Archaic Admixture (within Africa) a new paper (Science Jul. 30, 2026)

A paper published in the non-peer reviewed BioRxiv last March (see my post on it) has been now published in Science, on July 30, 2026 (Yulin Zhang et al., Recovering signatures of archaic hominin introgression using ancestral recombination graphs. Science 0,eaef8874 DOI:10.1126/science.aef8874). It discusses ghost introgressions in modern human populations. My original post highlighted its main points. Today, re-reading the article, I found some interesting points, which I discuss below.

Heterozygosity and archaic introgression

All research about Amerindians and all other non-Africans, stresses that they have higher homozygosity than Africans, a signal of a lower diversity in their genes. They are less heterozygous. I have argued in several posts that the higher heterozygosity observed in Africans could come from their recent admixture with archaics that survived until recently, within Africa.

This paper reported that (highlighting is mine) "Several additional lines of evidence support our results of ghost ancestry in modern humans. First, we find that genomic regions harboring ghost ancestry exhibit elevated heterozygosity levels, a pattern also observed for Neanderthal and Denisovan segments (fig. S25). The elevation in heterozygosity is consistent with a model of introgression from a deeply divergent lineage..."

The authors note that sub-Saharan Africans have the highest levels of super-archaic ghost admixture, and non-Africans have much lower values, but they attribute it to a bottleneck effect following the Out Of Africa (OOA) migration, ignoring the possibility of recent admixture within Africa: "We find that ghost ancestry peaks are over-represented in sub-Saharan African populations relative to non-African populations, which is consistent with the lower genetic diversity in non-Africans."

Africans and admixture there, in Africa

Regarding "deserts" where ghost presence is lacking, they attribute it to the same cause, the OOA migration: !We also identify 97 deserts of ghost ancestry (i.e., regions that are at least 10 Mbp long and have less than 0.1% frequency of ghost ancestry). These deserts are only found in non-African populations, with nearly half (43.3%) shared between different non-African groups, likely formed during the OOA bottleneck (supplementary section S6.3 and figs. S37 and S38). We do not identify any ghost ancestry deserts in sub-Saharan Africans." A plausible explanation for this is that ghosts introgressed within Africa, leading to a total lack of deserts there, while in the rest of the world, deserts point at a lack of superarchaic admixing.

In my original post I highlighted their comment about the source of the ghost population, I will once again quote the authors comments: "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."

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

Denisovan may have split from Homo erectus

A recent research article (not peer-reviewed) published in BioRxiv (Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations. Noel McAllister, Sebastian Zöllner, Xinjun Zhang, bioRxiv 2026.06.25.734355; doi: https://doi.org/10.64898/2026.06.25.734355), used simulations based on a specific computing program to explore the sites in our genomes where superarchaic introgression may be found. Introgression that reached us via Denisovans.

It looks into the genome of modern populations and finds that HLA/MHC loci have higher introgression scores than other sites. This, according to the authors, "...is consistent with previous evidence that immune-related loci retain archaic variants. At the same time, HLA/MHC is among the most polymorphic regions of the human genome and has been shaped by pathogen-mediated and balancing selection, both of which can preserve deeply divergent haplotypes and generate unusually deep local genealogies..." However, they caution that these high scores may not only be due to archaic introgression: " ...HLA/MHC is also one of the clearest examples of long-term balancing selection, which also preserves deeply diverged haplotypes without recent introgression... We therefore interpret the HLA/MHC signal cautiously. It should not be treated as definitive evidence for superarchaic ancestry by itself. Nonetheless, its repeated elevation across all three populations is notable and suggests that immune-related regions may be especially informative targets for future local haplotype, ARG-based, and functional analyses."

It makes sense that alleles linked to immunity, received from superarchaics, if they provide a benefit, will be preserved across generations.

The paper then discusses Denisovans and mentions an interesting fact, that Denisovans could have evolved from Homo erectus: "Our results also intersect with the recent paleoproteomic evidence suggesting that some Denisovan superarchaic ancestry may ultimately derive from populations related to H. erectus."

It also notes that population structure can be mistaken for introgression: "A further limitation is that deep population structure and introgression remain intrinsically difficult to separate. Structured ancestral populations can generate old coalescent times and divergent haplotypes, and some recent models have shown that deep structure may explain signals previously interpreted as archaic or ghost admixture."

