title: Recombination networks as genetic markers in a human variation study of the Old World.
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.
authors: Computational Biology Center, IBM T J Watson Research, Yorktown, USA.
authors: Asif
authors: A
authors: Javed
authors: Marta
authors: M
authors: Melé
authors: Marc
authors: M
authors: Pybus
authors: Pierre
authors: P
authors: Zalloua
authors: Marc
authors: M
authors: Haber
authors: David
authors: D
authors: Comas
authors: Mihai G
authors: MG
authors: Netea
authors: Oleg
authors: O
authors: Balanovsky
authors: Elena
authors: E
authors: Balanovska
authors: Li
authors: L
authors: Jin
authors: Yajun
authors: Y
authors: Yang
authors: Ganeshprasad
authors: G
authors: Arunkumar
authors: Ramasamy
authors: R
authors: Pitchappan
authors: Jaume
authors: J
authors: Bertranpetit
authors: Francesc
authors: F
authors: Calafell
authors: Laxmi
authors: L
authors: Parida
mesh_terms: D000349:Africa; D001209:Asia, Central; D001210:Asia, Southeastern; D002874:Chromosome Mapping; D041321:Chromosomes, Human, X / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D005202:Asia, Eastern; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D005838:Genotype; D005843:Geography; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008297:Male; D008877:Middle East; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D011995:Recombination, Genetic; D015203:Reproducibility of Results