PRDM9 and our Ancestry

In my previous post about John Hawks take on the ancestral groups that merged (80:20 ratio theory) to form modern humans, I mentioned that he cited several research papers in his analysis. Today I will look into one of them, by Loya, H., Gupta Hinch, A., Palamara, P. F., Speidel, L., & Myers, S. R. (2026). Genome-wide genealogies reveal deep admixtures forming modern humans. bioRxiv. https://doi.org/10.64898/2026.04.17.719197

Loya et al., use a new algorithm called Ghostbuster to study ancient admixtures, and after validating it with recent admixture events, use it to evaluate PRDM9 alleles found in modern and ancient humans.

The PRDM9 gene is linked to genetic recombination. It codes for a protein called PR domain zinc finger protein 9, that plays an important role during meiosis (cell division that produces sex-cells, like sperm and egg cells, which carry half the normal number of chromosomes), it latches on to certain spots of the DNA strand and defines how the DNA recombines (how it is shuffled, and where snippets are added or removed).

Like all alleles, PRDM9 comes in different variants, that arise from mutations. And, these alleles are what Loya and team studied.

PRDM9 Alleles

Before continuing with Loya et al.'s paper, I would like to mention the frequencies at which different PRDM9 alleles are found in modern human populations. For an enlightening paper on the role of PRDM9, see Paigen and Petkov, 2019; it informs in an over-simplified manner that the alleles found globally "generally agree... with their “out of Africa” origins." It says so because Africans have a greater variety of alleles: 50% of allele A, 13% allele C and the other 37% a mix of different variants. The non-Africans, after the bottleneck caused by the OOA migration are almost exclusively A: "with ~90% alleles A and B (mostly A), which only differ in a serine/threonine substitution that does not affect binding specificity" Regarding the Denisovans and Neanderthals, this paper states that their "PRDM9 alleles closely related to rare contemporary alleles that are limited to Africans." I found this rather vague, so I looked for more information on alleles and their frequencies in different populations.

Alleva et al., 2021 investigated this matter and found that the A allele is the most frequent one, ranging from 90% in Finns (highest value) to 48% among Yoruba people in Ibadan, Nigeria (YRI) and 49% in Luhya in Webuye, Kenya (LWK), in between are the Chinese Han with 75% (CHB). The B allele, on the other hand, is higher among the Chinese CHB, with 13% and YRI = 7%, and much lower in other populations (0 to 3%). Another variat named L14 allele is found in Africa, ranging between 11% in LWK, to 3% in YRI, and not present in other non-Africans. The most relevant one is the C allele, it is found in all populations: YRI = 10%, LWK = 8%, CHB = 6%, and also in South American Peruivians from Lima (PEL) = 8%, lower in Italians from Toscana (TSI) and Pakistanis from Lahore (PJL), both with 4%, lowest among Finns with 2%. So, it isn't an exclusive African variant, it is rare in Europe, but present there.

Then come many other variants at lower frequencies in all populations. They add up to a 16% of the global PRDM9 alleles, but they vary between different populations. Most of them at levels of 30% and 31% are found in Africans (LWK and YRI respectively), followed by Tuscans (TSI) with 14% —probably due to recent African admixture in historic times. The rest of the world has levels of 7% to 9% (PEL, CHB, FIN, PJL).

Some rare alleles are exclusive to certain populations, like M1, found at "enriched" levels in Chinese HAN yet absent in all other populations. The D allele was only found in Finns.

Below is an image depicting a Table from the Supplementary Material of Berg et al., 2011, which also provides some frequencies for Europeans, Indians from India, and Africans. Notice the different variants and how the rare ones are exclusive to some regions. I highlighted those higher than 4%. It does not include variant M1 (from the Chinese).

Figure S1 in Berg et al. 2011

Having said this, let's get back to Loya et al. who report that the most common one, PRDM9-A is found in all modern human beings at frequencies of 85% to 90%, and the PRDM9-C allele is less frequent globally, but high in Africa at 10% to 15% together with other rare variants (at 35% in Africa).

Their Ghostbuster algorithm provides evidence that the best model to explain this distribution is the following: there was an original basal lineage carrying the A allele as ancestral variant. Then it split into two stems, one carried the allele A (population HA), the other the allele C (population HC). These populations split and remained separated around one million years ago, then they met 300,000 years ago, merging, this was the time when modern humans, Homo sapiens appeared. Below is Figure 5c, from their paper, showing this scenario:

Original caption (c) Proposed model of deep human history showing the divergence and persistence of different PRDM9 lineages across Denisovans, Neanderthals, and ancestral humans over the past >1 million years. HA and HC denote population groups carrying PRDM9-A-like and PRDM9-C-like PRDM9 alleles, respectively. Fig 5c in Loya et al. 2026

The Neanderthals and Denisovans form part of population HC. Through introgression, the C allele entered modern humans, and the Neanderthals, through admixture with us, got the A allele and a 10% contribution from humans to their genome. Regarding the Denisovans, "Denisovan PRDM9 alleles are distinct from present-day human genotypes, and at least one allele is more similar to PRDM9-C than to PRDM9-A."

