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Andamanese Islander Genomic Analysis Indicates Single Origin for Modern Asians

NEW YORK (GenomeWeb) – A genomic analysis of the Andamanese Islanders of India suggests that all Asian and Pacific populations stem from a single origin and expansion out of Africa.

Researchers from Universitat Pampeu Fabra sequenced the whole genomes of 10 Andamanese individuals and compared them to sequences from 10 mainland Indians. The Andamanese and mainland Indians had been thought to have different origins owing to differences in morphology and language. One theory proposed that the Andamanese were the descendants of an early out-of-Africa migration whose ancestors didn't mix with other populations.

However, Fabra's Jaume Bertranpetit and his colleagues uncovered evidence of a single origin for all Asian and Pacific populations as well as traces of mixture with an ancient hominin, as they reported today in Nature Genetics. They also noted that the distinctive phenotypes of the Andamanese population could be traced to natural selection.

"[T]he distinctive morphology of the Andamanese probably has originated from strong adaptive selection, as demonstrated by the excess of genes under selection related to height and body mass, leading to possibilities of understanding the basic biology of a complex adaptation to an island environment," Bertranpetit and his colleagues wrote in their paper.

He and his colleagues sequenced the genomes of 70 Indians — 60 from mainland India and 10 from the Andaman Island populations of Jarawa and Onge — to about 15X coverage. From this, they noted that the Andamanese, hailing from a small and historically isolated population, were more highly related to one another, had higher inbreeding coefficients, and longer runs of homozygosity. Principal components analysis similarly clustered the Andamanese tightly together.

Through a combination of D-statistic, TreeMix, and MSMC-based cross-coalescent analyses, Bertranpetit and his colleagues traced the origins of the Andamanese to the same out-of-Africa event that peopled mainland India. For instance, D-statistics indicated that the Andamanese shared more alleles with each of the out-of-Africa populations than with sub-Saharan African populations, a finding also supported by TreeMix analyses. Those analyses also uncovered a closer relationship between the Andamanese, mainland Indians, and Asians than with Pacific populations.

The researchers noted that D-statistic analyses further found that the Andamanese shared more alleles with East Asians, Papuans, and mainland tribal Indians than with Europeans, suggesting that Europeans are an outgroup for all Asians and that there's one origin for all modern Asians.

The Andamanese also harbored roughly the same portion — between 2 percent and 4 percent — of Neanderthal alleles as other out-of-Africa populations, the researchers reported. This, they added, indicates that the Neanderthal-human mixing event took place early on, before the out-of-Africa populations separated from one another.

Bertranpetit and his colleagues also found, though, that the Andamanese as well as mainland Indian and Papuan populations have some 2 percent to 3 percent fewer African alleles than Europeans or East Asians do. As they could not account for this reduction through the low Andamanese population size, later admixture between European or East Asian populations with Africans, or through admixture with an out-of-African population from Eurasia, they suggested instead that it was due to admixture with an as-yet-unknown hominin population that diverged from modern humans some 300,000 years ago.

As the researchers predicted a common origin for all Asians, they also investigated the source of the distinct Andamanese phenotype. Using a hierarchical boosting approach, Bertranpetit and his colleagues uncovered 1,000 genomic regions exhibiting signs of selection among the Andamanese. These regions, they noted, included an excess of genes related to height and body shape. This indicates selective pressure on body type among the Andamanese, and, they added, could represent insular dwarfism, a known adaptation of large animals to a restricted environment.

"The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size," Bertranpetit and his colleagues wrote in their paper.