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Gene. 2015 Dec 15;574(2):345-51. doi: 10.1016/j.gene.2015.08.015. Epub 2015 Aug 11.

A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.

Author information

1
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia; BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia.
2
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
3
Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
4
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia; BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia. Electronic address: King.jordan@biology.gatech.edu.

Abstract

Uniparental genetic markers, mitochondrial DNA (mtDNA) and Y chromosomal DNA, are widely used for the inference of human ancestry. However, the resolution of ancestral origins based on mtDNA haplotypes is limited by the fact that such haplotypes are often found to be distributed across wide geographical regions. We have addressed this issue here by combining two sources of ancestry information that have typically been considered separately: historical records regarding population origins and genetic information on mtDNA haplotypes. To combine these distinct data sources, we applied a Bayesian approach that considers historical records, in the form of prior probabilities, together with data on the geographical distribution of mtDNA haplotypes, formulated as likelihoods, to yield ancestry assignments from posterior probabilities. This combined evidence Bayesian approach to ancestry assignment was evaluated for its ability to accurately assign sub-continental African ancestral origins to Afro-Colombians based on their mtDNA haplotypes. We demonstrate that the incorporation of historical prior probabilities via this analytical framework can provide for substantially increased resolution in sub-continental African ancestry assignment for members of this population. In addition, a personalized approach to ancestry assignment that involves the tuning of priors to individual mtDNA haplotypes yields even greater resolution for individual ancestry assignment. Despite the fact that Colombia has a large population of Afro-descendants, the ancestry of this community has been understudied relative to populations with primarily European and Native American ancestry. Thus, the application of the kind of combined evidence approach developed here to the study of ancestry in the Afro-Colombian population has the potential to be impactful. The formal Bayesian analytical framework we propose for combining historical and genetic information also has the potential to be widely applied across various global populations and for different genetic markers.

KEYWORDS:

Africa; Afro-Colombian; Bayes' rule; Combined evidence; Haplotype; Human ancestry; Mitochondrial DNA; Trans-Atlantic slave voyages

PMID:
26275940
DOI:
10.1016/j.gene.2015.08.015
[Indexed for MEDLINE]

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