  The shift from outcrossing to self-fertilization is among the most common
transitions in plants. Until recently, however, a genome-wide view of this
transition has been obscured by a dearth of appropriate data and the lack of
appropriate population genomic methods to interpret such data. Here, we present
novel analyses detailing the origin of the selfing species, Capsella rubella,
which recently split from its outcrossing sister, Capsella grandiflora. Due to
the recency of the split, most variation within C. rubella is found within C.
grandiflora. We can therefore identify genomic regions where two C. rubella
individuals have inherited the same or different segments of ancestral
diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based
on this analysis, we show that C. rubella was founded by multiple individuals
drawn from a diverse ancestral population closely related to extant C.
grandiflora, that drift and selection have rapidly homogenized most of this
ancestral variation since C. rubella's founding, and that little novel
variation has accumulated within this time. Despite the extensive loss of
ancestral variation, the approximately 25% of the genome for which two C.
rubella individuals have inherited different founding haplotypes makes up
roughly 90% of the genetic variation between them. To extend these findings, we
develop a coalescent model that utilizes the inferred frequency of founding
haplotypes and variation within founding haplotypes to estimate that C. rubella
was founded by a potentially large number of individuals 50-100 kya, and has
subsequently experienced a 20X reduction in its effective population size. As
population genomic data from an increasing number of outcrossing/selfing pairs
are generated, analyses like this here will facilitate a fine-scaled view of
the evolutionary and demographic impact of the transition to
self-fertilization.