The authors suggest that HA population contributed with 20% of the human ancestry. It was a larger population.

Who were these HA people?

The HA population lived for a long time, starting over one million years ago, and surviving until at least 300,000 years ago. It was widespread as it had to mix with the other HC population (in Africa, in accordance with the African origin of modern humans and demanded by the Out of Africa theory), and also in Eurasia, where it met the Neanderthals and admixed with them too. However it seems not to have been present in Eastern Asia because it didn't mix with Denisovans (though, later, modern humans and Denisovans mated there).

Considering the higher prevalence of the A allele outside of Africa, and the lower frequencies inside of Africa, the HA population was surely an established Eurasian lineage that partly migrated into Africa blending with HC there.

Due to the controversy around Mid Pleistocene fossils (the "muddle in the middle" conundrum), it is not an easy task to assign fossils to the HA population. Loya et al. timidly propose that "fossils attributed to H. heidelbergensis are a candidate for HA, as they possess the geographic and temporal properties suggested above." Perhaps they were a group living in the Europe, and the Levant, originating and descending from Eurasian Homo erectus, like the Homo antecessor whose remains have been found in Spain

Pending questions

If so, we can imagine that the superarchaic group from which HA and HC split is also Eurasian. This split took place long ago. Could the basal lineage be an ancestor of Homo erectus, a group that was present in Eurasia, like the Dmanisi hominins from the Caucasus?

The figure above shows that the subpopulation within HC that mixed with HA to form modern humans within Africa split from the remaining HC branch before this stem, in turn, split into Denisovans and Neanderthals. So, according to this figure, there is an "out of Africa" around 600,000 years ago, of the branch leading to Denisovans and Neanderthals, that totally removes this HC group from Africa (note that Africans do not carry Denisovan or Neanderthal alleles).

As mentioned further up, C allele is present at similar levels in Africa 10-8% as in Asian and American populations: Chinese and Peruvians 8-6%, but is much lower in Europe. Why? wouldn't admixing with Neanderthals (carrying C allele) enhance the frequency in Europe and Western Eurasia? Perhaps the predominance of a large HA population in Europe contributed to a higher frequency of A allele there, diluting the C allele frequencies.

Perhaps the most interesting part is the 35% of rare variants found in Africa, these probably derive from mutations in other archaic branches like H. naledi or Homo rhodesiensis they did not come from the HC or HA populations. They were archaics that blended into the modern Africans, and added their ancient, rare PRDM9 alleles. Another piece of evidence suggesting that diversity within Africa is due to the introgression of archaic hominins.

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

An older date for the arrival of Modern Humans in SE Asia

We have all heard about the Out of Africa theory (OOA) that proposes an initial, failed, migration of humans into the Levant, from Africa around 150,000 years ago (150 ky) that died out and left no trace in our modern lineage. Then came the second, and final migration around 50 ky ago which peopled Eurasia, Oceania, and later, America. But, as we will see in this post, this timeline is not so certain.

A paper by Friedline et al., 2023 (Early presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos) suggests that humans reached the southeastern side of Asia some 68,000 years ago.

The authors analyzed bone remains from Tam Pà Ling (TPL for short), and concluded that one of the specimens (known as TPL 6), "confirms the presence of H. sapiens by 70 ± 3 kyr, and TPL 7 extends this range to 77 ± 9 kyr, supporting an early dispersal of H. sapiens into Southeast Asia."

This adds evidence of en early presence of humans in the region. Another sites with old dates are the Sumatran one at Lida Ajer, which is around 73 ky old (Westway et al., 2017).

These dates are incompatible with the current OOA theory so how can these remains be fitted into it? The theory should be reevaluated and updated. Were these people survivors from the first "failed" migration? Did they evolve localy? Did they admix with Denisovans or archaics?

The article confirms that human beings lived at TPL for over 56,000 years! Several specimens were analyzed and they show affinities and differences with other humans from Asia.

Some highlighs regarding these people:

• "Geometric morphometric analyses of TPL 6 suggest descent from a gracile immigrant population rather than evolution from or admixture with local archaic populations."
• "The TPL fossils’ clear affinities to H. sapiens suggest that they descended from a gracile H. sapiens population from Africa, the Near East, or locally."
• "considerable shape and size variability is present at Tam Pà Ling... supporting previous observations that high levels of heterogeneity characterize Late Pleistocene modern human groups."
• "TPL 6 and potentially the younger fossils from Tam Pà Ling would represent an unsuccessful dispersal. Whether this dispersal disappeared prior to the main later dispersal or the distinct migrations experienced a period of co-habitation remains unclear with absence of ancient DNA from 50 to 10 kyr."

