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Flores Island Pygmy Genomes Provide Clues to Ancestry, Short Stature

NEW YORK (GenomeWeb) – The short stature found in a pygmy population from Indonesia's Flores Island seems to stem from selection affecting the fatty acid desaturase (FADS) gene cluster and height-related variants shared with other human populations rather than from archaic introgression from Homo floresiensis, a diminutive archaic hominin that once lived on the same island, according to a new study.

"[T]hese gene variants were present in a common ancestor of Europeans and the Flores pygmies," co-corresponding author Richard Green, a biomolecular engineering researcher at the University of California at Santa Cruz, said in a statement. He noted that the Flores pygmies "became short by selection acting on this standing variation already present in the population, so there's little need for genes from an archaic hominin to explain their small stature."

Green and colleagues from UCSC, Princeton University, and elsewhere performed array-based genotyping on 32 adults from a pygmy population from a Flores Island village called Rampasasa, including 10 individuals who were also profiled by whole-genome sequencing. By comparing these variant profiles to those in archaic hominins and present-day populations, they detected pygmy sequences stemming from Denisovan and Neanderthal hominins.

But the team did not detect significant gene flow from H. floresiensis (nicknamed the "hobbit" since its discovery well over a decade ago) or yet-to-be-discovered archaic species. Instead, the group's analyses hinted that diet-related pressures may have pushed selection affecting the FADS genes, contributing to body size in conjunction with polygenic selection on common height-related variants. The findings were published online today in Science.

"It suggests that something in the past caused their diet to change dramatically, and they adapted by natural selection favoring certain variants of those genes," Green said, explaining that island populations in general are "free to evolve in unrestrained directions based on the demands of a small ecosystem."

He and his co-authors profiled around 2.5 million SNPs across the genome in 32 adults from Rampasasa and selected 10 individuals for whole-genome sequencing based on reported family relationships and ancestry patterns gleaned from the variant data. The genomes were sequenced to a median average depth of almost 38-fold, they noted.

By bringing in available genome sequences from Melanesia and SNP profiles for another 2,507 representatives from 225 populations around the world, the team analyzed ancestry clusters in the Flores Island pygmies. For example, ancestry tracts in the Flores Island individuals suggested that the pygmy population has Near Oceanic population roots with more recent East Asian admixture.

When the researchers focused on archaic hominin ancestry in genome sequences for nine unrelated individuals from Flores Island, 27 Melanesians, more than 100 East Asians, and 91 Europeans, they found that the pygmy individuals had average levels of Neanderthal ancestry that were midway between that in populations from East Asia and Melanesia.

The Flores individuals had Denisovan ancestry as well, albeit at lower average levels than those found in Melanesian populations, but the authors found "no evidence that unknown sequences in Flores are enriched for older or more divergent lineages, as would be expected if they contained lineages inherited from a more deeply divergent hominin group, such as H. floresiensis or H. erectus."

Through a series of follow-up analyses, the team saw signs of selection for a haplotype influencing FADS1 and FADS2 gene expression, along with polygenic selection at height-related variants — a conclusion informed by a search for height-influencing loci using data for more than 456,000 individuals of European ancestry.

"We find that European height-associated loci are significantly more differentiated between Flores and other neighboring populations than expected under random genetic drift," the authors wrote. "Moreover, the Flores sample is significantly enriched for height-decreasing alleles."