BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Agriculture, Ningxia University, Yinchuan 750021, China; College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
Cell. 2022 May 12;185(10):1646-1660.e18. doi: 10.1016/j.cell.2022.03.034. Epub 2022 Apr 20.
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
不完全谱系分选（ILS）使得祖先的遗传多态性在快速物种形成事件中持续存在，导致基因树和物种树之间出现不一致。ILS 使得许多谱系的系统发育推断变得复杂，包括人类。然而，我们缺乏经验证据表明 ILS 会导致表型变异的不一致。在这里，我们进行了基因组分析，结果表明，南美monito del monte 是所有澳大利亚有袋类动物的姊妹谱系，尽管由于古代辐射期间的 ILS，其基因组的 31%以上与 Diprotodontia 更接近，而不是其他澳大利亚群体。整个基因组中普遍存在的冲突系统发育信号与现存有袋动物之间的一些形态变异一致。我们检测到数百个在 ILS 期间经历随机固定的基因，这些基因在非姊妹物种中编码相同的氨基酸。通过功能实验，我们证实了 ILS 如何直接导致形态特征的半同形现象，这些特征是在大约 6000 万年前的有袋动物快速物种形成过程中建立的。
