Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
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DOI：
10.1371/journal.pbio.3000494
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发表时间：
2019-12-01
期刊：
影响因子：
9.8
通讯作者：
Jetz, Walter
中科院分区：
文献类型：
--
作者：
Upham, Nathan S.;Esselstyn, Jacob A.;Jetz, Walter
大规模的时间尺度的生物多样性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，为数千个物种推断可靠的系统发育树涉及许多权衡，这限制了它们对比较生物学家的效用。为了为所有大约6,000种现存的哺乳动物建立一个强大的进化时间尺度，我们开发了一组可靠的树，这些树捕获了拓扑结构和发散时间中的根到尖的不确定性。我们的“骨干和补丁”的方法，树的建设适用于一个新组装的31个基因的超矩阵贝叶斯推理的两个层次：（1）骨干关系和年龄之间的主要血统，使用化石节点或尖端测年，和（2）物种水平的“补丁”的同源性与非重叠的内组，每个对应于一个代表性的血统在骨干。未采样DNA的物种要么被排除在外（“仅DNA”树），要么在分类学约束条件内使用从当地出生-死亡模型得出的分支长度进行估算（“完整”树）。加入时间尺度的补丁骨干的结果在现存的哺乳动物的物种水平的树与所有分支估计在同一建模框架下，从而促进率比较血统不同的有袋动物和胎盘动物。我们将我们的系统发育树与以前估计的哺乳动物范围内的进化和分歧时间进行比较，发现（1）节点年龄在研究中大致一致，（2）最近（尖端水平）的物种形成率在我们的研究中比以前的“超树”方法更准确地估计，其中未解决的节点导致分支长度的文物。哺乳动物系统发育历史的可信集合现在可以在下载，使比较生物学中长期存在的问题的调查成为可能。
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 , enabling investigations of long-standing questions in comparative biology.