Using genomic data to unravel the root of the placental mammal phylogeny
Using genomic data to unravel the root of the placental mammal phylogeny
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DOI：
10.1101/gr.5918807
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发表时间：
2007-04-01
期刊：
影响因子：
7
通讯作者：
Miller, Webb
中科院分区：
文献类型：
--
作者：
Murphy, William J.;Pringle, Thomas H.;Miller, Webb
胎盘哺乳动物的胚胎发生是选择未来基因组测序靶点和在核苷酸水平上解析祖先哺乳动物基因组的关键框架。尽管最近在定义超序关系方面取得了相当大的进展，但仍有几个分支没有得到很好的解决，包括胎盘树的根。在这里，我们分析了人类，犰狳，大象和负鼠的基因组序列组装，以确定信息编码插入缺失，这将作为罕见的基因组变化，以推断胎盘哺乳动物胚胎发育的早期事件。我们还通过包括来自> 30个正在进行的基因组项目的序列数据来扩大我们的物种采样，然后对额外分类群中的每个indel进行PCR和测序验证。我们的数据提供了支持的姐妹群之间的关系Afrotheria和Xenarthra（的adaptogenata假说），这反过来又是姐妹分类群Boreoeutheria。我们未能恢复任何indels支持的基础位置Xenarthra（Epitheria），这是建议的形态学和最近的逆转录分析，或假设与Afrotheria basal（Exafrico-placentalia），这是赞成的大型核基因数据集的系统发育分析。此外，我们确定了两个逆转录酶插入，也支持arctogenata和没有备择假设。基于这些系统发育推断的修订分子时间尺度表明，非洲兽和异节兽在1.03亿（95- 1.14亿）年前从其他胎盘哺乳动物中分化出来。我们讨论了这种拓扑结构对早期系统发育重建和重复为基础的推断的同源性的影响。
The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from > 30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafrico-placentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals similar to 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.