Papio baboon species indicative Alu elements

The Baboon Genome Analysis Consortium

    Research output: Contribution to journalArticle

    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 languageEnglish (US)
    Pages (from-to)1788-1796
    Number of pages9
    JournalGenome Biology and Evolution
    Volume9
    Issue number6
    DOIs
    StatePublished - Jun 1 2017

    Fingerprint

    Alu Elements
    Papio
    hybrid zone
    Genetic Markers
    phylogeny
    phylogenetics
    captive population
    genetic marker
    Y Chromosome
    Population Genetics
    Body Size
    Y chromosome
    mitochondrial DNA
    population genetics
    Pedigree
    Phylogeny
    population structure
    Mitochondrial DNA
    chromosome
    body size

    Keywords

    • Evolutionary biology
    • Population genomics
    • Retrotransposon

    ASJC Scopus subject areas

    • Ecology, Evolution, Behavior and Systematics
    • Genetics

    Cite this

    Papio baboon species indicative Alu elements. / The Baboon Genome Analysis Consortium.

    In: Genome Biology and Evolution, Vol. 9, No. 6, 01.06.2017, p. 1788-1796.

    Research output: Contribution to journalArticle

    The Baboon Genome Analysis Consortium 2017, 'Papio baboon species indicative Alu elements', Genome Biology and Evolution, vol. 9, no. 6, pp. 1788-1796. https://doi.org/10.1093/gbe/evx130
    The Baboon Genome Analysis Consortium. / Papio baboon species indicative Alu elements. In: Genome Biology and Evolution. 2017 ; Vol. 9, No. 6. pp. 1788-1796.
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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 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.",
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    KW - Population genomics

    KW - Retrotransposon

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