Papio Baboon Species Indicative Alu Elements

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.

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

“…In Preparation). Recent work also supports that the expansion of Alu elements is not unique to the olive baboon, but rather the Papio lineage as a whole [ 33 , 35 ].…”

“…The recent findings of the Baboon Genome Analysis Consortium, along with other recent studies of mobile elements in the baboon genome have provided a great deal of new information (Rogers et al: The comparative genomics, epigenomics and complex population history of Papio baboons. In Preparation) [ 33 , 35 ]. This study found 127 novel Alu element subfamilies, supporting the high Alu mobilization rate reported by the Baboon Genome Analysis Consortium (Rogers et al: The comparative genomics, epigenomics and complex population history of Papio baboons.…”

“…In Preparation). Previous work on Alu elements in baboons has already been informative for population structure, species identification, and as a polymorphic marker for hybrid individuals in the field [ 33 – 35 ].…”

Predicting the impacts of climate change on Papio baboon biogeography: Are widespread, generalist primates ‘safe’?

“…The less threatened African species include several remarkably flexible, ecologically generalist species like the Papio baboons (Codron, Lee‐Thorp, Sponheimer, de Ruiter, & Codron, , ; Jolly, ; Whiten, Byrne, Barton, Waterman, & Henzi, ), which adapt effectively to many anthropogenic contexts (Bergman & Kitchen, ; Hoffman & O'Riain, ; Warren, ). The genus Papio comprises six closely related taxa (Walker et al, ; Zinner, Wertheimer, Liedigk, Groeneveld, & Roos, ), usually given specific status despite a history of hybridization in contact zones (Charpentier et al, ; Jolly, Burrell, Phillips‐Conroy, Bergey, & Rogers, ; Wall et al, ; Wango et al, ). They are thought to have begun diverging approximately 2 million years ago (Zinner, Groeneveld, Keller, & Roos, ), and collectively occupy most of sub‐Saharan Africa (Winder, ).…”

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

“…Considered nearly homoplasy-free [ 48 , 49 ], most potential sources of homoplasy involving Alu elements can be resolved through Sanger sequencing [ 41 , 42 , 61 ]. Recent studies demonstrate the utility of Alu elements for Papio species identification, as well as retrieving population structure within distinct Papio species [ 28 , 29 ]. Furthermore, Alu elements have been successfully used to resolve controversial relationships between primates [ 38 , 39 , 42 , 64 ].…”