Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements.
Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements.
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DOI：
10.1093/gbe/evx168
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发表时间：
2017-09-01
影响因子：
3.3
通讯作者：
Faircloth BC
中科院分区：
文献类型：
--
作者：
Esselstyn JA;Oliveros CH;Swanson MT;Faircloth BC
真兽目哺乳动物的生殖发育包含了四足动物生命树中一些最具进化性的节点。我们结合全面的分类和字符采样，探讨三个最有争议的序数间关系胎盘哺乳动物。我们从72个已发表的基因组中进行了超保守元件基因座的计算机提取，并从另外28种哺乳动物中进行了超保守元件的体外富集和测序，导致了3，787个基因座的比对。我们分析了这些数据，使用串联和多物种结合系统发育的方法，拓扑测试，并探索支持个别位点，以确定真兽亚纲和树的姐妹群（Scandentia）和马（奇蹄目）的根。个别位点提供了弱，但往往是一致的拓扑假说的支持。虽然许多基因树缺乏公认的物种树的关系，摘要合并拓扑结构在很大程度上是一致的，从串联的推论。在真兽目的根源上，我们确定了对Xenarthra和Afrotheria之间姐妹关系的一致支持（即，属）。在其他感兴趣的节点，支持不太一致。我们建议Scandentia是Primatomorpha（Euarchonta）的姐妹，但我们未能拒绝Scandentia和Glires之间的姐妹关系。同样地，我们认为奇蹄目是鲸蹄目（真有蹄类）的姐妹，但奇蹄目和翼手目之间的姐妹关系仍然是合理的。
The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
0.7
作者：
Cao, J;Yang, EB;Chow, P
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Chow, P
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影响因子：
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通讯作者：
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