A New March 2026: Paper on Archaic introgressions in Humans

March 2026 has seen plenty of research papers published regarding hominins! This post will look into another introgression paper, that found not one, but two separate admixture events with archaics. One took place within Africa before Modern Humans set out on their Out of Africa migration, the second one affected people in Melanesia and Papua New Guinea, Oceanians.

This is the article: Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, Priya Moorja, (2026). Recovering signatures of archaic introgression using ancestral recombination graphs, nioRxiv 2026.03.03.709416; doi: https://doi.org/10.64898/2026.03.03.709416

Introgression Inside of Africa

They detected a first admixture with a ghost (unknown population) that added genes from a "super-archaic lineage" into the ancestors of all humans (Africans and Non-Africans), because it took place before the Out-Of-Africa event, in Africa.

"The ghost lineage, with a divergence time similar to Neanderthals, could plausibly correspond to Middle Pleistocene Homo groups or African Homo heidelbergensis populations that directly admixed with modern human ancestors before the OOA dispersal. For the super-archaic lineage, one potential candidate —compatible with the split time of approximately 1.8 Mya— is Homo erectus, as suggested by earlier studies."

The authors admit that it could have been one, single event, or there could have been more: "additional episodes of gene flow among structured African populations may have occurred but remain difficult to resolve with present data."

They noticed that the introgressed alleles could have been modified due to the action of natural selection perhaps because they provided adaptative benefits.

The paper says that their software (TRACE) found the following archaic ancestry in contemporary people from different regions, where N is Neanderthal, and D, Denisovan:

• Europeans. N: 0.99%; D: 0.03%.
• East Asians. N: 0.97%; D: 0.10%.
• South East Asians. N: 0.78%; D: 0.10%.
• Oceanians. N: 0.73%; D: 0.66%.

But, apart from Neanderthal and Denisovan alleles they also detected an introgression from a "ghost" source distantly related to Neanderthals and Denisovans: "Ghost segments exhibit deep divergence in marginal trees and show nearly identical genetic affinity to both sequenced Neanderthal and Denisovan genomes, indicating that they originated from an unsequenced lineage equally related to both archaic groups."

It was found in all modern humans at frequencies that ranged from 0.49 to 1.1%. This includes Sub-Saharan Africans.

Africans have more unique segments

The interesting part is that although non-Africans and Africans share alleles of the ghost introgression, "...both East and West Africans harbor a greater diversity of unique ghost segments." The authors don't attribute this enrichment and divergence to a recent or ancient admixture with archaics after the OOA event. Instead, they attribute it to the bottleneck caused by the OOA that led to the loss of these variants, now only found in East and West Africans.

Dates

The calculated "coalescence time" between human and ghost genes is, on average, 830,000 years (95% CI: 0.61–1.27 Mya).

This data leads the team to conclude that "an unknown archaic population, which diverged over 500,000 years ago, introgressed into the common ancestors of all modern humans prior to the OOA migration, resulting in similar patterns of ghost ancestry in non-Africans and Africans."

Denisovans injected super-archaic ancestry in Oceanians

Then they found a second introgression!

Previous studies have suggested that Denisovans may have mated with a super-archaic hominin (possibly Homo erectus), and as Papuans, Melanesians, and Southeast Asians have the highest level of Denisovan ancestry (they admixed when humans reached Sundaland, and the Philippines), the researchers wondered if the admixing led to a flow of super-archaic genes from Denisovans to humans.

They looked for super-archaic alleles contained within the Denisovan segments found in modern Oceanians. Their analysis revealed the 0.73% of Neanderthal and 0.66% of Denisovan ancestry mentioned further up, and also, a 0.33% introgression of super-archaic "ghost" ancestry.

"we infer that the super-archaic segments embedded within Denisovan ancestry tracts contributed almost 0.3% of the total detected Denisovan ancestry in Oceanians. This estimate constitutes a very conservative lower bound on the true fraction of super-archaic ancestry, as our analysis is restricted to Denisovan-introgressed regions in modern humans, requires segments longer than 20 kbp, and excludes loci where the sequenced Denisovan carries super-archaic ancestry. Using the marginal trees in SINGER, we estimate the coalescence time between these super-archaic segments and modern human lineages to be approximately 1.77 Mya (95% CI: 1.13–3.98 Mya), consistent with earlier reports."

