DOI: 10.5061/dryad.j6q573nf3
title: Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

description: Capsella is a model plant genus of the Brassicaceae, closely related to
 Arabidopsis. To disentangle its biogeographical history and intrageneric
 phylogenetic relationships, 282 individuals of all five currently
 recognised Capsella species were genotyped, using a restriction
 digest-based next generation sequencing method. Our analysis retrieved two
 main lineages within Capsella that split c. one million years ago, with
 western C. grandiflora and C. rubella forming a sister lineage to the
 eastern clade consisting of C. orientalis. The split was attributed to
 continuous latitudinal displacements of the Eurasian steppe belt to the
 south during early Pleistocene glacial cycles. During the interglacial
 cycles of the Late Pleistocene, hybridisation of the two lineages took
 place in the southwestern East European Plain, leading to the
 allotetraploid C. bursa-pastoris. Extant genetic variation within Capsella
 orientalis postdated any extensive glacial events. Ecological niche
 modelling showed that suitable habitat for C. orientalis existed during
 the Last Glacial Maximum around the north coast of the Black Sea and in
 southern Kazakhstan. Such a scenario is also supported by population
 genomic data that uncovered the highest genetic diversity in the south
 Kazakhstan cluster, suggesting that C. orientalis originated in
 continental Asia and migrated north- and possibly eastwards after the last
 ice age. Post-glacial hybridisation events between C. bursa-pastoris and
 C. grandiflora/rubella in the southwestern East European Plain and the
 Mediterranean gave rise to C. thracica. Introgression of C.
 grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean
 cluster within the already existing Eurasian C. bursa-pastoris
 cluster. This study shows that the continuous displacement and disruption
 of the Eurasian steppe belt during the Pleistocene was the driving force
 in the evolution of Capsella.
description: The supplementary material consists of two sets of
 files: 'caps_0_95_min141_max005_outfiles'
 represent the raw output files of the ipyrad analysis of a taxon sample
 containing all 282 accessions of the five investigated Capsella
 species. 0_95 refers to the ## [14] [clust_threshold]:
 Clustering threshold for de novo assembly in the ipyrad parameter
 file<br> min141 refers to the ## [21] [min_samples_locus]: Min #
 samples per locus for output in the ipyrad parameter file<br> max005
 refers to the ## [22] [max_SNPs_locus]: Max # SNPs per locus in the ipyrad
 parameter file
 'ori_0_95_min117_max005_outfiles' represent the raw
 output files of the ipyrad analysis of a taxon sample containing 235
 investigated Capsella orientalis accessions. 0_95
 refers to the ## [14] [clust_threshold]: Clustering threshold for de novo
 assembly in the ipyrad parameter file<br> min117 refers to the ##
 [21] [min_samples_locus]: Min # samples per locus for output in the ipyrad
 parameter file<br> max005 refers to the ## [22] [max_SNPs_locus]:
 Max # SNPs per locus in the ipyrad parameter file