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 sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.

中文翻译：

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系统基因组学揭示了两栖动物生命树中古代基因树的不一致

分子系统发育对两栖动物生命之树的许多部分提供了强有力的支持，但对更深层次节点的解析支持不足，包括家庭和命令之间的关系。为了阐明这些关系，我们通过开发针对数百个在整个类中有效的保守外显子的分类群特异性锚定混合富集协议，提供了关于两栖动物关系的系统发育视角。从 286 个物种（代表 94% 的科和 44% 的属）的 220 个基因座获得数据后，我们估计了现存两栖动物的系统发育，并确定了两栖动物系统发育最深分支的基因树-物种树冲突。我们对两栖动物单系的替代拓扑假设进行逐个位点的谱系询问，重点是间序关系。我们发现两栖动物系统发育深处的系统发育信号在不同位点之间差异很大，其方式与现存两栖动物祖先谱系中的不完整谱系分类一致。我们的结果压倒性地支持两栖动物的单一性以及青蛙和蝾螈之间的姐妹关系，这与 Batrachia 假设一致。物种树分析集中在现有两栖动物科之间关系的一小组拓扑假设上。这些结果澄清了两栖动物生命之树的几个有争议的部分，结合一组经过审查的化石校准，支持比以前报告的冠和有序两栖动物多样化更年轻的时间尺度。更广泛地说，我们的研究提供了对来源、量级、