It presents a scenario that I had not read about before: "Hominin evolution may have involved both long-lived structured populations and episodic admixture among deeply diverged groups." Which is very plausible, we can imagine, especially in Africa this scenario, with archaic populations and ancestral modern humans living in isolated, deeply structured populations admixing sporadically, and adding diversity to the Homo sapiens group.

The other branches of the human tree also followed that pattern, with Neanderthals in western Eurasia and Denisovans in the Eastern part of Asia. Mixing with modern humans as our ancestors met them.

Homo erectus has been shown to have admixed with Denisovans (see this post), but, this article suggests that Denisovans evolved from Homo erectus, which is a very reasonable assumption. I recently posted about Denisovans and Homo heidelbergensis being related (also Neanderthals), it is possible that the common ancestor for these groups evolved from erectus (via Homo antecessor) in Eurasia.

Evidence seems to be building a stronger case for an Eurasian origin for hominins.

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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 © 

Another paper on Introgressions (April 2026)

Continuing with the wide variety of introgression / admixture papers published over the past few years, today I add a new preprint (in Biorxiv, and therefore not peer-reviewed) published a few days ago, on April 12, 2026: Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic. Nicholas W Collier, Simon Gravel, Aaron P Ragsdale. bioRxiv 2026.04.11.717825; doi: https://doi.org/10.64898/2026.04.11.717825

Through the use of a very particular statistical model (described at the beginning of the paper, and well over my statistical abilities to understand), and genetic analysis of the autosomal DNA, the authors suggest a population structure and admixture, and population sizes for modern humans, Neanderthals, Denisovans, and super-archaics that mix to and fro over the past million years. The paper assumes "a fixed mutation rate of 1.3 × 10−8 per bp per generation and a generation time of 29 years" (I have previously posted about mutation rate, its variability, and generation times and the combined effect of them on calculating timelines.

The paper reports the following events and dates:

• Neandertal-Denisovan Common ancestor or ND lived from 779 to 726 kya and lasted for ~50.000 years.
• Ancestral Neanderthals or AN that around 123 kya split into Altai people in Siberia - who later became extinct, and the Western Neandrthals or WN
• Anatomically Modern Humans or AMH introgressed into AN 250 kya ago, and 110 kya into the western Neanderthal (WN) group, which later evolved into the Croatian Vindija and Chagyrskaya (Siberia) lineages.
• Denisovans received gene flow from a ghost lineage, a "Superarchaic" S that may be Homo erectus, it had split from our ancestors 2 million years ago.
• They reckon that the Ust’Ishim people from East Central Siberia dated to around 45 ky were the first humans in Eurasia to split from the other branches after the Out of Africa Event.

The arrows in the chart show the introgression: "broken one-headed arrows denote instantaneous gene flow events; solid double-headed arrows denote continuous gene flow." The percentages, and population sizes (N_e) are also represented:

Figure 6: Early hominin history in Eurasia with recurrent gene flow. From Nicholas W Collier, Simon Gravel, Aaron P Ragsdale, 2026.

The timeline is the following:

TND→AMH (ky) AMH–ND split time 798 CI: 748 – 827
TAN→Den (ky) AN–Denisova split time 688 CI: 639 – 734
TWN→Alt (ky) WN–Altai split time 123 CI: 117 – 137
TCha→Vin (ky) Chagyrskaya–Vindija split time 60.5 CI: 57.3 – 67.7
TYor→OOA (ky) Yoruba–OOA split time 56.9 CI: 53.6 – 60
TOOA→BE (ky) OOA–BE split time 54.7 CI: 49.7 – 57.6
TLos→Stu (ky) Loschbour→Stuttgart admixture time 29.4 CI: 13.2 – 35.9

The authors conclude that "Using these advances, we inferred a demographic model that broadly explained observed H2 patterns and integrated major supported features in hominin evolution, including recurrent interbreeding between Neanderthals and AMH, introgression from a distantly-related, unsampled lineage to Denisovans, and population structure in western Eurasian AMH."

