Neutral Genetic Diversity in Mixed Mating Systems.

Background/objectives: Systems of reproduction differ with respect to the magnitude of neutral genetic diversity maintained in a population. In particular, the partitioning of reproductive organisms into mating types and regular inbreeding have long been recognized as key factors that influence effective population number. Here, a range of reproductive systems are compared with respect to the maintenance of neutral genetic diversity.

Joint identity among loci under mutation and regular inbreeding.

This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci.

Wright's Hierarchical F-Statistics.

This perspective article offers a meditation on FST and other quantities developed by Sewall Wright to describe the population structure, defined as any departure from reproduction through random union of gametes. Concepts related to the F-statistics draw from studies of the partitioning of variation, identity coefficients, and diversity measures. Relationships between the first two approaches have recently been clarified and unified.

Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent.

We address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class.

Inductive determination of allele frequency spectrum probabilities in structured populations.

We present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate (θ).

Evolution of the sex ratio and effective number under gynodioecy and androdioecy.

We address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own genotype, while in our maternal control models, it depends on the genotype of its maternal parent.

A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types.

Genealogical histories in structured populations.

In genealogies of genes sampled from structured populations, lineages coalesce at rates dependent on the states of the lineages. For migration and coalescence events occurring on comparable time scales, for example, only lineages residing in the same deme of a geographically subdivided population can have descended from a common ancestor in the immediately preceding generation. Here, we explore aspects of genealogical structure in a population comprising two demes, between which migration may occur.

Effects of polymorphism for locally adapted genes on rates of neutral introgression in structured populations.

Adaptation to local conditions within demes balanced by migration can maintain polymorphisms for variants that reduce fitness in certain ecological contexts. Here, we address the effects of such polymorphisms on the rate of introgression of neutral marker genes, possibly genetically linked to targets of selection. Barriers to neutral gene flow are expected to increase with linkage to targets of local selection and with differences between demes in the frequencies of locally adapted alleles.

Sex-specific incompatibility generates locus-specific rates of introgression between species.

Disruption of interactions among ensembles of epistatic loci has been shown to contribute to reproductive isolation among various animal and plant species. Under the Bateson-Dobzhansky-Muller model, such interspecific incompatibility arises as a by-product of genetic divergence in each species, and the Orr-Turelli model indicates that the number of loci involved in incompatible interactions may "snowball" over time. We address the combined effect of multiple incompatibility loci on the rate of introgression at neutral marker loci across the genome.

Ancestral population genomics: the coalescent hidden Markov model approach.

With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the number of generations between speciation events. We use a hidden Markov model parameterized according to coalescent theory to infer the genealogy along a four-species genome alignment of closely related species and estimate population parameters.

Site frequency spectra from genomic SNP surveys.

Genomic survey data now permit an unprecedented level of sensitivity in the detection of departures from canonical evolutionary models, including expansions in population size and selective sweeps. Here, we examine the effects of seemingly subtle differences among sampling distributions on goodness of fit analyses of site frequency spectra constructed from single nucleotide polymorphisms. Conditioning on the observation of exactly two alleles in a random sample results in a site frequency spectrum that is independent of the scaled rate of neutral substitution (theta).

Importance sampling for the infinite sites model.

Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model.

The evolutionary forest algorithm.

Motivation: Gene genealogies offer a powerful context for inferences about the evolutionary process based on presently segregating DNA variation. In many cases, it is the distribution of population parameters, marginalized over the effectively infinite-dimensional tree space, that is of interest. Our evolutionary forest (EF) algorithm uses Monte Carlo methods to generate posterior distributions of population parameters.

Likelihoods from summary statistics: recent divergence between species.

We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation.

The evolutionary dynamics of self-incompatibility systems.

Self-incompatible flowering plants reject pollen that expresses the same mating specificity as the pistil (female reproductive tract). In most plant families, pollen and pistil mating specificities segregate as a single locus, the S locus. In at least two self-incompatibility systems, distinct pollen and pistil specificity genes are embedded in an extensive nonrecombining tract.

Evolution under tight linkage to mating type.

Recent large-scale sequencing studies of mating type loci in a number of organisms offer insight into the origin and evolution of these genomic regions. Extensive tracts containing genes with a wide diversity of functions typically cosegregate with mating type. Cases in which mating type determination entails complementarity between distinct transcription units may descend from systems in which close physical linkage facilitated the coordinated expression and cosegregation of the interacting genes.

On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation.

Pollen limitation affects plants with diverse reproductive systems and ecologies. In self-incompatible (SI) species, pollen limitation may preclude full reproductive compensation for prezygotic rejection of pollen. We present a model designed to explore the effects of incomplete reproductive compensation on evolutionary changes at a modifier locus that regulates the level of SI expression.

Maximum-likelihood estimation of rates of recombination within mating-type regions.

Features common to many mating-type regions include recombination suppression over large genomic tracts and cosegregation of genes of various functions, not necessarily related to reproduction. Model systems for homomorphic self-incompatibility (SI) in flowering plants share these characteristics. We introduce a method for the exact computation of the joint probability of numbers of neutral mutations segregating at the determinant of mating type and at a linked marker locus.

A simple method for computing exact probabilities of mutation numbers.

We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolutionary changes as a Markov process and determination of one-step transition matrices. We address the pattern of nucleotide diversity at a neutral marker locus linked to a determinant of mating type.

Patterns of variation within self-incompatibility loci.

Diverse self-incompatibility (SI) mechanisms permit flowering plants to inhibit fertilization by pollen that express specificities in common with the pistil. Characteristic of at least two model systems is greatly reduced recombination across large genomic tracts surrounding the S-locus, which regulates SI. In three angiosperm families, including the Solanaceae, the gene that controls the expression of gametophytic SI in the pistil encodes a ribonuclease (S-RNase).

Genealogy-dependent variation in viability among self-incompatibility genotypes.

Many hermaphroditic plants avoid self-fertilization by rejecting pollen that express genetically determined specificities in common with the pistil. The S-locus, comprising the determinants of pistil and pollen specificity, typically shows extremely high polymorphism, with dozens to hundreds of specificities maintained within species. This article explores a conjecture, motivated by empirical findings, that the expression of recessive deleterious factors at sites closely linked to the S-locus may cause greater declines in the viability of zygotes constituted from more closely related S-alleles.

INBREEDING AND THE COST OF MEIOSIS: THE EVOLUTION OF SELFING IN POPULATIONS PRACTICING BIPARENTAL INBREEDING.

The effect of biparental inbreeding on the conditions governing the evolution of selfing is examined using recursions in mating-type frequencies. Sibmating in combination with random outcrossing influences two key determinants of the adaptive value of selfing: 1) the meiotic cost of biparental reproduction and 2) the level of inbreeding depression due to deleterious mutations. Biparental inbreeding serves to maintain biparental reproduction by increasing relatedness between parents and their biparentally derived offspring and introduces the possibility of an optimal mating system that incorporates both modes of reproduction.

ON THE EVOLUTION OF PARTHENOGENESIS. II. INBREEDING AND THE COST OF MEIOSIS.

Quantitative models of genetic change were analyzed to study the effect of inbreeding on the conditions for the evolution of parthenogenesis. Although inbreeding has been proposed as a key factor that may resolve the apparent paradox between the success of biparental reproduction and the genetic advantages of uniparental reproduction, the results indicate that inbreeding does not greatly change the cost of meiosis in diploids and actually increases it in haplodiploids. Inbreeding increases parent-offspring relatedness and the reproductive value of females.