Murphy William J, Pringle Thomas H, Crider Tess A, Springer Mark S, Miller Webb
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
Genome Res. 2007 Apr;17(4):413-21. doi: 10.1101/gr.5918807. Epub 2007 Feb 23.
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 (Exafricoplacentalia), 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 approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.
胎盘哺乳动物的系统发育是选择未来基因组测序目标以及在核苷酸水平解析哺乳动物祖先基因组的关键框架。尽管最近在确定超目关系方面取得了相当大的进展，但仍有几个分支的解析度很差，包括胎盘树的根部。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，以识别信息丰富的编码插入缺失，这些插入缺失将作为罕见的基因组变化，用于推断胎盘哺乳动物系统发育中的早期事件。我们还通过纳入来自30多个正在进行的基因组项目的序列数据来扩大物种采样范围，随后对其他分类群中的每个插入缺失进行PCR和测序验证。我们的数据支持非洲兽总目和异关节总目之间的姐妹群关系（大西洋兽类假说），而这一关系又是北方真兽类的姐妹分类单元。我们未能找到任何支持异关节总目（真兽类）处于基部位置的插入缺失，这一位置是由形态学和最近的反转座子分析所暗示的，也未能找到支持非洲兽总目处于基部位置（非洲胎盘兽类假说）的插入缺失，这一假说是由大型核基因数据集的系统发育分析所支持的。此外，我们确定了两个反转座子插入，它们也支持大西洋兽类假说，而不支持其他假说。基于这些系统发育推断的修订分子时间尺度表明，非洲兽总目和异关节总目大约在1.03亿（9500万 - 1.14亿）年前与其他胎盘哺乳动物分化。我们讨论了这种拓扑结构对早期系统发育重建以及基于重复序列的系统发育推断的影响。
