Oceanians & Denisovans, a new paper

A paper published in Science last week reported that Near Oceanians, that is, people living in the islands close to Papua New Guinea in Melanesia (New Britain, New Ireland, Bouganville, etc.) and the Solomon Islands, mixed with three different types of Denisovans and still carry their genes nowadays because they play a role in the adaptability and survival of these people.

This is the paper: Patrick F. Reilly, Stephen Rong, Daniela Tejada-Martinez, Samantha L. Miller, Audrey Tjahjadi, Chang Liu, Jared Akers, Alysa Pomer, Margaret E. Prentice, D. Andrew Merriwether, Françoise R. Friedlaender, George Koki, Jonathan S. Friedlaender, Steven K. Reilly, Serena Tucci. Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania. Science, 2026; 392 (6803) DOI: 10.1126/science.adr6749

The authors state that they found "previously unidentified archaic sequence and three times more Denisovan sequence than previous studies... We uncovered evidence for introgression from three Denisovan-like groups into the ancestors of Near Oceanians, revealing a new twist on our interactions with archaic hominins." The Denisovan introgressions impact on genes that affect "TRPS1, a skeletal development gene previously found under selection in central African rainforest hunter-gatherers and highland Ecuadorians", and also genes invovled in immune system pathways.

The paper points out that bottlenecks and subsequent genetic drift, and isolation of the populations in the region have shaped their genetics, causing wide differences between different groups.

Regarding the Denisovan introgression, this study "found that Oceanic genomes carry ∼2.5-fold more archaic introgressed sequence from all origins per individual than European genomes... and 14-fold more Denisovan sequence per individual than East Asian genomes."

But, the distribution of Denisovan genes was not uniform, to the contrary, it varied "by almost twofold from the New Guinean Sepik and Goroka groups to New Britain’s Nakanai and the Polynesian outlier groups of Bellona and Rennell... Sepik individuals harbored the most Denisovan introgression, 25 times more than East Asians... In line with prior work, we found that the genomic proportion of Denisovan introgression in Island Southeast Asian and Near Oceanic groups increased with greater shared ancestry with New Guineans, with the Philippine Agta as the sole exception" (the Agta people carry a very high proportion of Denisovan genes with a very low New Guinean shared ancestry, perhaps an indication of admixture within the Philippines).

Neanderthal genes

Interestingly, the authors say there is a high level of Neanderthal admixture in this Oceanian population, and refer to table S6 in the Supplementary material. Checking the table I found that the highest Neanderthal content is found in the Surui people of the Amazonian region in South America! the second highest is found in the Santa Cruz islanders of Oceania. See the adapted image below, from Table S6 in this paper:

However, the authors downplay the highest levels of average Neanderthal genetic content found in these Oceanians by using the excuse of bottlenecks. See how the try to minimize or understate this fact: "We found that despite harboring 41% more Neanderthal introgression per individual and having ~45% larger sample size in our dataset, Oceanic genomes had 28% less Neanderthal coverage than Central and South Asian genomes (tables S6 and S7). One possible explanation for reduced archaic coverage is a population bottleneck after admixture, which would also lead to increased homozygosity of archaic tracts. In support of this, we found both elevated homozygosity of archaic tracts and 2.3 to 3.4% less archaic coverage than expected given per-individual levels of introgression in five Oceanic groups with bottleneck signals..."

Denisovans

As you can see, the Denisovan levels are highest in Oceanians, and those living in Island South East Asia, followed far away by Amerindians and East Asians.

The paper states that "Denisovan introgression likely occurred in multiple pulses from multiple distinct Denisovan-like groups... We recapitulated previous findings of introgression from two Denisovan-like groups in East Asians... and found evidence for introgression from three distinct Denisovan-like groups with differing genetic affinity to the Altai Denisovan into almost all sampled Oceanic populations... we show that these signals are more widespread than previously thought, highlighting the complex dynamics of Denisovan admixture with modern humans."

Implications

It is time to look at who the Denisovans were, and also, the route followed by the Neanderthal admixture into both, Oceanians, Amerindians and East Asians. We also need to understand more about the differences between the Densivoan populations. Their evolution in Altai, East Asia, and especially Sahul and Sunda. Their presence in American Native genes is also relevant.

The simple model of humans meet Neanderthals in the Levant on their Out of Africa migration and mingle with Denisovans on their trek along South Asia into East Asia and Oceania is missing something.

