Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella

TL;DR

This study uses genome analysis to trace the origin and demographic history of the selfing plant species Capsella rubella, revealing it was founded by multiple individuals from a diverse ancestral population and has experienced rapid genetic homogenization.

Contribution

The paper introduces novel population genomic methods to identify founding haplotypes and reconstruct the recent evolutionary history of a selfing species from outcrossing ancestors.

Findings

C. rubella was founded by multiple individuals from a diverse ancestral population.

Most ancestral variation has been rapidly lost due to drift and selection.

Approximately 90% of genetic variation between individuals is within shared founding haplotypes.

Abstract

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.