The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

/pdf/detecting-the-number-of-clusters-of-individuals-using-the-16mlx2qlv8.pdf

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

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

spag e d i version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling. spag e d i is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.

spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels

Genetics and analysis of quantitative traits

Population genetics studies using microsatellites, and data on their molecular dynamics, are on the increase. But, so far, no consensus has emerged on which mutation model should be used, though this is of paramount importance for analysis of population genetic structure. However, this is not surprising given the variety of microsatellite molecular motifs. Null alleles may be disturbing for population studies, even though their presence can be detected through careful population analyses, while homoplasy seems of little concern, at least over short evolutionary scales. Interspecific studies show that microsatellites are poor markers for phylogenetic inference. However, these studies are fuelling discussions on directional mutation and the role of selection and recombination in their evolution. Nonetheless, it remains true that microsatellites may be considered as good, neutral mendelian markers.

Microsatellites, from molecules to populations and back

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-294X.2002.01576.x

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis.

Studies of bioinvasions have revealed various strategies of invasion, depending on the ecosystem invaded and the alien species concerned. Here, we consider how migration (as a demographic factor), as well as ecological and evolutionary changes, affect invasion success. We propose three main theoretical scenarios that depend on how these factors generate the match between an invader and its new environment. Our framework highlights the features that are common to, or differ among, observed invasion cases, and clarifies some general trends that have been previously highlighted in bioinvasions. We also suggest some new directions of research, such as the assessment of the time sequence of demographic, genetic and environmental changes, using detailed temporal surveys.

A general eco-evolutionary framework for understanding bioinvasions

Selfing, the fusion of male and female gametes from a single genetic individual or colony, is possible in many plants and also in hermaphrodite animals. We review the occurrence of selfing and mechanisms for its avoidance, in functionally hermaphrodite animal and plants. We discuss means by which selfing can be detected and briefly review techniques for estimation of selfing frequencies in natural populations. Although many functionally hcmaphrodite species are probably almost complete outcrossers or inbreeders, mixed mating systems are also found in both plant and animal populations. We review theories for the advantages and disadvantages of selfing, and for the maintenance of mixed mating systems, together

The Evolution of the Selfing Rate in Functionally Hermaphrodite Plants and Animals

Excluding insects, hermaphroditism occurs in about one-third of animal species, providing numerous opportunities for the evolution of selfing. Here we provide an overview of reproductive traits in hermaphroditic animal species, review the distribution of selfing rates in animals, and test for ecological correlates of selfing. Our dataset (1342 selfing-rate estimates for 142 species) is 97% based on estimates derived from the analysis of population structure (FIS-estimates) using genetic markers. The distribution of selfing is slightly &#x1d5e8;-shaped and differs significantly from the more strongly &#x1d5e8;-shaped plant distribution with 47% of animal t-estimates being intermediate (falling between 0.2 and 0.8) compared to 42% for plants. The influence of several factors on the distribution of selfing rates was explored (e.g., number of populations studied per species, habitat, coloniality, sessility, or fertilization type), none of which significantly affect the distribution. Our results suggest that genetic ...

https://bioone.org/journals/evolution/volume-60/issue-9/06-246.1/ANIMALS-MIX-IT-UP-TOO--THE-DISTRIBUTION-OF-SELF/10.1554/06-246.1.pdf

Philippe Jarne

Papers

Microsatellites, from molecules to populations and back

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis.

A general eco-evolutionary framework for understanding bioinvasions

The Evolution of the Selfing Rate in Functionally Hermaphrodite Plants and Animals

Animals mix it up too: the distribution of self-fertilization among hermaphroditic animals