DOI: 10.5061/dryad.zpc866tgb
title: Multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang involving homoploid and tetraploid hybrids

description: Reaumuria songarica is a constructive shrub widely distributed
 in temperate deserts of arid Central Asia. Previous studies
 inferred that the populations of R. songarica in the Gurbantunggut Desert
 (GuD) originated from homoploid hybridizations between its
 eastern and western lineages and may have evolved into an incipient
 species. To further reveal the genetic composition of different hybrid
 populations and determine the species boundary of this independent hybrid
 lineage, we hereby investigated the overall
 phylogeographic structure of R. songarica based on
 variation patterns of five cpDNA sequences and one nrITS
 sequence in 32 populations. Phylogenetic analyses demonstrated
 that in the GuD lineage, the Wuerhe
 population evolved directly from the ancestors, whereas the
 others were derived from hybrids between the eastern and western lineages.
 PCoA and genetic barrier analysis strongly supported that the GuD
 lineage was further divided into two genetic groups: the
 southern group near the Tianshan Mountains (GuD-S) and
 the northern group (GuD-N). The populations in GuD-S group had
 consistent genetic composition and the same ancestral parents, indicating
 that they belong to the homoploid hybrid lineage. However, the mixed GuD-N
 group had undergone genetic admixture of the eastern and western lineages
 on nrITS and cpDNA, and some populations were allopolyploid.
 Additionally, BEAST analyses revealed that the
 origins of the GuD-S and GuD-N
 groups were later than 0.5 Ma.
description: The cpDNA dataset includes the sequences of
 <em>pet</em>B-<em>pet</em>D,
 <em>trn</em>S2-<em>trn</em>G2,
 <em>atp</em>H-<em>atp</em>I,
 <em>ndh</em>A and
 <em>pet</em>N-<em>psb</em>M fragments from 243
 individuals of <em>Reaumuria songarica</em>. The sequences of
 91 individuals were newly sequenced in this study, and others were
 downloaded from our previous study (Yin et al., 2015).
 The nrITS dataset was collected from 230 individuals of
 <em>Reaumuria songarica</em>. All processed and downloaded
 nrITS sequences were separated into two haplotypes by the PHASE program
 integrated into the DnaSP software. The PCR primer and
 amplification procedures for these DNA markers can be found online in the
 supplementary data of this article.  
description: # Multiple origins of the desert shrub *Reaumuria songarica* in northern
 Xinjiang involving homoploid and tetraploid hybrids
 [https://doi.org/10.5061/dryad.zpc866tgb](https://doi.org/10.5061/dryad.zpc866tgb) The nrITS sequences and concatenated cpDNA sequences of *Reaumuria songarica* individuals. ## Description of the data and file structure The data files (RS_ITS_clean_data_final_phased_XiaoFei_Ma.fas and RS_cpDNA_concatenate_sequence_XiaoFei_Ma.fas) are in fasta format. The individuals belong to different populations. The capital letter string in the name of each individual is the population name, e.g. FK. The concatenated sequences of cpDNA are *pet*B-*pet*D, *trn*S2-*trn*G2, *atp*H-*atp*I, *ndh*A, and *pet*N-*psb*M fragments in order from beginning to end. The nrITS sequences of each individual were phased into two haplotype sequences.