The analysis of the next oldest remains from the site, TPL, dated to 70 ky, shows that it has "affinities to Pleistocene archaic humans (e.g., non-H. sapiens Middle Pleistocene hominins and Neanderthals from Africa and Eurasia), plotting outside of the range of variation of early and Upper Paleolithic H. sapiens. This is mainly due to its large bi-mental breadth, an archaic feature also found in early H. sapiens and Neanderthals and associated with a wide ramus". An intriguing hint, in my opinion, of admixture with archaics in Euyrasia. The authors point out, however, that it had "a well-developed chin (mental osseum rank 537), a trademark of our species". They also compared TPL to the Chinese fossil Zhiren 3, which is around 100 ky old, and is more archaic, yet also has a prominent chin. The explanation for this feature is admixture of humans with archaics in Asia.

The authors point out the doubts surrounding the age of Zhiren, which could either be "an example of an early dispersal of H. sapiens that was unsuccessful. Alternatively, if the geological age is overestimated it could also be an example of one of the earliest inhabitants from a late dispersal."

Two other specimens, TPL1 and TPL2 are curious; they are 52-40 ky old, but have some oddities. TPL2 is small: 140–153 cm (less than 5 feet tall). TPL1, on the other hand has a roubust skull, with strong brow ridges, jutting lower jaw, which according to the authors "can be generally interpreted as a retention of ancestral morphology rather than admixture with local archaic populations". Why discard admixture with H. erectus or Denisovans? No explanation is given.

The paper concludes "TPL 6... provides direct evidence of an early, possibly unsuccessful, dispersal from Africa or the Near East towards Southeast Asia by 70 ± 3 kyr. TPL 6 is remarkably gracile implying that it descended from a gracile immigrant population and not the outcome of local evolution from, or admixture with, H. erectus or Denisovans. Our semilandmark geometric shape analyses of the other craniomandibular fossils from Tam Pà Ling (TPL 1, 2, and 3) are consistent with previous studies attributing them to H. sapiens, and their considerable shape and size variability suggests that high levels of heterogeneity characterize Late Pleistocene modern human groups."

The TPL6 is gracile, so they interpret it as lacking admixture with archaics. But, why did the other early specimens, TPL 1, 2 & 3, show such high variability, a mix of ancient, robust, and modern features? Doesn't this mosaic of old and modern features hint at admixture?

It seems likely that the first humans reached Southeast Asia much earlier than proposed by the current OOA theory. Their mosaic features hint at admixture with archaics in Asia. Possibly, humans could have originated outside of Africa after splitting from Neanderthal/Denisovans, and spread west into Africa, and east into the domains of the still extant Homo erectus.

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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 © 

Neanderthals, Denisovans, territory and admixture

Icame across an interesting map while browsing the Internet, it shows the habitats where Denisovans and Neanderthals could have lived in Eurasia. Mind you, habitats or ecological regions suitable for them, which does not necessarily mean that they lived in this whole territory. It also found overlapping areas where both populations could have met, and exchanged genes.

The paper was published in 2023: Jiaoyang Ruan et al., Climate shifts orchestrated hominin interbreeding events across Eurasia. Science 381, 699-704 (2023). DOI:10.1126/science.add4459.

Neanderthal-Denisovan habitat overlap (dotted area). Fig 2 A in Ruan et al.

Denisovans and Neanderthals coexisted in Eurasia from around 400 ky ago to 30 ky ago. They met and mixed several times. This paper looked into the climate and how it altered their habitat forcing them to move east, west, north and south as it worsened or improved during the Ice Ages.

The paper points out the different enviornments each group lived in: "Both Neanderthals and Denisovans are simulated to have lived primarily in environments characterized by annual temperature, precipitation, and NPP of ~−10° to 20°C, ~500 to 1300 mm/year, and ~200 to 800 g of carbon per square meter per year, respectively. Yet, compared to Neanderthals, Denisovans were present in hot and humid climates, which points to a comparatively wider niche space. Whereas Neanderthals were more abundant in temperate forests, Denisovans were present in both boreal forest and tundra." Denisovans lived in Southeast Asia, but fossil preservation in that area is poor, so no remains have been found, but there are genetic markers of Denisovans in the modern humans living in that region, the Phillipines and Papua New Guinea.

During the marine isotope stage (MIS) 5 around 135-105 kya, the Neanderthals spread into Northeastern and Central Europe, and further east into Southern Siberia. During the cold glacial maximum periods, they retreatedinto refugia in Southern Europe and around the north of the Black Sea. The authors suggest that these differnt habitats during the glaical and interglacial periods can explain the divergence of Neanderthal haplogroups, and their split (See my post on Western and Eastern Neanderthals Were Very Divergent).

