Computational Biology
@ Comenius University in Bratislava

Jerilyn A. Walker, Vallmer E. Jordan, Cody J. Steely, Thomas O. Beckstrom, Cullen L. McDaniel, Corey P. {St Romain}, Emily C. Bennett, Arianna Robichaux, Brooke N. Clement, Miriam K. Konkel, {Baboon Genome Analysis Consortium}, Mark A. Batzer. Papio Baboon Species Indicative Alu Elements. Genome Biology and Evolution, 9(6):1788-1796. 2017. Tomas Vinar is a member of the Baboon Genome Analysis Consortium.

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Download from publisher: https://doi.org/10.1093/gbe/evx130

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Abstract:

The genus of Papio (baboon) has six recognized species separated into Northern
and Southern clades, each comprised of three species distributed across the
African continent. Geographic origin and phenotypic variants such as coat color
and body size have commonly been used to identify different species. The
existence of multiple hybrid zones, both ancient and current, have complicated
efforts to characterize the phylogeny of Papio baboons. More recently,
mitochondrial DNA (mtDNA) and Y-chromosome genetic markers have been utilized for
species identification with particular focus on the hybrid zones. Alu elements
accumulate in a random manner and are a novel source of identical by descent
variation with known ancestral states for inferring population genetic and
phylogenetic relationships. As part of the Baboon Genome Analysis Consortium, we 
assembled an Alu insertion polymorphism database of nearly 500 Papio-lineage
specific insertions representing all six species and performed population
structure and phylogenetic analyses. In this study, we have selected a subset of 
48 species indicative Alu insertions and demonstrate their utility as genetic
systems for the identification of baboon species within Papio. Individual
elements from the panel are easy to genotype and can be used in a hierarchical
fashion based on the original level of uncertainty. This Alu-48 panel should
serve as a valuable tool during the maintenance of pedigree records in captive
populations and assist in the forensic identification of fossils and potential
hybrids in the wild.