There is no Denisovan to AMH admixture in this model, it seems to only focus on Northern and Western Eurasians, and does not consider Eastern, Southern or Southeastern Asians and Oceanians.

Effective Populations

I found the Effective population sizes to be of interest (the N_e). As you can see, the Ancient basal root at the top of the image (A) has a large population from which the Superarchaics (S), the modern humans (AMH) split from and conserve a large population size, the ancestor of Neanderthals and Denisovans (ND) has a tiny population and remain that size, so do the N, Denisovans, and the original Out of Africa migration group (bottleneck). The Yoruba people retain a large population.

The paper says that the original Ancestral population had an N_e of 16500 individuals (CI: 15900 – 17300) and then it says "We fixed the effective size of the Superarchaic lineage (S) to 20,000" So the superarchaics splitting from the Ancestral line into Eurasia didn't suffer a bottleneck? Why?

Yet the other groups splitting from the Ancestral group did! The authors explain this large Superarchaic population size as follows: "We justified fixing the population size of S with the observation that changing the effective size of a ghost lineage which makes a small ancestry contribution to a sampled lineage has a negligible effect on E[H2]." So, their model and formulation allows these unrealistic assumptions.

The upper part of the image further down, shows how the Superarchaic introgression into Denisovans affects the population sizes and dates, their model calculates an outcome with a minor impact on effective populations or the timelines.

Interestingly, they note that small effective population sizes may be an artifact, because they can be "plausibly explained by geographic population structure. With spatial structure, recent ancestors are expected to live in closer proximity, and to therefore have a higher probability of sharing parents, than ancient ancestors. Strong structure therefore causes recent coalescence rates to be larger than ancient ones,a pattern which is interpreted as a small recent effective size in a panmictic model."

The paper also notes that "using a lower mutation rate inflated effective size and time parameters, while a higher rate diminished them." They show tables with the effects of different mutation rates as can be seen in the lower part of the image below. The image shows the effects of Superarchaic introgression into Denisovans and the effect of different mutation rates on Ages and N_e of the hominin clades. The original can be seen in tables S8 and S9 in the Supplementary Information of this paper:

The impact of a slower mutation rate can be seen in the older split between ND and our lineage and an older ND split into Denisovans and Neanderthals, but does not affect on more recent events. The impact of mutation rates on the effective population size (N_e) is also variable, some populations have a bigger effective population (A, AMH, Altai, Vindija, Chagyrskaya, Denisovan) while others smaller (ND, Yoruba).

I have already posted about mutation rates and how it impacts on N_e and heterozygosity, and mentioned the same effect reported by the authors of this paper: For a given heterozygosity, lower mutation rates increase effective population size. I also posted about the effect of mutation rates on dating splits, lower rates lead to deeper (older) split dates.

However, this paper does not explain why the same mutation rate affects N_e in opposite ways (there is a complex explanation about their model in the Appendix that mentions some effects on the Effective Population size). It does admit that the model, like all models is a simplification of reality: "... we made many approximations to simplify our models. We treated populations as discrete entities, with random mating, piecewise-constant sizes, and instantaneous divergence. Some of these assumptions allow us to model the evolution of HR statistics, while others are useful for formally testing tractable demographic models. Of course, the true evolutionary history includes unmodeled populations, continuously fluctuating population sizes, population structure induced by the spatial distribution of individuals, and variable migration rates... We also made a number of simplifying biological assumptions. We assumed that the genome-wide average germline mutation rate was constant across all lineages throughout the modeled period... We also assumed a constant generation time for all lineages throughout the studied period."

Interesting work.

Introgression Index

Visit my index post, with all the introgression posts in one single place.

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

All the Introgression posts in one place

I decided to index the posts and the papers that I cited in them, to have in one single post, links to all of them. Over the years I posted about Neanderthal, Denisovan, Ghost, Super-Archaics, and unknown archaics introgressing (or not) with Modern Humans or with the ancestors of our lineage at different times (before the split with Neanderthals and Denisovans, or after that split), and also with humans injecting alleles into Neanderthals! Very confusing, and sometimes contradictory.

Our lewd ancestors and their dallies

What is the basis of these events? Politely termed admixture and introgression, the only way our ancestors could have exchanged genes is through sexual intercourse. They were sexually aggressive.

