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

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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.