Vallmer E. Jordan, Jerilyn A. Walker, Thomas O. Beckstrom, Cody J. Steely, Cullen L. McDaniel, Corey P. {St Romain}, {Baboon Genome Analysis Consortium}, Kim C. Worley, Jane Phillips-Conroy, Clifford J. Jolly, Jeffrey Rogers, Miriam K. Konkel, Mark A. Batzer. A computational reconstruction of Papio phylogeny using Alu insertionpolymorphisms. Mobile DNA, 9:13. 2018. Tomas Vinar is a member of the Baboon Genome Analysis Consortium.

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Background: Since the completion of the human genome project, the diversity of
genome sequencing data produced for non-human primates has increased
exponentially. Papio baboons are well-established biological models for studying 
human biology and evolution. Despite substantial interest in the evolution of
Papio, the systematics of these species has been widely debated, and the
evolutionary history of Papio diversity is not fully understood. Alu 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 Alu
insertion polymorphisms unique to the Papio lineage. To complete these analyses, 
we created a computational algorithm to identify novel Alu insertions in
next-generation sequencing data. Results: We identified 187,379 Alu insertions
present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These
elements were characterized using genomic data sequenced from a panel of twelve
Papio baboons: two from each of the six extant Papio species. These data were
used to construct a whole genome Alu-based phylogeny of Papio baboons. The
resulting cladogram fully-resolved relationships within Papio. Conclusions: These
data represent the most comprehensive Alu-based phylogenetic reconstruction
reported to date. In addition, this study produces the first fully resolved
Alu-based phylogeny of Papio baboons.