Mapping Human Genetic Diversity in Asia

Abstract

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

“…The mtDNA data also contradict genome-wide SNP data that says FEN and FEnN groups do not differ. 8 As previously suggested, the isolation of FEN group ancestors from those of FEnN groups with subsequent recent admixture could support the SNP data. 14 Group isolation is well documented in FE group ethnography and is fairly evident in contemporary groups, reinforced by cultural practices such as within-group marriages.…”

“…These South Asian affinities support the hypothesis of a migration path through South Asia for the ancestors of FEN groups (and other Asia-Pacific groups) as they peopled the Asia-Pacific region. [8][9][10] Ancient, Late Pleistocene affinities with Australia and Near Oceania is evident with haplogroup P. FEN group Y-STR haplotypes under haplogroups C-RPS4Y and K-M9 also were observed to have associations with Australian and Melanesian haplotypes. 14 Genome-wide SNPs also showed an ancient association between the Mamanwa FEN group and groups from Australia and New Guinea.…”

“…This is consistent with STRUCTURE/frappe results from a genome-wide SNP study where a South Asian component is present in Southeast Asian groups including the AetaZ and Agta FEN groups. 8 It could be argued that through the Srivijaya and Majapahit, thalassocratic empires based in Indonesia, 44 Indian influence and possibly haplogroups M52'58 and M52a were brought to the Philippines as early as the fifth century AD. However, Indian influence through these trade empires were indirect and mainly commercial; moreover, other Southeast Asian groups served as filters that diluted and/or enriched any Indian influence that reached the Philippines.…”

“…A survey of genome-wide singlenucleotide polymorphisms (SNPs) of Asian groups show that six FE groups (five FEN and one FEnN) and three RC groups do not differ from each other or from other Austronesian speaking groups, and that there was a single migration wave into Asia from which all Asian groups are descended. 8 Genome-wide SNPs show that gene flow occurred into the common ancestors of New Guineans, Australians and the Mamanwa FEN group from Denisovans. 9 Genome-wide SNPs also show an ancient association between Australia, New Guinea and the Mamanwa FEN group, which supports the view that these populations represent the descendants of an early 'southern route' migration out of Africa.…”

SAQC: SNP Array Quality Control

“…Single-nucleotide polymorphisms (SNPs), the most abundant genetic markers in the human genome, have been widely used in genetic and genomic research such as studies of disease gene mapping [1-6], medical and clinical diagnostics [7-9], forensic tests [10-12], genome structure of linkage disequilibrium and recombination [13-18], chromosomal aberrations [19-24], and genetic diversity [25-27]. Modern high-throughput and high-resolution SNP array genotyping techniques, such as the Affymetrix GeneChip (Affymetrix Inc., Santa Clara, CA, USA) [28,29] and Illumina BeadChip (Illumina Inc., San Diego, CA, USA) [30-32], provide genotype and fluorescence intensity data on hundreds of thousands of SNPs for each study sample.…”