Regarding Denisovans, the paper finds that due "to glacial cooling, Denisovan habitats vanish in Scandinavia, mildly increase in its core areas from eastern Europe to Siberia, and show massive fragmentation in Asia."

Where did they interbreed?

In a previous post, I wondered where did Denisovans and Neanderthals admix, Ruan et al. answer that question: Both species overlapped for around 400,000 years and there were hotspots like the Altai region where Denisova cave is found, occupied by Neanderthals and Denisovans (yellow star in map above). The authors find that there were six interbreeding episodes between the two groups: "the five younger events cluster during the warm MIS 5, whereas the oldest event, although with considerable dating uncertainty, occurs in the cooler MIS 6. Because some of these events occurred thousands of years earlier than the fossil dates, they could have happened in places far away from the places where the specimens were found. Our simulation of Neanderthal-Denisovan overlap suggests that these MIS 5 interbreeding events took place in central-southern Siberia... By contrast, the MIS 6 event likely happened in eastern Europe."

They note that there was "bidirectional gene flow" between both groups in Siberia. And that European Neanderthals don't have signs of admixture suggesting the Denisovans didn't mingle with them in Europe, however, they also point out that "large-sample genetic analyses have recently revealed Denisovan ancestry in modern European populations in France and in Iceland, which suggests the possibility for more widespread and prevalent interbreeding than previously thought. These results are consistent with our model simulations, which indicate the presence of suitable Denisovan habitats in Europe under optimal orbital conditions" It isn't clear if they suggest that Denisovans intereacted with modern humans in Europe, or with Neanderthals who later admixed with modern humans. Another option is that Eastern Siberian modern humans picked up their Denisovan genes there, and then moved into Europe later, carrying them with them.

I did find interesting the extended Neanderthal habitat, reaching into Central, Western, and Eastern Africa, India, Korea, Eastern China, Southern Mongolia, Myanmar, Saudi Arabia, Yemen, Morocco. Not so long ago, Neanderthals had been confined to Western Europe and the Middle East. Now we see them spread across Eurasia. This has many interesting implications.

The paper also included a map with sites where Denisovan and Neanderthal remains have been found the caption reads: "Neanderthal and Denisovan locations and their corresponding climate and biome conditions. (A) Hominin fossil, archaeological, and genetic data compiled for HSMs; candidate Denisovans (dashed circle)". I reproduced it below.

The lonely brown circle on the right side of the map, is the easternmost Neanderthal outpost in Eastern Asia (in the map above) is Jinsitai Cave, North China. We will look into it in my next post.

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

China is redefining hominin evolution

A paywalled paper published three days ago (Feb. 24, 2026) in Nature (Yang, SX., Martinón-Torres, M. & Petraglia, M. Palaeoanthropological evidence from China is changing the picture of hominin evolutionary history. Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-026-02983-w) reports on the recent research, datings and findings in China that have upended conventional beliefs about the evolution of our species.

"Abstract
Recent palaeoanthropological discoveries in China indicate that eastern Asia had an important role in the evolutionary history of the genus Homo over the past 2 million years. New taxonomic proposals have been made to re-group archaic human fossils, including those considered to be Denisovans, as Homo juluensis and Homo longi. The hypothesis that the affinities of Yunxian 2, dated to about 1 million years ago, also infer an early divergence of the Homo sapiens lineage further underscores China’s pivotal role in global evolutionary narratives. Here we explore key biological and cultural evidence emerging from the Chinese record and its evolutionary implications, raising questions about the relationships between ‘transitional’ clades and their differing adaptive capabilities. Rather than an evolutionary cul-de-sac, China now appears as a dynamic evolutionary crossroad where multiple Homo lineages may have arisen, interacted and adapted to shifting environments. The growing fossil and genetic evidence point to a diversity of populations whose demographic history and gene flow exchange helped to shape the broader mosaic of our species."

In my next two posts I will look into two very papers that report two remarkable findings: an earlier age for the first Out Of Africa event that saw Homo erectus enter Asia (or possibly, even an australopithecine) leave Africa 1.95 million years ago, and also a much older date for erectus' arrival in China. Plus two other papers mentioning sites that are possibly over 2 million years old in China.

I am not a Sinophile, and not because I dislike the Chinese people or their culture, quite the opposite. I have visited China many times before I retired as I worked for several years with companies there, visited customers, traveled the country extensively. I spent vacations there, with my wife, and I also have Chinese friends. I enjoy the food, the rich history, the diverse culture, and its natural sights. I am reluctant to embrace China because I am at odds with the system that governs that great nation. The Chinese Communist party, allied with the People's Liberation Army, is a one-party system that perpetuates a caste, an elite, living in luxury, backed by force that has, for the past 77 years destroyed and ignored the human rights (as we see them with our Western eyes) of its people, jailed opposition, suppressed free press, and supported dictators (like the ones who govern Iran, North Korea, and Russia). Then there are the territorial claims in the South China Sea (Spratly Islands), and its heavy handed attitude with South Korea, and Japan. Add to that the official silence over the origin of the Covid-19 pandemic, and how it has gradually eroded the rights agreed upon with Britain for Hong Kong ("One country, two systems", for 50 years) and is slowly but surely imposing its totalitarian views and police-state grip there. The increasingly aggressive stance with Taiwan, the Republic of China, a thriving democracy, is also troubling.

