DOI: 10.5061/dryad.1ns1rn8w3
title: The evolutionary history of Cardamine bulbifera shows a successful rapid postglacial Eurasian range expansion in the absence of sexual reproduction

description: Background and Aims Sexual reproduction is known to drive plant
 diversification and adaptation. Here we investigate the evolutionary
 history and spatiotemporal origin of a dodecaploid (2n = 12x = 96)
 Eurasian deciduous woodland species, Cardamine bulbifera, which reproduces
 and spreads via vegetative bulb-like structures only. The species has been
 among the most successful range-expanding understorey woodland plants in
 Europe, which raises the question of the genetic architecture of its gene
 pool, since its hexaploid (2n = 6x = 48) but putatively outcrossing
 closest relative, C. quinquefolia, displays a smaller distribution range
 in Eastern Europe towards the Caucasus region. Cardamine bulbifera belongs
 to a small monophyletic clade of four species comprising also C. abchasica
 (2n = 2x = 16) and C. bipinnata (unknown ploidy) from the Caucasus region.
 Methods We sequenced the genomes of the two polyploids and their two
 putative ancestors using Illumina short-read sequencing technology (×7–8
 coverage). Covering the entire distribution range, genomic data were
 generated for 67 samples of the two polyploids (51 samples of C.
 bulbifera, 16 samples of C. quinquefolia) and 6 samples of the putative
 diploid taxa (4 samples of C. abchasica, 2 samples of C. bipinnata) to
 unravel the evolutionary origin of the polyploid taxa using phylogenetic
 reconstructions of biparentally and maternally inherited genetic sequence
 data. Ploidy levels of C. bulbifera and C. quinquefolia were analysed by
 comparative chromosome painting. We used genetic assignment analysis
 (STRUCTURE) and approximate Bayesian computation (ABC) modelling to test
 whether C. bulbifera represents genetically differentiated lineages and
 addressed the hypothesis of its hybrid origin. Comparative ecological
 modelling was applied to unravel possible niche differentiation among the
 two polyploid species. Key Results Cardamine bulbifera was shown to be a
 non-hybridogenous, auto-dodecaploid taxon of early Pleistocene origin, but
 with a history of past gene flow with its hexaploid sister species C.
 quinquefolia, likely during the last glacial maximum in shared refuge
 areas in Eastern Europe towards Western Turkey and the Crimean Peninsula
 region. The diploid Caucasian endemic C. abchasica is considered an
 ancestral species, which also provides evidence for the origin of the
 species complex in the Caucasus region. Cardamine bulbifera successfully
 expanded its distribution range postglacially towards Central and Western
 Europe accompanied by a transition to exclusively vegetative propagation.
 Conclusions A transition to vegetative propagation in C. bulbifera is
 hypothesized as the major innovation to rapidly expand its distribution
 range following postglacially progressing woodland vegetation throughout
 Europe. Preceding and introgressive gene flow from its sister species C.
 quinquefolia in the joint refuge area is documented. This transition and
 ecological differentiation may have been triggered by preceding
 introgressive gene flow from its sister species in the joint East European
 refuge areas.
description: The High-Throughput Sequencing
 in three Illumina lanes produced over 2 billion reads (5 M - 82 M
 reads/individual) with 28 million reads/individual on average (details are
 provided with Suppl. Table S1 in the original manuscript). Over 1.1
 billion reads (about 53%) mapped to the plastome and were used in the de
 novo assemblies of plastid genomes, and over 746 million reads (about 36%)
 could be mapped to the reference genome of <em>Cardamine
 hirsuta</em>. Finally, this resulted in a mean 7.4fold coverage of
 the nuclear genome (using <em>C. hirsuta</em> as reference)
 and a 14,263fold coverage of the plastid genome. The raw sequencing data were
 submitted to the NCBI SRA database under GenBank BioProject
 PRJNA760465.
description: The data files contain: Suppl. Mat. 1: the
 concatenated SNP matrix for nuclear encoded NGS data<br>Suppl. Mat.
 2: the NEXUS matrix/file for ML tree reconstruction of plastome data
 including position of genes in alignment<br>Suppl. Mat. 3: the
 family-wide NEXUS matrix/file of plastome data Suppl.
 Mat. 4 (Zenodo): the bash script used processing raw NGS data and r_script
 to run ABC modelling