Research by Emma Nelson, Campbell Rolian, Lisa Cashmore, Susanne Shultz, 2010 (Digit ratios predict polygyny in early apes, Ardipithecus, Neanderthals and early modern humans but not in Australopithecus. Proceedings of the Royal Society B, 2010; DOI: 10.1098/rspb.2010.1740) reported that the finger bones of fossil ancestors (bones that are affected by sex hormones in the womb), can predict their levels of promiscuity and competitiveness (polygynous hominins! who had more than one mate). This study found that Ardipithecus ramidus, Neanderthals, and early anatomically modern human (like Qafzeh 9) were more polygynous than modern humans, while Australopiths had a lower polygyny. Strong sex drives that led to many mating events.

Below I list my posts with the corresponding citations, and the outline of the research in them.

• May 2018: Archaic hominins admixed with Pygmies in Africa, citing: Psing Hsun Shieh et al, 2016. Summary: at least one introgression of archaics into pygmies ~9 kya.
• May 2018: More on archaic introgression into H. sapiens in Africa: the source of African's genetic diversity, citing: Hammer et al., 2011. Summary: modern Africans' DNA has a ~2% introgression that took place ~35 kya, from an archaic that split from our lineage 700 kya.ed DNA, ) that introgressed ~35 kya from an archaic population that split from the ancestors of anatomically modern humans ~700 kya
• May 2019: Archaic Ghost population admixed with Modern Humans in Africa, citing: Lorente-Galdos et al, 2019. Summary: a divergent ghost archaic population that split from the ancestors of modern humans 528 kya introgressed into Africans at the following frequencies:~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka.
• September 2019: Super Archaic Hominin admixture with Denisovans, Neanderthals and Africans, citing: Hubisz, Williams, and Siepel, 2019. Summary: (i) 1% of Denisovan genes introgressed from super-archaic hominin that diverged from Human lineage 1 million years ago (MYA). (ii) 0.75% of Altai Neanderthal, and 0.70% of Vindija Neanderthal introgressed from super-archaic. (iii) Some of it passed from Denisovans to Humans. (iv) Detected super-archaic admix in Africans. (v) 3% of Neanderthal genes are an introgression from Anatomically Modern Humans ~200-300 kya.
• June 2019: Archaic humans admixed with modern humans in Africa, citing: S. Langley, Miga, Karpen, C. Langley, 2018. Summary:a distinct, old introgressed archaic lineage (~1.1 MYA) consistent with recent admixture with an extinct archaic in Africa.
• October 2025: Neanderthals and Denisovans in India?, citing: Kerdoncuff, Laurits Skov, Nick Patterson, et. al., 2024. Summary: Beside their introgressed Neanderthal and Denisovan ancestry, 0.37 to 0.48% of Indian ancestry is from another unknown archaic.
• October 2025: Archaic admixture in humans that is neither Denisovan or Neanderthal, citing: Tucci et al., 2018, Mondal, Bertranpetit & Lao, 2019. Summary: The first paper did not find any unknown archaic introgression in SE Asian pygmies, the second one did: a third introgression in all Asian and Oceaninans from an extinct population of the Neanderthal-Denisovan clade or a one that diverged early from Denisovans. First Neanderthals admixed with humans 1.3% frequency 69 kya, then Denisovans introgressed in Oceanians 1.6% frequency, 43 kya, and the unknwon archaic added 2.6% 51 kya. The archacic dates back to 304 kya. Teixeira and Cooper, 2019. Also support a third introgression with an extinct hominin (not Neanderthal or Denisovan), and finally Yuan et al., 2021 suggest that the most recent, of two, Out of Africa events may have mated with undiscovered archaics in South Asia or that ancestors of Neanderthals and Denisovans admixed with superarchaics.
• February 2026: On the Diversity of Africans, citing: Durvasula and Sankararaman, 2020. Summary: introgression into four West African populations, with frequencies of 2 to 19% from an archaic population that diverged before the split of Neanderthals and modern humans. It took plase 43 kya (95% HPD: 6 - 124 kya).

Continues below, after the picture with Hollywood's fantasy about love 1 million years ago (the actors look too tanned and clean don't they?).