Nevertheless, I am glad that research is uncovering new findings in China. This will help us understand how our ancestors peopled Asia, America, and the interplay between the different branches of hominins.

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

Asian evolution of Hominins (2024 paper)

Today's post shares a paper on the dispersal and evolution of hominins in Eastern and Southeastern Asia. It has plenty of interesting insights on the time line and geographic dispersal of our ancient ancestors in Asia.

The paper is the following: Rikai Sawafuji, Takumi Tsutaya, Naoyuki Takahata, Mikkel Winther Pedersen, Hajime Ishida, (2024). East and Southeast Asian hominin dispersal and evolution: A review. Quaternary Science Reviews. Volume 333, 1 June 2024, 108669. https://doi.org/10.1016/j.quascirev.2024.108669.

It summarizes current knowledge, and theories, as well as suggesting some future research avenues. A very good paper!

I enjoyed the description of Homo erectus. This hominin has always fascinated me since I was a teen, when I read about it in my elder sister's highschool biology book (no internet in the 1970s). At that time there was the Peking Man, and the Java Man from Solo Rivr, and no African erectus. I also read about the Rhodesia Man, Neanderthals, Cro-Magnons, and the Australopithecines in Africa, more primitive and smaller. It seemed a complex mixture of different people. Now, over 50 years later, the panorama is still obscure!

"There are various views on the classification of H. erectus, e.g., H. erectus from Africa as a separate species called H. ergaster (Tattersall et al., 2015). In this review, we use the broader definition of H. erectus (H. erectus sensu lato) and consider the African H. erectus as part of the same taxon.
H. erectus is currently recognized as the first hominin to spread out of Africa and is thought to have migrated eastward across Eurasia and then southward into Southeast Asia. The fossil records are concentrated in Europe, China, and Java, with little data available for the intermediate areas.
Some of the earliest probable fossils of H. erectus are the ∼2.04 Ma cranium found at Drimolen, South Africa (Herries et al., 2020) and ∼2 Ma mandible at Melka Kunture, Ethiopia (Mussi et al., 2023), while the earliest generally accepted evidence of their presence out of Africa was discovered at Dmanisi, Georgia, and dated to ∼1.8 Ma (Ferring et al., 2011; Lordkipanidze et al., 2013).
In China, recent findings have suggested an earlier hominin presence although the evidence is scarce and primarily based on stone tools found at Shangchen, dated to ∼2.1 Ma (Zhu et al., 2018), and on hominin teeth dated between 2.42–1.8 Ma at Jianshi-Longgu Cave (Li et al., 2017a). These findings, which might predate the Dmanisi fossils, suggest the intriguing possibility that either H. erectus or another hominin arrived in China earlier than the time of Dmanisi (Cartmill and Smith, 2022). However, due to the scarcity of comprehensive fossil records, these conclusions must be approached with caution, as definitive identification of these early hominins in China remains challenging.
Fossils and lithics of likely H. erectus found in China include ∼1.66 Ma stone tools from Majuangou III in the Nihewan Basin (Zhu et al., 2004) and 1.7–1.6 Ma stone tools from Shangshazui (Ao et al., 2013), and a ∼1.63 Ma cranium from Lantian-Gongwangling, near Shang Chen (Zhu et al., 2015). Two ∼1.7 Ma incisors have also been found in Yuanmou, South China (Zhu et al., 2008), though their age determination remains questioned (Bae, 2010). Taken together with the fossil and lithic evidence, the conservative age of the emergence of H. erectus in China is about 1.7–1.6 Ma."

The interesting part is the suggestion of hominin presence in China ~2.4 to 2.1 Ma, older than the earliest South African fossils (~2.04 Ma), also that they were not Homo erectus but "...another hominin arrived in China earlier than ... Dmanisi." This could imply the presence of Homo habilis or even Australopithecines in Asia.

The following image shows how the different lineages of hominins coexisted in Asia during the past 2 million years.

Chronology of the genus Homo in EA/SEA.. Source

The image below shows the distribution of hominins in Eastern and Southeastern Asia.

The Story and Timeline of Hominins in Asia

The paper gives a brilliant description of the dispersal of hominins in East Asia and Southeast Asia.

