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Population Study Points to Pronounced Denisovan Ancestry in Philippine Population

NEW YORK – An Uppsala University-led team has documented particularly high levels of Denisovan archaic hominin ancestry in an Indigenous Negrito population in the Philippines with the help of population genetic data and computational analyses.

"[O]ur findings unveil a [more] complex intertwined history between modern and archaic humans in the Asia-Pacific region than previously appreciated," senior and co-corresponding author Mattias Jakobsson, a human evolution researcher affiliated with Uppsala University, the University of Johannesburg, and SciLifeLab, explained in an email.

Based on new genotyping data for 1,107 individuals from 118 populations in the Philippines, along with available genetic data for other global populations in the past, the researchers found that Ayta Magbukon Negrito individuals carry significantly more Denisovan ancestry than other populations profiled so far.

Their findings, published in Current Biology on Thursday, suggested that Denisovan DNA is roughly 30 percent to 40 percent more prevalent in Ayta Magbukon genomes than in sequences from Denisovan-admixed Australasian or Papuan populations, where pronounced Denisovan ancestry has been detected in the past.

The enhanced Denisovan ancestry appeared to stem from relatively low rates of mixing between the Ayta Magbukon population and individuals arriving in the Philippines since the archaic admixture took place. In contrast, the genetic data pointed to Denisovan DNA dilution in other populations in the region through interactions with incoming East Asian populations with far lower levels of Denisovan ancestry.

"Some groups, though, such as the Ayta Magbukon, minimally admixed with the more recent incoming migrants," Jakobsson said in a statement. "For this reason, the Ayta Magbukon retained most of their inherited archaic tracts and were left with the highest level of Denisovan ancestry in the world."

For their analyses, the investigators considered roughly 2.3 million variants across the genome in 1,107 individuals spanning 118 ethnic groups in the Philippines, including representatives from 25 Negrito populations with distinct ethnolinguistic histories. Using an analytical approach that takes Neanderthal ancestry into account, they estimated that Denisovan DNA makes up some 5 percent of the genome, on average, in Ayta Magbukon individuals.

The team suggested that the especially pronounced Denisovan ancestry in the Ayta Magbukon population is likely related to lower-than-usual mixing with individuals from other modern human populations that moved into the region, since analytical methods to mask East Asian ancestry revealed Denisovan ancestry that reached 46 percent across the Philippine Negrito populations considered, Jakobsson noted.

From these and other results, the authors speculated that the Island Southeast Asia region may have once been home to several Denisovan or Denisovan-related archaic hominins groups, perhaps including a recently described archaic species known as Homo luzonensis.

"In the Asia-Pacific region, there were likely diverse Islander Denisovan populations, who later differentially admixed with incoming modern humans across multiple locations and at various points in time," Jakobsson said, adding that the current findings "are consistent with a model of an independent interbreeding event between Negritos and Denisovans within the Philippines, suggesting that Denisovans may have been in the islands long before the presence of any modern human ethnic group."

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