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 fourspecies genome alignment of closely related species and estimate population parameters. We analyze a basic, panmictic demographic model and study its properties using an extensive set of coalescent simulations. We assess the effect of the model assumptions and demonstrate that the Markov property provides a good approximation to the ancestral recombination graph. Using a too restricted set of possible genealogies, necessary to reduce the computational load, can bias parameter estimates. We propose a simple correction for this bias and suggest directions for future extensions of the model. We show that the patterns of ILS along a sequence alignment can be recovered efficiently together with the ancestral recombination rate. Finally, we introduce an extension of the basic model that allows for mutation rate heterogeneity and reanalyze human-chimpanzee-gorilla-orangutan alignments, using the new models. We expect that this framework will prove useful for population genomics and provide exciting insights into genome evolution. B IOLOGICAL sequence data, and particularly the variation therein, contain information about the evolutionary processes that shaped the present-day organisms. Coalescent theory provides tools for comparative sequence analysis to investigate the history of populations, by studying the genealogy of the sampled sequences (Hein et al. 2005). More recently, with the rapid accumulation of molecular data, multiple-loci studies have become possible, allowing for the estimation of population genetics parameters such as speciation times and ancestral population sizes (Rannala and Yang 2003; Burgess and Yang 2008). The availability of complete genome sequences for closely related species opens a new area of research, by providing virtually as many loci as possible, yet for a single sequence from a limited number of species. While such data cannot be used to study contemporary populations, they contain information about ancestral population processes, particularly when speciation events are sufficiently close in time that incomplete lineage sorting (ILS) occurs.Consider a site in an alignment of human, chimpanzee, and gorilla. The most likely evolutionary scenario is that going backward in time, the human and chimpanzee sequences coalesce first within the humanchimpanzee (HC) ancestral population and then meet the gorilla sequence within the human-chimpanzeegorilla (HCG) ancestral population (Figure 1, case HC1). Because of genetic drift, we expect the sequences to have an older common ancestor in some regions, falling back in the HCG ancestral population. The two lineages would have been passe...

The self-incompatibility (S) locus of flowering plants offers an example of extreme polymorphism maintained by balancing selection. Estimates of recent and long-term effective population size (Ne) were determined for two solanaceous species by examination of S-allele diversity. Estimates of recent Ne in two solanaceous species differed by an order of magnitude, consistent with differences in the species' ecology. In one species, the evidence was consistent with historical population restriction despite a large recent Ne. In the other, no severe bottleneck was indicated over millions of years. Bottlenecks are integral to founder-event speciation, and loci that are subject to balancing selection can be used to evaluate the frequency of this mode of speciation.

No abstract

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. Biparental inbreeding serves to promote uniparental reproduction by reducing the relative inbreeding depression suffered by uniparental offspring. The net effect of these two antagonistic trends depends upon the extent to which mutational load accounts for differences in the numbers of the two types of offspring. A brief summary of the empirical literature suggests that: 1) biparental inbreeding may occur in populations exhibiting mixed mating systems; 2) while inbreeding depression represents an important factor, it does not account entirely for differences in offspring number between the two modes of reproduction.

S-allele diversity in Solanum carolinense was surveyed in two natural populations, located in Tennessee and North Carolina, with a molecular assay to determine the genotype of individual plants. A total of 13 different S-alleles were identified and sequenced. There is high overlap between the two populations sampled, with 10 alleles shared in common, one allele found only in Tennessee, and two found only in North Carolina. The number of alleles in this species appears to be extremely low compared with other species with gametophytic self-incompatibility. Sequence comparisons show that most alleles are extremely different one from another in their primary sequence and a phylogenetic analysis indicates extensive trans-specific evolution of S-lineages. In addition, some alleles appear to be derived much more recently. The implications of these observations are discussed in the light of recent theoretical results on S-allele population diversity and persistence.