Denisovans must have been a thriving group, all along the eastern, central and southern regions of Asia, perhaps also, Oceania when they were met by Homo sapiens, smoke screens arguing bottlenecks, genetic drift, and isolation can't explain away the fact that a group in the Amazon jungle has the highest levels of Denisovan ancestry in the whole world.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Chinese study finds link between Denisovans and Homo erectus

A paper published yesterday in the prestigious journal Nature (Quiamei Fu, et al., 2026, Enamel proteins from six Homo erectus specimens across China, https://doi.org/10.1038/s41586-026-10478-8) identified protein from the teeth of Homo erectus remains of ~400,000 years of age from 3 sites in China, and found that "all specimens from all three sites share two amino acid variants. Of these, A253G in AMBN is previously unknown and has not been identified in other human lineages, including H. erectus from Dmanisi (Georgia), Homo antecessor from Atapuerca (Spain), Denisovans, Neanderthals and modern humans. The other variant, AMBN(M273V), has previously been identified in Denisovans, and our evidence now indicates it may have been introduced through populations related to these Middle Pleistocene H. erectus. The regions in the Denisovan genome attributed to super-archaic introgression, some of which later passed to modern humans, are likely to have originated from H. erectus. Late Middle Pleistocene H. erectus may have coexisted with Denisovans in parts of East Asia, where these interactions are presumed to have occurred." A clear link between Denisovans and erectus!

This new variant does not appear in any other primate except these Homo erectus.

AMBN(M273V) from erectus to Denisovan to human!

Then, is the second protein now found in Homo erectus was originally detected in Denisovans.

This discovery suggest that it was passed on from erectus to Denisovans.

This variant known as AMBN(M273V), results from a mutation (single-nucleotide polymorphism or SNP), at rs564905233, where adenine switched to guanine: A→G. Surprisingly, this mutation is also found in humans, and is believed to have introgressed into them, from Denisovans. The paper mentions its frequency as follows: "... 21% in the Philippines, 1.17% in India, 0.71% in Papua New Guinea, and is absent from most other modern human populations." Interestingly Denisovans have admixed mainly with humans from the Southeastern Asia region, including Papua New Guinea and Sunda islands.

Previous studies (see my posts: here, here and here) suggested that Denisovans admixed with superarchaic ancestors, a group that split from ours over 1 million years ago. The authors point out that "genomic studies reveal that Denisovans received 0.5–8% gene flow from a hominin whose ancestors diverged more than 1 Ma from the common lineage ancestral to Neanderthals, Denisovans and modern humans, and about 15% of these ‘super-archaic’ DNA regions introgressed from Denisovans into Asian and Oceanian individuals. This situation is similar to what we observe with AMBN(M273V). Consequently, this variant is not exclusive to Denisovans but appears to have been introduced into them through a population linked to Middle Pleistocene H. erectus from Zhoukoudian, Hexian, and Sunjiadong."

So the Homo erectus in China had sex with Denisovans and passed on alleles that eventually ended up in South East Asians and Oceanians! Below is Fig. 4 in this paper, captioned: " A possible model of gene flow related to AMBN(M273V) among H. erectus associated with the populations of Zhoukoudian, Hexian and Sunjiadong, Denisovans and modern humans."

The paper also clarified the status of two specimens from Hexian, which carry the new AMBN(A253G) mutation found in Homo erectus but absent in Denisovans like (Denisova 3, Penghu 1, and Harbin) this suggests that the Hexian remains belong to the H. erectus clade.

It would be interesting to find if the variant shared by erectus with humans via the Denisovans is found in other groups beyond SE Asia and PNG. For instance, in America, and in ancient human remains. However, the paper states that it is "absent" in most other human populations.

In coming posts, I will address the ancient sites of 400 to 800 ky of age, found in Siberia, which could have been the home of pre-Denisovan people, even Homo erectus, who, as we will see, may have advanced northeast, across Beringia and into America at that early date.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

More papers on Denisovan introgression in PNG and superarchaic mix in Africans

Although it was published last June, a paper by Hsieh et al, is very interesting, and worthy of a post (free access to it her: A global map for introgressed structural variation and selection in humans. bioRxiv [Preprint]. 2025 Jun 24:2025.06.24.661368. doi: 10.1101/2025.06.24.661368. PMID: 40667000; PMCID: PMC12262424). It is not peer-reviewed so its conclusions should be taken with caution.

The paper looks into the introgression of archaics into modern people in Papua New Guinea and I highlight the following findings:

It Adds diversity

The authors state that "some archaic sequences likely contributed to human phenotypic variation" and that they were not necessarily bad for us (deleterious as other papers have suggested). Instead the paper proposes that "many introgressed loci in our genome show signatures of positive selection." They go on to add that Structural Variants or SVs, "such as insertions, deletions, and inversions, contribute disproportionately to human genetic diversity by affecting more genomic sequences than SNVs."

Denisovan and Neanderthal admixture in PNG

The authors noticed that "Unexpectedly, PNG individuals carry more Neanderthal sequences than Denisovan, contradicting the expected genome-wide estimates of ∼4% Denisovan and ∼2% Neanderthal ancestry" This is surprising, and they try to explain it as follows: "[caused by the differences between the sequenced Denisovan genome and the actual Denisovan population that interbred with the ancestors of the PNG as well as complex demographic histories in Oceania." Translated: We don't know why this happened!