One Million Years B.C. (1966), prehistoric love and survival, with Rachel Welch and John Richardson. Source

• February 2026: Diversity in Africa. Some explanations on why it is so diverse, citing: Skoglund et al., 2017, Jakobsson et al., 2025 and Padilla-Iglesias et al., 2025. Summary: deep stratification in Africa may come from admixture with an unknown archaic African group predating the divergence of Humans from Neandertals and Denisovans. Western Africans may have introgressed with archaics.
• February 2026: Did Humans admix with Neanderthals? Paper in Nature says NO, citing: Tournebize and Chikhi, 2025. Summary: There was no admixture between humans and Neanderthals, it is an artifact of mistaken models.
• April 2026: Human Ancestors Interbred with Two Distinct Populations of Superarchaics, citing: Rogers, Islam, Brand, and Webster, (2026). Summary: at least two distinct superarchaic populations admixed with us: one into archaic Eurasian populations (Denisovans and Neanderthal-Denisovan ancestors), an superarchaic that diverged earlier from the human lineage than did the second superarchaic, that admixed within Africa, contributing DNA to early modern humans.
• April 2026: A New March 2026: Paper on Archaic introgressions in Humans, citing: Zhang, Biddanda, Johnson, O’Dushlaine, Moorja, (2026). Summary: two introgressions with super-archaics. (i) inside of Africa with a ghost population that diverged from ours over 500 kya it is found in all humans, Africans and non-Africans. (ii) Superarchaic admixture at 0.3% frequency in Oceanians. This population diverged 1.77 Mya from humans. (iii) All non-Africans carry admixture with Neanderthals and Denisovans.
• April 2026: Another Paper on Introgressions (April 2026), citing: Nicholas W Collier, Simon Gravel, Aaron P Ragsdale. (2026). Summary: Through statistical models and genetic analysis of the autosomal DNA, the authors suggest a population structure and admixture, and population sizes for modern humans, Neanderthals, Denisovans, and super-archaics that mix to and fro over the past million years

Last Updated on April 18, 2026

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

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 © 

An Eurasian origin for Homo Sapiens (2021 paper)

I found an interesting paper published four years ago (Árnason, Ú. The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia. Hereditas 158, 36 (2021). https://doi.org/10.1186/s41065-021-00197-7) that provides an analysis showing that Homo sapiens sapiens or modern humans originated in Eurasia!!

The author summarizes his "Out of Eurasia" findings as follows: He identified "potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH [Out of Eurasia Hypothesis] at the same time ... they lent no support to the OOAH [Out of Africa Hypothesis].

The paper places Homo erectus at the base of the nuclear DNA tree: "Homo erectus, He, has been placed at the root of the tree consistent with He entering Eurasia from Africa > 2 million years ago". The following image appears with the caption that is given below.

Fig. 1 in Arnason (2021). Source

Fig. 1. Captioned: "The nuDNA phylogeny leading to Hss, Homo sapiens sapiens. Blue: Eurasian lineages. Red: African lineages. H. erectus has been placed at the root of the tree in accordance with the artefact sequence related to the Eurasian existence of He 2,12 MYBP. The divergence between Hs, H. sapiens, and Ha, H. antecessor, has been dated to ≈ 850,000 YBP, that between Hss and Hsn, H. s. neanderthalensis, to ≈ 800,000 YBP and that between Lund and Mbuti/San to ≈ 250,000 YBP. Hsn divides into Hsnn, Neanderthals proper, and Hsnd, Denisova, with Hsnn dividing further into SH-Hsnn (Hsnn at Sima de los Huesos) and Hsnn*, a branch arising as the result of the mtDNA introgression that took place from Hss into Hsnn* ≈ 500,000 YBP". Where Hsn is Neanderthal, HSnd, Denisovan.

