Stewart Alexander A, Wiens John J
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA.
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA.
Mol Phylogenet Evol. 2025 Mar;204:108272. doi: 10.1016/j.ympev.2024.108272. Epub 2024 Dec 15.
Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22-45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.
最近经过时间校准的两栖动物系统发育树在现存蝾螈的科级关系上达成了一致，但它们的抽样方案不同，推断出的分歧时间也大不相同。例如，一项基于220个核基因座的近期系统基因组学研究的分类群抽样有限（41个物种），估计的分歧时间相对较近，而一项基于15个基因和481个物种的更广泛的超级矩阵研究估计，主要类群的分歧时间要早2200万至4500万年。在这里，我们结合了系统基因组学和超级矩阵方法，以基于分子标记估计迄今为止最大的蝾螈系统发育树。我们的矩阵包含765种蝾螈和503个基因（总体缺失数据为92.3%）。我们比之前最大的蝾螈系统发育树多纳入了284个物种（增加了59%），并对目前所有已描述蝾螈物种的约93%进行了抽样。我们的年代测定分析纳入的蝾螈化石校准点是之前研究的两倍多。树拓扑结构的最大似然估计得出的科级关系与早期研究一致。尽管许多物种存在大量缺失数据，但几乎所有物种都被归入了预期的属。整棵树的自展支持率总体较高，但在一些基因抽样有限的类群中支持率较低（例如，一些疣螈科蝾螈）。年代测定分析得出的主要类群的年龄估计值通常介于之前系统基因组学和超级矩阵分析的结果之间。我们还提供了一组200个经过时间校准的树，用于比较分析。
