Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

中文翻译：

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推断哺乳动物树：在生态，进化和保护方面存在问题的物种级系统发育集。

大型的，有时间尺度的系统发育是将进化过程与现代生物多样性模式联系起来的基础。然而，为数千个物种推断出可靠的系统发育树涉及许多折衷，这限制了它们对比较生物学家的实用性。为了为所有大约6,000种活的哺乳动物建立可靠的进化时间表，我们开发了可靠的树集，以捕获拓扑和发散时间中从根到顶的不确定性。我们的“骨架和修补”树木构建方法将新组装的31基因超矩阵应用于贝叶斯推断的两个级别：（1）主要化石之间的骨干关系和年龄，使用化石节点或尖端测年法，以及（2）物种级“补丁” 具有不重叠基团的系统发育，每个基团对应于骨干中的一个代表性谱系。未采样DNA的物种被排除在外（“仅DNA”树），或使用从本地出生死亡模型得出的分支长度（“完整”树）在分类学约束内进行估算。将按时标度的斑块连接到主干，可以得到现存哺乳动物的树种级树，所有分支都在相同的建模框架下进行估算，从而促进了与有袋动物和胎盘动物不同的血统之间的比率比较。我们将我们的系统树与以前对整个哺乳动物的系统发生和发散时间的估计进行了比较，发现（1）研究之间的结节年龄基本一致，并且（2）在我们的研究中估计了最近的（尖端水平）物种形成速率比以前的“超级树” 方法，其中未解决的节点导致分支长度伪像。现在可以从http://vertlife.org/phylosubsets下载可靠的哺乳动物系统发生史集，从而能够研究比较生物学中长期存在的问题。