Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT).

Polyploid formation is a major mode of sympatric speciation in flowering plants. Unlike other speciation processes, polyploidization is often assumed to confer instant reproductive isolation. Shared polymorphism across ploidy levels has therefore often been attributed to multiple polyploid origins, whereas the alternative hypothesis of introgressive hybridization has rarely been rigorously tested. Here, we sequence 12 nuclear loci representing 6 genes duplicated by polyploidy in 92 accessions of the tetraploid Capsella bursa-pastoris together with the corresponding loci in 21 accessions of its close diploid relative Capsella rubella. In C. bursa-pastoris accessions from western Eurasia, where the 2 species occur in partial sympatry, we find higher levels of nucleotide diversity than in accessions from eastern Eurasia, where C. rubella does not grow. Furthermore, haplotypes are shared across ploidy levels at 4 loci in western but not in eastern Eurasia. We test whether haplotype sharing is due to retention of ancestral polymorphism or due to hybridization and introgression using a coalescent-based isolation-with-migration model. In western but not in eastern Eurasia, there is evidence for unidirectional gene flow from C. rubella to C. bursa-pastoris. An independent estimate of the timing of dispersal of C. bursa-pastoris to eastern Eurasia indicates that it probably predated introgression. Our results show that polyploid speciation need not result in immediate and complete reproductive isolation, that postpolyploidization hybridization and introgression can contribute significantly to genetic variation in a newly formed polyploid, and that divergence population genetic analysis constitutes a powerful way of testing hypotheses on polyploid speciation.

Polyploidization, often accompanied by hybridization, has been of major importance in flowering plant evolution. Here we investigate the importance of these processes for the evolution of the tetraploid crucifer Capsella bursa-pastoris using DNA sequences from two chloroplast loci as well as from three nuclear low-copy genes. The near-absence of variation at the C. bursa-pastoris chloroplast markers suggests a single and recent origin of the tetraploid. However, despite supporting a single phylogeny, chloroplast data indicate that neither of the extant Capsella diploids is the maternal parent of the tetraploid. Combined with data from the three nuclear loci, our results do not lend support to previous hypotheses on the origin of C. bursa-pastoris as an allopolyploid between the diploids C. grandiflora and C. rubella or an autopolyploid of C. grandiflora. Nevertheless, for each locus, some of the C. bursa-pastoris accessions harbored C. rubella alleles, indicating that C. rubella contributed to the gene pool of C. bursa-pastoris, either through allopolyploid speciation or, more likely, through hybridization and introgression. To our knowledge, this study is the first of a wild, nonmodel plant genus that uses a combination of chloroplast and multiple low-copy nuclear loci for phylogenetic inference of polyploid evolution.