Fig. 2 in Arnason (2021). Source

Fig. 2's Caption reads: "The mtDNA relationships of Hs demonstrating the paraphyly of the African Hss populations as resolved by PPA. Blue: non-African taxa; red: African taxa. Hsnn*: Hsnn other than SH-Hsnn. The arrowheads signify the mtDNA introgression that gave rise to Hsnn*. The limitation of Hsnn to Eurasia places the mtDNA introgression in this continent, reversing the direction of Hss evolution behind OOAH. The Hss part of the tree underlines the phylogenetic continuity among non-African populations and the paraphyly of the African populations including the two Yoruba [1]. AuAb: Australian aborigines; PNG: Papua New Guinean; Han: Chinese; Lund: The first described non-chimaeric human mtDNA molecule [19]; French: A European, as representing previous genomic findings"

An interesting hypothesis that has surely been torn apart by those who support the OOA theory. Nevertheless, since 2021, findings in China have provided some additional support to the notion that there were evolved humans in Asia at least 200,000 years ago besides the Denisovans.

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Ancient H. erectus introgression into Denisovans and Neanderthals

A recent paper used statistical tools to look into ancient introgressions in the modern human line. The authors reported in their abastract that "We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions—comprising at least about 4Mb—were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.".

You can read the full text of the paper here (Hubisz MJ, Williams AL, Siepel A (2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16(8): e1008895. https://doi.org/10.1371/journal.pgen.1008895).

Some higlights:

• The program they used "calls nearly 0.5% introgression from the Neanderthal into each of the African individuals. These calls are likely explained by a combination of false positives and back-migration into Africa from Europe. However, another possibility is that some regions introgressed into Neanderthals from ancient humans may be assigned the wrong direction". So they did find Neanderthal introgression in Africans but seem to write it off as a fabricaton of the program or false positives, and maybe back-migration.
• "We identify 1% of the Denisovan genome as introgressed from a super-archaic hominin—roughly double the estimated false positive rate (0.49%) for this event. Our apparent weak power for these events (another group has estimated ∼6% introgression) suggests that the super-archaic divergence may have been somewhat recent (perhaps closer to 1Mya than 1.5Mya). Still, this analysis resulted in 27Mb of sequence that may represent a partial genome sequence from a previously unsequenced archaic hominin. In addition, ARGweaver-D predicted that a small fraction of the Neanderthal genomes is introgressed from a super-archaic hominin (0.75% for Altai and 0.70% for Vindija), an event that has not been previously hypothesized. However, these fractions only slightly exceed the estimated false positive rate (0.65%), so these results are likely dominated by spurious predictions."
  This is indeed interesting. The time frame means surely an introgression from Homo erectus into Denisovans, in Asia. And also a probable admixture of H. erecrtus with Neanderthals!
• The introgression between the super-archaic into Denisovans was relatively recent: "...suggests that tmig > 225kya for the for the Sup→Den event"
• "our analysis suggests that at least about 4Mb of modern human genomes derives from an unknown but highly diverged archaic hominin, possibly Homo erectus, through at least two separate introgression events".
• The authors validate an early admixture of Humans into Neanderthals in Asia some 200 to 300 kya: "Our follow-up analysis based on the frequencies of introgressed elements among the two diploid Neanderthal genomes suggests that the Hum→Nea gene flow occurred roughly between 200 and 300kya, within the limits of accuracy imposed by our assumed demographic model, mutation rates, and generation time. As previously noted, because contact between modern humans and Neanderthals most likely took place in Eurasia, this timeline appears to be inconsistent with a genetic exchange involving the direct ancestors of most present-day Eurasians, who migrated out of Africa ∼50kya. Instead, our timeline suggests an earlier migration, occurring at least 200kya.". Yet they assume (without explaining why) that "These early migrating humans may later have gone extinct, leaving a genetic trace only in introgressed segments in Neanderthals."
• They "only detected a low rate of Sup→Afr introgression, somewhat below our estimated false positive rate." which is attributed to using a large population size, based on the assumption of their model -Africa as cradle of mankind had the largest population size.
• On ancient introgressions: "It is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans. Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."
• The authors did not discriminate between Africans and Non-Africans in this study: "When analyzing non-African humans, we only included the “recent” migration bands from Neanderthals and Denisovans into humans, whereas when looking for older introgression events, we excluded the “recent” bands as well as non-African humans. Throughout this paper, all humans are placed in the same population; we do not model divergences within human populations... on this time scale, the European/African split is very recent, so that we did not model the population divergence among modern humans or recent growth in out-of-Africa populations".

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall ©