Luo Xin, Hu Quanjun, Zhou Pingping, Zhang Dan, Wang Qian, Abbott Richard J, Liu Jianquan
MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.
State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou, China.
Mol Ecol. 2017 Jun;26(11):3037-3049. doi: 10.1111/mec.14097. Epub 2017 Apr 1.
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.
当一个祖先已经灭绝时，重建一个多倍体物种的起源尤其具有挑战性。在这种情况下，多倍体中发现的基因组的已灭绝供体可能被视为一个“幽灵”物种，因为它的先前存在是通过其基因组在多倍体中的存在而被认可的。在本研究中，我们旨在确定中华山蓼（2n = 40）的多倍体起源，已知其仅有一种同属物种，即二倍体高山山蓼（2n = 14）。为此进行了基因组原位杂交（GISH）、转录组、系统发育和种群动态分析以及生态位建模。GISH显示中华山蓼包含14条来自高山山蓼的染色体和26条来自未知祖先的染色体。转录组分析表明，在与高山山蓼分化后，大约在1200万年前（Ma）发生了基因组加倍，大约在6 Ma时发生了第二次基因组加倍，从而产生了中华山蓼。中华山蓼除了含有一组与高山山蓼聚类的基因序列外，还含有与高山山蓼中存在的基因序列不同的同源基因序列。溯祖模拟表明，中华山蓼大约在6 - 7 Ma时扩大了其分布范围，可能是在第二次多倍体化事件之后，而高山山蓼的分布范围扩大得要晚得多。还表明，在更新世气候振荡期间，这两个物种的分布范围都收缩并重新扩大。生态位建模同样表明，这两个物种都经历了其分布范围的变化以响应第四纪气候变化。与中华山蓼起源相关的未知“幽灵”四倍体物种的灭绝可能是由于中华山蓼对其现今分布区域反复出现的气候变化具有更强的适应性。