MUC19

They observed the presence of a rare introgressed SV, the MUC19 segment: "... an introgressed variable number tandem repeat (VNTR) haplotype at the MUC19 locus with an uncertain archaic origin." I posted about MUC19 last March, because it is supposedly enriched among Amerindians, giving them adaptative advantages, and it is believed to have originated in Denisovans, and passed on to humans via Nenaderthals. These people in PNG have the variant. So it is not so uncommon as believed.

The timing of the introgression

The authors estimate that one of the SV introgressions, an insertion in chromosome 16 "diverged from the others about 596 thousand years ago (kya; range: 322–870 kya)" which is a rather wide range! and attribute it to Denisovans and that the actual "admixing" between Denisovans and the ancestors of the PNG people took place between 60 and 170 kya. Which is older than you would expect and consistent, in my opinion, with an early out of Africa event, or, perhaps a non-African modern human group mixing with Denisovans 170,000 years ago.

Centromeres

If you imagine a chromosome pair with its characteristic "✘" shape, the centromere is the place where the chromosome arms narrow down and meet. Since humans are diploid, we have 23 pairs of chromosomes (each with one paternal and one maternal chromosome) with a total of 46 individual chromosomes. Each chromosome of the pair links with the other one to form the typical "X" shape: "❱" to the left, and "❰" to the right join at the centromere (located at the apex of each single chromosome).

During cellular division (which I will oversimplify in this description) the cell sends fibers that attach to the centromere and and pulls the chromosomes apart, half going to one side, the other half going to the opposite side of the dividing cell. So centromeres play an important role in regulating the division of cells, and reproduction, where the sexual cells carry half the chromosome load compared to regular ones.

The paper goes on to look into centromeres, and reports that it found "11 centromeres likely derived from archaic hominins" and looks into them in detail.

The authors state, for instance, that the PNG people carry a centromere lineage (haplotype 2 chromosome 4) that is older than those found in other modern humans: "[it] diverged from the rest of the modern human lineages 489,447 – 507,131 years ago... also observed evidence for archaic origins for the chromosome 22 centromeres... The lineage that gave rise to the[m] ... diverged from other modern human lineages approximately 580,661 years ago (95% HPD interval: 469–694 kya... sugesting that these centromeres are likely introgressed from archaic hominins into the early ancestors of the PNG."

African divergence and superarchaic introgressions

An earlier paper by Langley et al., 2019 aldo studied the centromere region (they call them Cenhaps, large-scale haplotypes that span the centromere-proximal regions or CPRs in chromosomes). They reported that they found that Africans carry a very ancient, basal, diverged variant of a centromere not found outside of Africa in humans, and it predates the split of Neanderthal-Denisovans from the Modern human branch. The authors find that non-Africans carry another varaint closer to Neanderthals than Denisovans (proof of the admixture of OOA humans with Neanderthals). The superarchaic admixture in Africans comes from a 1.1 million-year-old hominin, and happened recently. The full text is the following:

"The most diverged, basal clade in the chr12 CPR is common in Africa, but, like the most diverged chrX cenhap, is not represented among the descendants of the out-of-Africa migrations (Bae et al., 2017). The great depth of the lineage of this cenhap is further supported by comparison to homologous archaic sequences (Green et al., 2010; Prüfer et al., 2014; Prüfer et al., 2017). Consistent with the hypothesis that this branch split off before that of Neanderthals/Denisovans, members of this cenhap share fewer matches with derived SNPs on the Neanderthal and Denisovan lineages (DM) and exhibit strikingly more ancestral non-matches (AN) than other chr12 cenhaps (see Figure 3b). This putatively archaic chr12 cenhap represents a large and obvious example of the potentially introgressed sequences within African populations inferred from model-based analyses of the distributions of sequence divergence (Hammer et al., 2011; Hsieh et al., 2016; Durvasula and Sankararaman, 2019). The small out-of-Africa cenhap nested within a mostly African subclade appears to be a typical Eurasian archaic introgression with higher affinity to Neanderthals (DM/(DN + DM)=0.91 and DM/(DM +AN)=0.90) than to Denisovans (Figure 3b). This bolsters the conclusion that the basal African cenhap represents a distinctly older archaic lineage. Unfortunately, there are too few coding bases in this region to support confident estimation of the TMRCAs of these ancient chr12 cenhaps. Based on the numbers of SNPs underlying the cenhaps, this basal cenhap is twice as diverged as the apparent introgressed Neanderthal cenhap, placing the TMRCA at ~1.1 MYA, assuming the Neanderthal TMRCA was 575KYA (Prüfer et al., 2017). While there is no direct evidence of recent introgression, the large genomic scale of the most diverged chr12 cenhap (relative to apparent exchanges in other cenhaps) is consistent with recent admixture with an extinct archaic in Africa
... Two examples are chromosome 8, containing an ancient cenhap limited to Africa with an estimated TMRCA of ~730 KYA, and chr10 that appears to harbor another clear Neanderthal cenhap introgression..."

Again, and this time from another source, we see proof of ancient surviving archaic hominins in Africa mating with Africans, recently, and in the process, adding to their diversity and divergence.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©