Data from: Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor

Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a ‘ghost’ species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6–7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown ‘ghost’ tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs.

当多倍体物种的祖先已灭绝时，重建其起源尤为困难。在此类情况下，多倍体中留存的基因组所对应的已灭绝供体祖先，可被视为“幽灵”物种（ghost species）——其既往存在仅能通过该基因组在多倍体中的留存得以证实。本研究旨在明确中华山蓼（Oxyria sinensis，2n=40）的多倍体起源，目前该属仅报道有一种同属物种——二倍体肾叶山蓼（Oxyria digyna，2n=14）。为此，我们开展了基因组原位杂交（Genomic in situ hybridization，GISH）、转录组学、系统发育与群体遗传学分析，以及生态位建模实验。GISH分析结果表明，中华山蓼的染色体组包含14条源自肾叶山蓼的染色体，以及26条来自未知祖先的染色体。转录组分析显示，中华山蓼在与肾叶山蓼分化后（二者的分化伴随约1200万年前的一次全基因组复制事件），又于约600万年前（Ma）发生了第二次全基因组复制，进而形成当前的中华山蓼。研究发现，中华山蓼的同源基因序列中，既有与肾叶山蓼基因序列聚为一类的序列，也存在与其显著分化的序列。溯祖模拟结果显示，中华山蓼可能在第二次多倍化事件后约600万至700万年前（Ma）发生了分布扩张，而肾叶山蓼的分布扩张时间则晚得多。此外，研究还发现，在更新世气候波动期间，两个物种的分布范围均经历了收缩与再扩张过程。生态位建模结果同样表明，两个物种的分布范围均因第四纪气候变化而发生了改变。参与中华山蓼起源的未知“幽灵”四倍体物种（ghost tetraploid species）之所以灭绝，可能是由于中华山蓼更能适应其现今分布区域内反复出现的气候波动。