Data from: Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa-pastoris)

Polyploidization is a dominant feature of flowering plant evolution.
However, detailed genomic analyses of the inter-population diversification
of polyploids following genome duplication are still in their infancy,
mainly because of methodological limits, both in terms of sequencing and
computational analyses. The shepherd’s purse (Capsella bursa-pastoris) is
one of the most common weed species in the world. It is highly
self-fertilizing, and recent genomic data indicate that it is an
allopolyploid, resulting from hybridization between the ancestors of the
diploid species Capsella grandiflora and Capsella orientalis. Here, we
investigated the genomic diversity of C. bursa-pastoris, its population
structure and demographic history, following allopolyploidization in
Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread
across Europe, the Middle East and Asia, using genotyping-by-sequencing,
leading to a total of 4,274 SNPs after quality control. Bayesian
clustering analyses revealed three distinct genetic clusters in Eurasia:
one cluster grouping samples from Western Europe and Southeastern Siberia,
the second one centered on Eastern Asia and the third one in the Middle
East. Approximate Bayesian computation (ABC) supported the hypothesis that
C. bursa-pastoris underwent a typical colonization history involving low
gene flow among colonizing populations, likely starting from the Middle
East towards Europe and followed by successive human-mediated expansions
into Eastern Asia. Altogether, these findings bring new insights into the
recent multistage colonization history of the allotetraploid C.
bursa-pastoris and highlight ABC and genotyping-by-sequencing data as
promising but still challenging tools to infer demographic histories of
selfing allopolyploids.