The age given above points at Homo erectus, who was present in Eurasia 1.77 Mya.

The two introgressions. Copyright © 2025 by Austin Whittall

I prepared the map above to show what the paper says: An archaic ghost population in Africa (red circle) admixes with Modern Humans prior to the OOA (blue circle). These introgressed modern humans go into Eurasia (losing some of the archaic alleles due to founder effects and bottlenecks, and also spread across Africa (violet arrows) where the archaic signal remains stronger, one group heads towards SE Asia, Sunda and Melanesia, where Denisovans (green) live. These Denisovans had previously admixed with a Super-Archaic (yellow) somewhere in Asia (dashed yellow line). (2) is the Denisovan-Oceanian admixture, and (1) is the admixture within Africa. The red population is linked distantly to Denisovans and Neanderthals.

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

Denisovans and their abilities

I came across an interesting paper: Guy S. Jacobs, Georgi Hudjashov, Lauri Saag, et. al., (2019), Multiple Deeply Divergent Denisovan Ancestries in Papuans, Cell,Volume 177, Issue 4,2019, pp. 1010-1021.e32, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2019.02.035.

It explores three different Denisovan introgressions into the people that live in Papua New Guinea, and the relationship between the three Denisovan groups that admixed over a period of tens of thousands of years, in separate events (Modern humans met and shared genes with Denisovans several times).

I found it quite interesting:

Variety of Denisovans

"Here, we use a statistical approach on new genomes from ISEA and Papua to identify two new Denisovan groups (D1 and D2) and describe the relationships between these archaic hominins long before they first interacted with anatomically modern humans. Both groups branched off early from the Altai Denisovan clade at 283 and 363 kya and were reproductively isolated from the individuals at Denisova cave in Siberia and from each other. Yet both groups bred with modern humans, contributing around 4% of the genomes of Papuans, including over 400 gene variants enriched for traits involving immunity and diet. Some of this introgression is restricted to modern New Guinea and its surrounding islands and may have occurred as late as the very end of the Pleistocene, making the admixing D1 Denisovan population among the last surviving archaic hominins in the world."

Ancient Mariners

The Denisovans had a wide geographic range and had evolved in Asia for hundreds of thousands of years. They had split and differentiated in Siberia, Melanesia and Southeast Asia. Could they have moved northwards, into Beringia and crossed it into America?

The paper highlights the mobility and abilities of Denisovans in dealing with the sea (underline is mine:

"The genetic diversity within the Denisovan clade is consistent with their deep divergence and separation into at least three geographically disparate branches, with one contributing an introgression signal in Oceania and to a lesser extent across Asia (D2), another apparently restricted to New Guinea and nearby islands (D1), and a third in East Asia and Siberia (D0). This suggests that Denisovans were capable of crossing major geographical barriers, including the persistent sea lanes that separated Asia from Wallacea and New Guinea. They therefore spanned an incredible diversity of environments, from temperate continental steppes to tropical equatorial islands. The emerging picture suggests that far from moving into sparsely inhabited country, modern humans experienced repeated and persistent interactions as they expanded out of Africa into this highly structured archaic landscape across Eurasia. This genetic contact yielded a rich legacy, including hundreds of gene variants that continue to contribute to the adaptive success of anatomically modern humans today."

The paper explicitly mentions their seafaring capabilities, and also, that they survived until quite recently, far longer than the Neanderthals:

" this would imply that at least some Denisovan populations had the ability to cross large bodies of water, such as the one represented by the Wallace Line. This idea does not seem implausible given archaeological evidence of archaic hominin dispersals—notably, the discovery of stone tools in the Philippines dating to 700 kya (Ingicco et al., 2018) and the related finding of H. floresiensis on the island of Flores (Brown et al., 2004), both across substantial water boundaries that persisted throughout the Pleistocene. Such geographical barriers would limit gene flow and might help to explain the extent of divergence between the D1 Denisovan population and other Denisovan groups. Second, the late date for the D1 introgression and geographic structure in modern populations suggests that Denisovans survived until 30 kya, and perhaps as recently as 14.5 kya. This is longer than Neanderthals, who died out around 40 kya."

Capabilities that could have taken them along the eastern shores of Asia, into America.

