High levels of inbreeding cause populations to become composed of homozygous, inbred lines. High levels of homozygosity limit the effectiveness of recombination, and therefore, retard the rate of decay of linkage (gametic phase) disequilibrium (LD) among mutations. Inbreeding and recombination interact to shape the expected pattern of LD. The actual extent of nucleotide sequence level LD within inbreeding species has only been studied in Arabidopsis, a weedy species whose global range has recently expanded. In the present study, we examine the levels of LD within and between 18 nuclear genes in 25 accessions from across the geographic range of wild barley, a species with a selfing rate of Ϸ98%. In addition to examination of intralocus LD, we employ a resampling method to determine whether interlocus LD exceeds expectations. We demonstrate that, for the majority of wild barley loci, intralocus LD decays rapidly, i.e., at a rate similar to that observed in the outcrossing species, Zea mays (maize). Excess interlocus LD is observed at 15% of two-locus combinations; almost all interlocus LD involves loci with significant geographic structuring of mutational variation.nucleotide polymorphism ͉ population structure ͉ Wall's B ͉ interlocus linkage disequilibrium ͉ inbreeding U nder recurrent self-fertilization, the level of heterozygosity decays at the rate of one-half per locus, per generation (1). Thus, within a few generations a self-fertilizing population is expected to be entirely composed of a collection of homozygous lines. An important consequence of this mating system is an extreme reduction in the rate of effective recombination. Consequently, the decay of linkage disequilibrium (LD) will be arrested. This expectation has generally been borne out in studies of natural populations; within-population levels of LD for isozyme polymorphisms are generally higher in populations of self-fertilizing plants than in outcrossers (2, 3). Many plant species have a mixed mating system with a mixture of outcrossing and self-fertilization, where occasional outcross events produce new heterozygous lines, that within a few generations, sort out into homozygous lines (4). Under this scenario, LD decays at a rate that is a function not only of recombination distance but also the level of outcrossing (5-7).It has long been argued that the evolutionary potential of predominantly self-fertilizing species is limited by both reduced genetic diversity and a reduction in potential for effective recombination (e.g., refs. 8 and 9, reviewed in ref. 10). Recombinational potential is important because linkage drag, where selection acts on the net fitness of advantageous and disadvantageous mutations that are in LD with one another, both retards the rate of fixation of advantageous mutations and leads to the fixation of deleterious mutations. Despite the theoretical possibility of linkage drag, many of our most important crops, such as wheat, barley, beans, and tomatoes, are predominantly selffertilizing species. Therefore, the empirical me...

Mutations arise in a single individual and at a single point in time and space. The geographic distribution of mutations reflects both historical population size and frequency of migration. We employ coalescence-based methods to coestimate effective population size, frequency of migration, and level of recombination compatible with observed genealogical relationships in sequence data from nine nuclear genes in wild barley (Hordeum vulgare ssp. spontaneum), a highly self-fertilizing grass species. In self-fertilizing plants, gamete dispersal is severely limited; dissemination occurs primarily through seed dispersal. Also, heterozygosity is greatly reduced, which renders recombination less effective at randomizing genetic variation and causes larger portions of the genome to trace a similar history. Despite these predicted effects of this mating system, the majority of loci show evidence of recombination. Levels of nucleotide variation and the patterns of geographic distribution of mutations in wild barley are highly heterogeneous across loci. Two of the nine sampled loci maintain highly diverged, geographic region-specific suites of mutations. Two additional loci include region-specific haplotypes with a much shallower coalescence. Despite inbreeding, sessile growth habit, and the observation of geographic structure at almost half of sampled loci, parametric estimates of migration suggest that seed dispersal is sufficient for migration across the Ϸ3,500-km range of the species. Recurrent migration is also evident based on the geographic distribution of mutational variation at some loci. At one locus a single haplotype has spread rapidly enough to occur, unmodified by mutation, across the range of the species.

Determining accurate phylogenetic relationships among the members of the woody Sonchus alliance presents challenges because of an insufficient level of molecular variation and the convergent evolution of similar morphological traits in island settings. To obtain a better resolved phylogeny and to test the potential role of hybridization and introgression, we sequenced all members of the alliance with multiple populations for the ITS of nrDNA and over 4000 base pairs of coding and noncoding regions of cpDNA. The cpDNA phylogeny is not well resolved in the core members of the alliance (i.e., subg. Dendrosonchus and genus Taeckholmia), but like the ITS tree, it has identified basal lineages of monotypic genera. The cpDNA data set was not significantly different from that of ITS, and subsequent combined analysis provided a better resolved and supported phylogeny within the alliance. The combined ML tree identified the same basal lineages, suggested nonmonophyly of Dendrosonchus and Taeckholmia, and did not support either Boulos' or Aldridge's infrasubgeneric classification system. Assessment of the role of hybridization and introgression was limited due to poor resolution in the cpDNA phylogeny. The combined analysis supports a Gran Canaria origin for the alliance and two subsequent long distance dispersal events to Madeira and Cape Verde islands.

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Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter (r) relative to estimates of the mutation parameter (u) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of r/u are much greater than expected, with a meanr/û % 1.5, similar to estimates from outcrossing species. We also estimater with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination. T HERE are two sources of genetic diversity, mutation and recombination. Mutation, broadly defined here as novel heritable change in nucleotide state, introduces new variants while recombination reassorts the variants along a chromosome into novel combinations or haplotypes. Recombination can occur through both homologous crossover and homologous (intralocus) gene conversion, processes that occur as part of meiosis in diploid (or higher ploidy) organisms (Wiuf and Hein 2000). Under the Holliday junction model (Holliday 1964), homologous gene conversion is thought to occur when only a short tract of the alternate chromosome (usually a few hundred base pairs) is incorporated during meiotic exchange (e.g., Stahl 1994).Inbreeding dramatically reduces the role of recombination. Recurrent inbreeding can rapidly increase homozygosity; the recombination process continues to exchange chromosomal segments during gamete formation but with little effective recombination of mutations. Thus the primary impact of inbreeding is expected to be a reduction of the contribution of recombination, relative to mutation, to total genetic diversity.Under coalescent theory and assuming a standard neutral model, the impact of inbreeding can be measured as a reduction in the ratio of the recombination parameter r to the mutation parameter u, i.e., r/u (where r ¼ 4N e r and u ¼ 4N e m and where N e is the effective population size, r is the rate of recombination, and m is the rate of mutation) (symbols used are listed in Table 1). It is predicted that both r and u are reduced by inbreeding, but the impact on recombination is expected to be much greater (Nordborg 2000). Nordborg (2000) showed that r is predicted to be reduced under partial self-fertilization based on the relat...