Peak Denisovan Ancestry Is Found In The Philippines

A few years ago, it was discovered that Denisovan ancestry makes up the largest percentage of a modern population in a group of people in the Philippines (these peoples also have the typical level of Neanderthal ancestry found in non-African modern humans).

This implies the co-existence of the earliest modern human Negrito people and Denisovans during the early to middle Upper Paleolithic era (ca. 50,000 years ago).  

The extinction of the last Neanderthals in Europe was about 29,000 years ago, although Neanderthal admixture with modern humans was mostly 100,000 to 35,000 or so years ago.

This was perhaps 50,000 years after the extinction of Homo erectus, based upon the youngest known Homo erectus remains, although an extinction date 70,000 years ago in line with the Toba eruption and first contact wiht modern humans is a plausible possible extinction date that later discoveries could support.

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. 

Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. 

We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. 

Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

Maximillian Larena, et al., "Philippine Ayta possess the highest level of Denisovan ancestry in the world" 31(19) Current Biology 4219-4230 (August 12, 2021 in print October 11, 2021) (open access). 

The body text discusses the estimated timing of admixture and divergence and the amount of East Asian admixture in the relevant populations:

East Asian-related Admixture in Negritos 

To determine the presence of East Asian admixture among Philippine Negritos, we implemented the test D(Mbuti;EastAsian,Papuan,X); with Balangao Cordilleran utilized as a surrogate for the least admixed East Asian source. We find that all Philippine Negritos display varied levels of gene flow from East Asians, with Ayta Magbukon presenting as the least admixed. 

To estimate the levels of East Asian and Australasian-related ancestries in Negritos, we implemented the qpAdm tool of Admixtools v5.0 software package. We first prepared a new dataset with reference ancient samples, by merging Phil_1KGP_SGDP_1.92M dataset with published ancient DNA data to produce the Phil_1KGP_SGDP_Ancient_1.92M dataset, which was then haploidized and filtered to keep transversion sites only, producing the Phil_1KGP_SGDP_Ancient_Transv_317K dataset with 317,220 SNPs. 

The ‘left’ populations include Balangao Cordilleran of the Philippines as the surrogate for the least admixed East Asian source and Papuan as the surrogate for the least admixed Australasian source. The outgroup or ‘right’ populations include Juhoansi, Mbuti, Mota, Loschbour, Anzick1, Ust’Ishim, Sumiduouro, and Karitiana. 

Overall, there is a wide variation in the magnitude of admixture with East Asians. For instance, Ayta Magbukon and Ayta Ambala presented as the least admixed Negrito populations, with an East Asian-related ancestry of only ∼10%–30%. On the other hand, both Agta Bulusan and Agta Matnog have the highest levels of admixture, possessing ∼79%–85% East Asian-related ancestry. To estimate the date of admixture, we utilized MALDER, which applies a weighted linkage disequilibrium (LD) statistic-based method and allows detection of multiple admixture events. Philippine non-Negritos, Amis, Atayal, mainland East Asians, and Australopapuans were set as putative source populations, while all Philippine Negrito groups were set as target populations. The mean date of admixture between Negritos and East Asians among all ethnic groups within the Philippines was estimated to ∼2,281 years (95% CI: 2,083 – 2,523 years). 

This time frame is largely historically consistent with the arrival of Austronesian mariners in the Philippines. 

Divergence Time between Negritos and Papuans 

To estimate the divergence time between Philippine Negritos versus Papuans, we utilized the ‘TT’ method, which is based on computing sample configurations in a population divergence model. This approach estimates the number of generations since a population divergence for a pair of individuals (or populations), and the method produces direct estimates in generations that are unaffected by the effective population size of the population of each of the individuals in the comparison. We utilized the publicly available genome sequence data on Papuans and our newly generated sequence data on Ayta Magbukon. 

The estimated divergence time between Ayta Magbukon Negrito and Papuans is ∼85 kya (95% CI: 76 – 95 kya). This unusually old divergence time may be attributed to the deeply diverging Denisovan ancestries found in both Papuans and Ayta Magbukon. 

To correct the effect of archaic introgression, we filtered out all the archaic sequences (that were identified using the S’ method) in both Ayta Magbukon and Papuans. The estimated divergence time between Ayta Magbukon Negritos and Papuans, using the filtered data, is 53 kya (95% CI: 41-64 kya). This estimated date falls shortly after the divergence between Australasians and East Asians/West Eurasians, which was previously estimated to ∼58 kya (95% CI: 51 – 72 kya).

The Denisovan populations that were sources for populations in the Philippines and Papuan populations respectively, might have been 100,000 or more years diverged from each other.