Clearly, a complex pattern is being pieced together in Asia, with the Denisovans appearing to have been well established there long before the "Out of Africa" event.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

More on the Amerindian - Australasian link: Denisovans?

I I have already posted about this The link between Negritos, Papuans and Amerindians!, but the paper by P. Skoglund et al., published online on July 21, 2015 [1], found a close relationship between the genetic makeup of some Amazonian Native Americans and a group of Oceanian or Austalasian people. Namely, the team found "genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".

Being beind a paywall, since that first posts I have read other online sources who have accessed the paper found some interesting points to share in this post:

Skoglund et al., found that the Amazonian Amerindians like the Suruí, the Xavante and Karitiana share around 1 or 2% of their genes with aboriginal Andamanese, Papuans and Australians. Furthermore, the 12,600 year-old remains from Anzic, Montana, US, don't have any links to these Australasians suggesting that the Anzic child and modern Amazonians have different origins.

Their explanation is the following:

A simple migration from Melanesia north to Bering and then south into America does not seem likely because there are no traces of Australasian genes along the route. It is improbable that they would have covered such a long route without dallying with the locals and spreading their genes.

Instead they suggest that an ancestral population which is now extinct (that is why their genes cannot be found in Asia), lived in eastern Asia and split into two groups, one that moved south into South East Asia, PNG and Australia and another that marched north across eastern Asia and entered America.

They named these mysterious people as "Population Y" (Y from the Tupi word "Ypykuéra", which means "ancestor").

As I am not constrained by the rigidity of orthodox science, I can suggest that there is a Denisovan link involved in this process:

As Austronesians have a very high share of Denisovan genetic input, the hypothetical "Population Y" may well be the group that admixed with Denisovans, and therefore Denisovan genes in America could have this origin.

An alternative explanation however for the lack of "Population Y" traces in Asia could be that the Denisovans lived both in Asia and America, and admixed with the first wave of humans that went into America and also with the first wave through their Asian homeland: the ancestors of the modern Australasians. Later, they became extinct, but their genes lived on. Later still, Asians with a different genetic make up entered America and swept the first people away. Nowadays only 2% of the old genome survives in the Amazonian forests.

Since the very old hg M mtDNA was found in some ancient native remains in America, but is also found in parts of South East Asia, PNG, India and Tibet. Could this be a signal of the first people to reach America from South East Asia?

We have evidence of humans in Southern Asia aroung 120 kya, a very archaic population of humans; and they probably moved into America and mixed with Denisovans there or in Asia. What is the mtDNA of these people? If the hypothetical Out of Africa move took place earlier, then they could be Haplogroup M. We will have to wait for more evidence.

Source

[1] Pontus Skoglund, et al. (2015) Genetic evidence for two founding populations of the Americas, Nature 525, 104–108 (03 September 2015) doi:10.1038/nature14895.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Unique Amerindian Genetic Trait

My previous post dealt with the anomalous prevalence of Alzheimer's Disease among American Natives, today's deals with another "unique" Amerindian genetic trait, that extends to what in USA are known as Latinos (people with mixed ancestry that includes Native Americans): one that protects against breast cancer.

Breast Cancer incidence by Race USA. From [1]

The table above clearly shows how American Natives and Latinos have the lowest incidence of Breast Cancer among American women.

The cause according to a paper [2] by Laura Fejerman et al.,(2014) is a mutation in chromosome 6: "Here we carry out a genome-wide association study of breast cancer in Latinas and identify a genome-wide significant risk variant, located 5′ of the ​Estrogen Receptor 1 gene (​ESR1; 6q25 region). The minor allele for this variant is strongly protective (rs140068132: odds ratio (OR) 0.60, 95% confidence interval (CI) 0.53–0.67, P=9 × 10−18), originates from Indigenous Americans and is uncorrelated with previously reported risk variants at 6q25."

This mutation is the reason that "Latina women, those with a high proportion of Indigenous American ancestry are at a lower risk of developing breast cancer..." [2].

This mutation must have appeared in America otherwise the purported ancestors of Amerindians (as per the Out of Africa theory) would also carry this variant. By the way, the prevalence of Cancer among Amerindians is almost 1/3 of that found among White American women and half of that found among African American women. The Asian Americans' ratio is also almost twice that of American Natives. (these are supposedly the closest genetic relatives to Amerindians).