"As more and more pieces are continuously added to our understanding of hominins, their geographical distribution and persistence, new questions arise, and details about how the different hominins dispersed and why they went extinct still remain unclear. From current fossil records and genetic evidence, one plausible and coherent scenario of hominin dispersal is the following: H. erectus emerged in Africa and expanded into the Eurasian continent around 2 Ma, later occupying Europe, East Asia (China) and Southeast Asia (Java).
Subsequently, the common ancestor of H. sapiens, Neanderthals and Denisovans split into two groups: one was in Africa (later leading to H. sapiens) and the other settled around the Middle East at some point. The latter interbred with a super-archaic hominin group (possibly H. erectus) around 700–600 ka.
The Eurasian hominin group then split into two groups. One settled in the West (Europe and Western Asia) leading to Neanderthals, while the other settled in Asia leading to Denisovans. Denisovans interbred with H. erectus in Eurasia, occupying their niche. At some point, Denisovans also expanded into East and Southeast Asia, where the groups diverged into different subgroups (D0, D1, D2, D3, the details are in the chapter of Denisovans). Meanwhile, H. erectus may have become extinct around 400 ka in East Asia and 100 ka in Southeast Asia. Denisovans reached the Altai region, eventually meeting and interbreeding with Neanderthals several times around 140–80 ka. Meanwhile, some H. sapiens left Africa before 200 ka. This initial migration was unsuccessful, but interbreeding with Neanderthals at this time left traces in their genome (Peyrégne et al., 2023). There were several subsequent out-of-Africa events, which might have reached Asia, but the populations that led to our ancestors left Africa around 55 ka. They interbred with Neanderthals in West Asia and with Denisovans in EA/SEA. Note that we consider the super-archaic hominin contributing to the Denisovan genome to be H. erectus. While there is a possibility that hominins other than H. erectus and Denisovans migrated into Asia or evolved from H. erectus, this is not considered here due to the lack of evidence."

The suggestion that (no date given for this event) the ancestor of modern humans, Neanderthals and Denisovans moved out of Africa, settled in the Middle East and some 700-600 ya mating there with H. erectus is very interesting!

The further admixing of Denisovans with erectus as they moved across Eurasia is not often mentioned. And the final comment that "... there is a possibility that hominins other than H. erectus... migrated into Asia or evolved from H. erectus," is worth exploring as there is no evidence to prove it happened. But, it is possible and likely.

The paper also has some interesting comments on the four lineages of Denisovans (with a neat map), and their history:

Denisovans

"The common ancestor of Denisovans and Neanderthals which occupied around the Middle East interbred with a super-archaic hominin, and afterwards the Denisovan ancestors diverged from the Neanderthal ancestral group and moved into Asia. Some of them spread towards Papua and settled in Island Southeast Asia (D1). Another group remained in South or Southeast Asia (D2), and from there, another group moved further north into East Asia (D0, D3). During the early phase of this migration, they encountered a super-archaic hominin population and interbred. The D0 group settled somewhere in East Asia. The D3 group reached the Altai in Siberia (D3), where they met and interbred with Neanderthals."

The section dedicated to small-sized hominins Homo floresiensis and Homo luzonensis is great, I learned that the latter's "finger and toe bones are elongated and curved, a feature similar to australopithecines". Nevertheless, evidence suggests both "tiny" hominins may descend from H. erectus.

Ancient Mariners

It is remarkable that these two groups of people (and a third responsible for stone tools found in Sulawesi) crossed open sea, settled in islands, and lived there in isolation until their demise when modern humans reachd the area. Navigating abilities is something seldom discussed in any paper, including this one, which only says "Although it is unclear how each hominin crossed the sea, they succeeded intentionally or accidently"

It is evident that even archaic forms of hominins like erectus crossed open sea. Could they have reached America? (See my post about their navigating skills, and this post on Neanderthal "sailors").

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

Archaic admixture in humans that is neither Denisovan or Neanderthal

We all carry some genetic material inherited from our ancestors after they mated with Denisovans and Neanderthals (except maybe Africans since those two hominins were Eurasian and didn't live in Africa, but received it later as Asians and Europeans moved into Asia and mingled with the locals).

Interestingly, there is evidence showing that there may be other older genetic material admixed when our ancient ancestors exchanged body fluids with some unknown hominins. This post looks into the evidence of such "ghost" ancestors.

A paper published in Science back in 2018 (Serena Tucci et al., Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science 361, 511-516(2018). doi:10.1126/science.aar8486) explored the pygmies in Flores Island (not the Hobbit, but the short statured humans).

The authors investigated archaic admixture:

"We searched for signatures of admixture with an unknown archaic hominin source by analyzing significant S* sequences that did not match the Neanderthal or Denisovan genomes (hereafter called “unknown” sequences). We found no evidence that unknown sequences in Flores are enriched for older or more divergent lineages, as would be expected if they contained lineages inherited from a more deeply divergent hominin group, such as H. floresiensis or H. erectus. Although it is difficult to exclude very low levels of admixture from such groups given current methodological limitations, our data are inconsistent with substantial levels of ancestry from a deeply divergent hominin lineage."

