Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage so...分子系统发育研究已为两栖动物生命之树的诸多分支提供了强有力的支持，但在深层节点的解析上，包括各科与各目之间的系统发育关系，其支持度仍较低。为阐明此类关系，本研究开发了一套类群特异性的锚定杂交富集（Anchored Hybrid Enrichment）实验方案，靶向针对两栖纲内数百个具备高效通用性的保守外显子，以此从系统基因组学视角解析两栖动物的系统发育关系。本研究对286个物种（涵盖该类群94%的科与44%的属）的220个基因位点完成数据获取后，估算了现生两栖动物的系统发育树，并鉴定了两栖动物系统发育最深分支处的基因树-物种树冲突。我们针对两栖动物单系性的不同拓扑结构假设开展了逐位点谱系学探究，重点关注目间的系统发育关系。研究发现，两栖动物系统发育深层的系统发育信号在不同基因位点间差异极大，这一模式与不完全谱系分选（incomplete lineage sorting）的特征相符……