Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/77874
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Type: Journal article
Title: Recombination networks as genetic markers in a human variation study of the Old World
Author: Javed, A.
Mele, M.
Pybus, M.
Zalloua, P.
Haber, M.
Comas, D.
Netea, M.
Balanovsky, O.
Balanovska, E.
Jin, L.
Yang, Y.
ArunKumar, G.
Pitchappan, R.
Bertranpetit, J.
Calafell, F.
Parida, L.
Adler, C.
Cooper, A.
Dersarkissian, C.
Haak, W.
Citation: Human Genetics, 2012; 131(4):601-613
Publisher: Springer
Issue Date: 2012
ISSN: 0340-6717
1432-1203
Contributor: Adler, Christina Jane
Cooper, Alan
Der Sarkissian, Clio Simone Irmgard
Haak, Wolfgang
Statement of
Responsibility: 
Asif Javed, Marta Melé, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, GaneshPrasad ArunKumar, Ramasamy Pitchappan, Jaume Bertranpetit, Francesc Calafell, Laxmi Parida, The Genographic Consortium
Abstract: We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.
Keywords: Genographic Consortium; Chromosomes, Human, X; Humans; Reproducibility of Results; Chromosome Mapping; Genetics, Population; Population Dynamics; Evolution, Molecular; Recombination, Genetic; Genotype; Haplotypes; Polymorphism, Single Nucleotide; Geography; Models, Genetic; Africa; Asia, Central; Asia, Southeastern; Middle East; Far East; Europe; Female; Male; Genetic Variation
Description: Christina J. Adler, Alan Cooper, Clio S. I. Der Sarkissian and Wolfgang Haak are members of The Genographic Consortium
Rights: © Springer-Verlag 2011
RMID: 0020127517
DOI: 10.1007/s00439-011-1104-8
Appears in Collections:Environment Institute publications
Earth and Environmental Sciences publications

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