So, they didn't find proof of ancient unknown hominin admixture, but it could taken place and been present in tiny amounts below the threshold of detection.

A second paper published in 2019, in Nature (Mondal, M., Bertranpetit, J. & Lao, O. Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat Commun 10, 246 (2019). https://doi.org/10.1038/s41467-018-08089-7) used artificial intelligence (AI) to investigate admixture with hominins. They found proof that it took place:

"In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage."

The paper calls all ancient hominins Eurasian Extinct Hominins or EEH, it includes Denisovans, Neanderthals and another yet unknown hominin that they named "Xe". It also provided a timeline for these three events:

"...the introgression of Neanderthals with AMH [anatomically modern humans] out of Africa was 1.3% ... and occurred 69 Kya (CI from 56 Kya to 88 Kya; assuming a generation time of 29 years), whereas the split between African and OOA populations took place 121 Kya (CI from 78 Kya to 167 Kya); (ii) the Denisovan introgression to Oceanian populations was 1.6% (CI from 0.4% to 2.5%) and took place 43 Kya (CI from 29 Kya to 50 Kya); finally, (iii) the estimated amount of introgression in the AMH ancestor of current Asian populations by the extinct archaic population Xe was 2.6% (CI from 0.7% to 4.6%) at 51 Kya (CI from 45 Kya to 58 Kya)."

Who were these Xe hominins?

The authors state that Xe is old, "Xe appeared 304 Kya (CI from 211 Kya to 375 Kya) from an admixture event of Denisovans and Neanderthals that would have occurred only 14 Kya after the divergence of Denisovans and Neanderthals (314 Kya; CI from 300 Kya to 343 Kya)."

They nest it in the group of hominins that comprises Denisovans and Neanderthals: "we have an overwhelming support for the existence of a third extinct branch of the Neanderthal–Denisovan clade"

Three admixtures

A third paper also from 2019 (J.C. Teixeira, & A. Cooper, Using hominin introgression to trace modern human dispersals, Proc. Natl. Acad. Sci. U.S.A. 116 (31) 15327-15332, https://doi.org/10.1073/pnas.1904824116) reported that modern humans admixed with "at least 3 different hominin groups ... in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line.

All humans "outside of Africa" admixed with Neanderthals after leaving that continent: "The first of these events occurred between a small AMH population and Neandertals somewhere in western Eurasia around 55 to 50 thousand years before present (ka), and created a genomic signal of about 2% introgressed Neandertal DNA that is now found in non-African populations."

Then came two separate admixing episodes with Denisovans belonging to different populations of Denisovans:

"there were at least 2 pulses of hominin “Denisovan-like” introgression from very distinct groups, one of which was quite distant from the known Altai Denisovan genome. South Asian and Australo-Papuan populations only carry signals from this 'distant Denisovan group,' while East Asians appear to have both the 'distant' and standard Altai-type Denisovan ancestry components."

They mention a study that reported that this 'distant Denisovan group' "is actually so genetically divergent that it is equidistant to both Neandertal and Denisovans, and probably represents an entirely new hominin group.". They call these people extinct hominin 1 (EH1).

The paper suggests that this admixture (EH1 and AMH) took place somewhere in South Asia before humans split into different groups heading into South Asia, the Andaman Islands, East Asia, ISEA (Island South East Asia) and Oceania. The authors tentatively place this event in northern India.

Then they cite the 2018 paper mentioned further up (pigmies in Flores) as follows: "[it] reported an enigmatic unknown genomic signature whose source appears to be as divergent from modern-day humans as Neandertals and Denisovans (although the study did not highlight the finding). The unknown genomic component was detected exclusively in Flores, raising the possibility of an additional introgression event with a further extinct hominin (EH2), and implies it must also have crossed Wallace’s Line."

The Wallace Line is a sea barrier that splits Australia, New Guinea and Melanesia from South East Asia and ISEA, it was proposed by Alfred Russel Wallace (1823–1913). He was a British biologist and naturalist who (few know this fact) came up with the theory of evolution on his own. He wrote to Charles Darwin in 1858 (the most famous naturalist of his time) with a summary of his discovery and Darwin who had been working on the theory of natural selection since his journey on HMS Beagle in 1834 but was afraid of publishing his theory. Darwin disclosed it to Wallace, and both presented their theory to the Linnean Society in 1858. Shortly after Darwin published his "On the origin of Species by Means of Natural Selection".

The Wallace Line separates species of birds, reptiles, and mammals that can't cross deep and wide swaths of sea (i.e. marsupials in Australia, and Komodo dragons in Komodo). It was crossed by hominins who could navigate across the sea like the Hobbit of Flores Island, and modern humans.

