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- Title
A computational reconstruction of <italic>Papio</italic> phylogeny using <italic>Alu</italic> insertion polymorphisms.
- Authors
Jordan, Vallmer E.; Walker, Jerilyn A.; Beckstrom, Thomas O.; Steely, Cody J.; McDaniel, Cullen L.; St. Romain, Corey P.; The Baboon Genome Analysis Consortium; Worley, Kim C.; Phillips-Conroy, Jane; Jolly, Clifford J.; Rogers, Jeffrey; Konkel, Miriam K.; Batzer, Mark A.
- Abstract
Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. <italic>Papio</italic> baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of <italic>Papio</italic>, the systematics of these species has been widely debated, and the evolutionary history of <italic>Papio</italic> diversity is not fully understood. <italic>Alu</italic> elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of <italic>Alu</italic> insertion polymorphisms unique to the <italic>Papio</italic> lineage. To complete these analyses, we created a computational algorithm to identify novel <italic>Alu</italic> insertions in next-generation sequencing data. Results: We identified 187,379 <italic>Alu</italic> insertions present in the <italic>Papio</italic> lineage, yet absent from <italic>M. mulatta</italic> [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve <italic>Papio</italic> baboons: two from each of the six extant <italic>Papio</italic> species. These data were used to construct a whole genome <italic>Alu</italic>-based phylogeny of <italic>Papio</italic> baboons. The resulting cladogram fully-resolved relationships within <italic>Papio</italic>. Conclusions: These data represent the most comprehensive <italic>Alu-</italic>based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved <italic>Alu-</italic>based phylogeny of <italic>Papio</italic> baboons.
- Subjects
PRIMATES; PHYLOGENY; GENETIC polymorphisms; RETROTRANSPOSONS
- Publication
Mobile DNA, 2018, Vol 9, p1
- ISSN
1759-8753
- Publication type
Article
- DOI
10.1186/s13100-018-0118-3