics-in-geographically-structured-populations-defining-ew64yk3nst.pdf

Genetics in geographically structured populations: defining, estimating and interpreting FST

Genetic and evolutionary consequences of small population size in plants: implications for conservation.

Section One: Population biology and genetics of rare species Section Two: Distribution and sampling of genetic variation Section Three: Management and assessment of off-site collections Section Four: Conservation strategies for genetic diversity.

Genetics and conservation of rare plants.

Genetics and Conservation of Rare Plants

We present a framework for fitting multiple random walks to animal move- ment paths consisting of ordered sets of step lengths and turning angles. Each step and turn is assigned to one of a number of random walks, each characteristic of a different behavioral state. Behavioral state assignments may be inferred purely from movement data or may include the habitat type in which the animals are located. Switching between different behavioral states may be modeled explicitly using a state transition matrix estimated directly from data, or switching probabilities may take into account the proximity of animals to landscape features. Model fitting is undertaken within a Bayesian framework using the WinBUGS software. These methods allow for identification of different movement states using several properties of observed paths and lead naturally to the formulation of movement models. Analysis of relocation data from elk released in east-central Ontario, Canada, suggests a biphasic movement behavior: elk are either in an ''encamped'' state in which step lengths are small and turning angles are high, or in an ''exploratory'' state, in which daily step lengths are several kilometers and turning angles are small. Animals encamp in open habitat (agricultural fields and opened forest), but the exploratory state is not associated with any particular habitat type.

/pdf/extracting-more-out-of-relocation-data-building-movement-u7bx9wghqb.pdf

Kent E. Holsinger

Papers

Genetics in geographically structured populations: defining, estimating and interpreting FST

Genetic and evolutionary consequences of small population size in plants: implications for conservation.

Genetics and conservation of rare plants.

Genetics and Conservation of Rare Plants

Extracting more out of relocation data: building movement models as mixtures of random walks