Multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang involving homoploid and tetraploid hybrids
Data files
Aug 14, 2024 version files 1.26 MB
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README.md
864 B
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RS_cpDNA_concatenate_sequence_XiaoFei_Ma.fas
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RS_ITS_clean_data_final_phased_XiaoFei_Ma.fas
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Abstract
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.
README: Multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang involving homoploid and tetraploid hybrids
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.
Methods
The cpDNA dataset includes the sequences of petB-petD, trnS2-trnG2, atpH-atpI, ndhA and petN-psbM fragments from 243 individuals of Reaumuria songarica. 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 Reaumuria songarica. 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.