The power of ancient retroposed sequences to resolve problematic mammalian evolutionary questions

系统基因考古学阐明哺乳动物系统发生树。高通量的序列数据经常导致在解决哺乳动物进化的一些主要步骤的混乱。例如，有三个相互冲突的假设存在重要的独立证据，其中胎盘哺乳动物亚类（分支）形成胎盘树的基础：xenarthran分支，afrotherian分支，或xenarthran和afrotherian一起作为一个分支。为了解决这一问题以及哺乳动物进化中的其他当前不确定性，我们将识别和表征遗传学上提供信息的逆转录元件，即数百万年来复制并重新插入基因组中新位置的基因组序列，留下独特的足迹，可用于追溯生物体的共同祖先。我们将分析哺乳动物基因组中这些元素的存在和不存在，以澄清：（1）单系性（共同祖先）胎盘动物和有袋动物，（2）胎盘动物的基础关系，（3）灵长类动物的姐妹群，（4）啮齿类动物的主要分支，（5）兔形目动物进化的细节，（6）在laurasiatherian内的内部进化关系，（7）afrotherian，（8）xenarthran分支。哺乳动物进化树各个层次的进化关系的确认知识将为比较基因组学提供坚实的基础。

Phylogenomic Archaeology to Elucidate the Mammalian Phylogenetic Tree. Highthroughput sequence data frequently contribute to confusion in solving some of the major steps in mammalian evolution. For example, there exists significant independent evidence for three conflicting hypotheses for which placental mammalian subdivision (clade) forms the base of the placental tree: the xenarthran clade, the afrotherian clade, or xenarthrans and afrotherians together as one clade. To resolve this and other current uncertainties in mammalian evolution we will identify and characterize phylogenetically informative retroposed elements, genomic sequences that, over millions of years, replicated and reinserted into new locations in genomes, leaving unique footprints useful for retracing the common ancestry of organisms. We will analyze the presence and absence of these elements in mammalian genomes to clarify the: (1) monophyly (common ancestry) of placentals plus marsupials, (2) basal relationships of placentals, (3) sister groups of primates, (4) major branches in rodents, (5) details of lagomorph evolution, (6) internal evolutionary relationships within the laurasiatherian, (7) afrotherian, and (8) xenarthran clades. A confirmed knowledge of the evolutionary relationships at all levels of the mammalian tree will provide a solid foundation for comparative genomics.