Papio baboon species indicative Alu elements

The Baboon Genome Analysis Consortium

doi:10.1093/gbe/evx130

Papio baboon species indicative Alu elements

The Baboon Genome Analysis Consortium

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

6 Citations (Scopus)

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 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 language	English
Journal	Genome Biology and Evolution
Volume	9
Issue	6
Pages (from-to)	1788-1796
Number of pages	9
ISSN	1759-6653
DOIs	https://doi.org/10.1093/gbe/evx130
Publication status	Published - 1 Jun 2017

Keywords

Evolutionary biology
Population genomics
Retrotransposon

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10.1093/gbe/evx130

Cite this

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title = "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 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.",

keywords = "Evolutionary biology, Population genomics, Retrotransposon",

author = "Walker, {Jerilyn A.} and Jordan, {Vallmer E.} and Steely, {Cody J.} and Beckstrom, {Thomas O.} and McDaniel, {Cullen L.} and {St Romain}, {Corey P.} and Bennett, {Emily C.} and Arianna Robichaux and Clement, {Brooke N.} and Konkel, {Miriam K.} and Batzer, {Mark A.} and Jeffrey Rogers and Harris, {R. Alan} and Muthuswamy Raveendran and Yue Liu and Shwetha Murali and Vilgalys, {Tauras P.} and Walker, {Jerilyn A.} and Konkel, {Miriam K.} and Jordan, {Vallmer E.} and Steely, {Cody J.} and Beckstrom, {Thomas O.} and Thomas, {Gregg W.C.} and Pagel, {Kymberleigh A.} and Vikas Pejaver and Catacchio, {Claudia R.} and Nicoletta Archidiacono and Mario Ventura and Alessia Marra-Campanale and Antonio Palazzo and Oronzo Capozzi and Archana Raja and John Huddleston and Quick, {Veronica Searles} and Anis Karimpour-Fard and Dominik Schrempf and {de Manuel Montero}, Marc and Konstantinos Billis and Martin, {Fergal J.} and Matthieu Muffato and Georgios Athanasiadis and Christina Bergey and Andrew Burrell and Jade Cheng and Laura Cox and James Else and Kalle Lepp{\"a}l{\"a} and Kasper Munch and Thomas Mailund and Mikkel Schierup and {The Baboon Genome Analysis Consortium}",

year = "2017",

month = jun,

day = "1",

doi = "10.1093/gbe/evx130",

language = "English",

volume = "9",

pages = "1788--1796",

journal = "Genome Biology and Evolution",

issn = "1759-6653",

publisher = "Oxford University Press",

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TY - JOUR

T1 - Papio baboon species indicative Alu elements

AU - Walker, Jerilyn A.

AU - Jordan, Vallmer E.

AU - Steely, Cody J.

AU - Beckstrom, Thomas O.

AU - McDaniel, Cullen L.

AU - St Romain, Corey P.

AU - Bennett, Emily C.

AU - Robichaux, Arianna

AU - Clement, Brooke N.

AU - Konkel, Miriam K.

AU - Batzer, Mark A.

AU - Rogers, Jeffrey

AU - Harris, R. Alan

AU - Raveendran, Muthuswamy

AU - Liu, Yue

AU - Murali, Shwetha

AU - Vilgalys, Tauras P.

AU - Walker, Jerilyn A.

AU - Konkel, Miriam K.

AU - Jordan, Vallmer E.

AU - Steely, Cody J.

AU - Beckstrom, Thomas O.

AU - Thomas, Gregg W.C.

AU - Pagel, Kymberleigh A.

AU - Pejaver, Vikas

AU - Catacchio, Claudia R.

AU - Archidiacono, Nicoletta

AU - Ventura, Mario

AU - Marra-Campanale, Alessia

AU - Palazzo, Antonio

AU - Capozzi, Oronzo

AU - Raja, Archana

AU - Huddleston, John

AU - Quick, Veronica Searles

AU - Karimpour-Fard, Anis

AU - Schrempf, Dominik

AU - de Manuel Montero, Marc

AU - Billis, Konstantinos

AU - Martin, Fergal J.

AU - Muffato, Matthieu

AU - Athanasiadis, Georgios

AU - Bergey, Christina

AU - Burrell, Andrew

AU - Cheng, Jade

AU - Cox, Laura

AU - Else, James

AU - Leppälä, Kalle

AU - Munch, Kasper

AU - Mailund, Thomas

AU - Schierup, Mikkel

AU - The Baboon Genome Analysis Consortium

PY - 2017/6/1

Y1 - 2017/6/1

N2 - 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.

AB - 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.

KW - Evolutionary biology

KW - Population genomics

KW - Retrotransposon

UR - http://www.scopus.com/inward/record.url?scp=85044248871&partnerID=8YFLogxK

U2 - 10.1093/gbe/evx130

DO - 10.1093/gbe/evx130

M3 - Journal article

C2 - 28854642

AN - SCOPUS:85044248871

SN - 1759-6653

VL - 9

SP - 1788

EP - 1796

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

IS - 6

ER -

Papio baboon species indicative Alu elements

Abstract

Keywords

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