Papio baboon species indicative Alu elements

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10 Scopus citations


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 ofmultiple 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.

Original languageEnglish
Pages (from-to)1788-1796
Number of pages9
JournalGenome Biology and Evolution
Issue number6
StatePublished - Jun 1 2017

Bibliographical note

Funding Information:
The authors would like to thank all the members of the Batzer Lab for their helpful suggestions and the Baboon Genome Analysis Consortium. Special thanks to Dr. Laura Cox and Deborah Newman from the Southwest National Primate Research Center, Texas Biomedical Research Institute for their generous help providing SFBR-Y pedigree records. This research was supported by the National Institutes of Health R01 GM59290 (M.A.B.). A.R. was supported in part by the Louisiana Biomedical Research Network (LBRN) with funding from the National Institute of General Medical Sciences of the National Institutes of Health under Award Number P20GM103424 and by the Louisiana Board of Regents Support Fund. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or Louisiana Board of Regents. B.N.C. was funded in part by the National Institutes of Health Award Number 5T35OD011151-12 and the LSU School of Veterinary Medicine.

Publisher Copyright:
© The Author(s) 2017.


  • Evolutionary biology
  • Population genomics
  • Retrotransposon

ASJC Scopus subject areas

  • Medicine (all)


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