Is this also due to a bottleneck? or is did it appear during the "Beringian standstill"?

What does the genome of Neanderthal or Denisova tell us about this mutation? I have tried to find information but have not found anything. It may be a mutation inherited from them. Found only in America.

But what about Papuans, who have a high proportion of Denisovan genes? I found two papers (here) and (here) which inform extremely low levels of cance: roughly 8 to 20 times lower than the ratio among Ameridians"!: from 1958 to 1988, the incidence of breast cancer was betwenn 6.9 and 2.4 per 100,000 women.

Do Papuan women have a genetic mutation that protects them too? or is it just lifestyle? Or are these numbers not adjusted by age?

I found another interesting source (global Cancer atlas) which lists cancer prevalence among all human populations. I selected Breast Cancer Incidence and got this map:

Clearly this differs from the other information: dark blue= EU, Australia, America and NZ, Argentina... countries with a high prevalence of White Europeans that eat beef. And low prevalence in "poor" countries where fatty foods are not so common... Asia, Africa, Bolivia. The quality of the data is also variable, ranging from "A" in the US to "C" in China or "G" in Bolivia (19.2 per 100,000 cases) so it makes me wonder how reliable this information is.

Anway, the intersting point is the mutation in Chromosome 6 found among Native American women.

Sources

[1] Zhang and Olopade in Hereditary Breast Cancer. Edited by Caludine Isaacs, T.Rebbeck. pp.234
[2] Laura Fejerman, et al.,(2014). Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25, Nature Communications 5, Article number: 5260 doi:10.1038/ncomms6260

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Denisovans Amerindians and Austronesians

A paper by Pengfei Qin and Mark Stoneking (Denisovan Ancestry in East Eurasian and Native American Populations bioRxiv preprint first posted online April 3, 2015; doi: http://dx.doi.org/10.1101/017475), takes a look at the Denisovan content in modern Homo sapiens genes.

Below is one of the maps posted in the supporting information (from page 8) which shows (blue shades) the higher introgression of Denisovan DNA into humans in Australia, New Guinea and Melanesia, while the Neandertal content is given by the red shades (higher in Asia, America and Europe. Green tint is the neutral African area.

Neandertal and Denisovan DNA in modern humans. From Fig. S4 B in Pengfei and Stoneking.

They put forward two possible ways for the admixture of Denisovan and Homo sapiens genes. Allow me to quote them:

"However, there are (at least) two potential alternate scenarios that could explain these results. First, Denisovan admixture could have occurred in a population that was ancestral to both EE/NA (East Asia and Native American) and Oceanian populations; second, admixture could have occurred in a population that was ancestral specifically to Mamanwa, Australians, and New Guineans (as suggested previously (2)), followed by a back-migration from New Guinea to mainland East Asia. This putative back-migration would then have spread both New Guinea and Denisovan ancestry throughout East Asia and Siberia, and ultimately to the Americas."

The first option (admixture in Siberia near Denisova), would be followed by additional dilution in East Asia of Denisovan genes when more modern humans migrated into East Asia and admixed with the population that had originally received the Denisovan input. While this did not take place in Oceanian peoples.

In my opinion the back-migration out of Australia is unlikely. But what if... there was a sizeable populations of Denisovans in South East Asia and Sahul. Humans arrived and mixed with them. The higher the density of Denisovans or ratio of Denisovans to H. sapiens, the higher their "input" of genes into the mixed offspring of human - Denisovan matings. So PNG, Australia had a higher ratio of Denisovans than East Asia... or America (why must we always assume that the introgression took place once in one place?). Because admixture could have taken place in several locations: America, Asia and Austronesia.

Who are these Denisovans? The most likely candidate is an ancestor that lived in Asia and had left Africa before Humans and before Neandertals... that spells Homo erectus. They did live in Sahul and China (maybe America but that is not considered by mainstream science).

The interesting thing is that Neanderthal (see the red hues in the map above) genes are very strong in America among Native Americans too, suggesting (a) Modern Humans mixed with them in Asia and brought the Neandertal genes with them into America or (b) Admixture took place in America: modern humans met and mated with Neandertals in the New World.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©