The paper conclues that "as AMHs first moved through the area, they interbred with EH1 in South Asia, Denisovans in ISEA and the Philippines, and potentially EH2 in Flores. Strikingly, of these hominin groups, only Denisovans are currently known, and even in this case, the evidence stems solely from genomics. The region was clearly occupied by several hominin groups, which probably lived in relative isolation from one another for hundreds of thousands of years, and appear to have contributed unique patterns of ancestry to current populations."

Two OOA Events and introgression of superarchaics

A fourth paper published in Nature in 2021 (Yuan, K., Ni, X., Liu, C. et al. Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nat Commun 12, 6232 (2021). https://doi.org/10.1038/s41467-021-26503-5) also looked into this matter. It proposed a two-wave Out-Of-Africa migration with different introgressions.

" The results in this study could not be explained by a single-wave “Out-of-Africa” model; in particular, the independent Denisovan-like introgression in Papuans occurred much earlier (64.0–61.9 kya) than both admixtures of Neanderthal-like DNA in the Papuan populations (first wave 61.7–53.0 kya, second wave 35.2–28.9 kya).
It was also before the first-wave Neanderthal-like introgression in East Asia (56.9–49.1 kya) and that in South Asia (58.2–53.2 kya).
We proposed a two-wave “Out-of-Africa” model to reconstruct the archaic–modern admixture history. The first wave out of Africa happened around 120 kya. We estimated that the first Denisovan-like introgression event occurred 118.8–94.0 kya, which indicated there might have been an archaic–modern admixture that happened around 120–80 kya in the Middle East. Skhul and Qafzeh hominins in Israel, which died around 120–80 kya, exhibit a mix of traits found in archaic and AMHs.
Then, the first wave of modern human ancestors migrated to Asia and Oceania. Madjedbebe, the oldest known site showing the presence of humans in Australia, suggests humans have been in these areas since at least 60–50 kya, which is much closer to the time of Denisovan-like introgression in Oceania (64.0–61.9 kya).
The second wave of modern humans went out from Africa around 60 kya to the Middle East. During that period, a branch of Neanderthals who lived in Amud Cave, Levant (60–50 kya) might have encountered our ancestors. This also corresponded to the first wave of Neanderthal-like introgression into Eurasian genomes (58.8–49.1 kya). The second-wave modern humans moved worldwide through the Middle East and may have encountered Altai Neanderthals, European Neanderthals, Altai Denisovan, or some other undiscovered archaic hominins in South Asia."

The last sentence leaves the door open to admixture with "some other undiscovered archaic hominins". They also find it "plausible that the ancestors of Neanderthals and Denisovans interbred with some superarchaics... The potential admixture history of archaic and African references used in the analysis could affect the power of detecting introgression sequences and result in underestimation of the admixture proportion."

We have posted about archaic introgressions within Africa (here, here, here, and here) several times, it adds diversity to the Africans making them appear more "basal" than they really are; this distorts inferences made by using their genomes.

Below is a map from this paper showing the two OOA (Out-Of-Africa) migrations. The caption from the paper is the following: "Migration pathways of H. sapiens are supported by archeological evidence. Translucent red and blue represent possible ranges for contact between archaic and modern humans. The waves, admixture proportions, and dates inferred in our study are labeled in boxes in white. kya thousand years ago."

Fig 5. in Yuan, K., Ni, X., Liu, C. et al., (2025). Source

Indeed the history of mankind is complex, and the simple Out-Of-Africa event with modern humans who replaced all previous hominins, erasing them into oblivion is not correct. We had sex with them time and time again, both ways, then natural selection acted, preserving the valuable traits, discarding the unhealthy ones. Asia, has a rich past, which only now we are starting to uncover.

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

The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

• Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes"). This is what one would expect.
• Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
• They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
• And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

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

The most recent information on Admixture with archaic hominins

A paper (Using hominin introgression to trace modern human dispersals, Joao C. Teixeira and Alan Cooper, PNAS first published July 12, 2019 https://doi.org/10.1073/pnas.1904824116 - behind a pay wall), reports admixture with several groups of hominins other than Denisovans and Neanderthals during the dispersal of modern humans around the globe.

The abstract says the following:

"bstract The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic."

Apparently the following admixture events took place between our unchaste ancestors and the other humans they met during their travels:

1. Neanderthals: in the Middle East (?) 50 - 55 kya
2. Unknown human similar to Neanderthals and Denisovans. More recent than 50 kya. In Northern India. Modern Punjabi and Bengal populations have some DNA from this admixture event.
3. Humans that headed into Central and Eastern Asia: Admixture with Denisovans.
4. Humans heading south into the Malaysian Peninsula: mixed with a relative of the Denisovans which had split from those living in Central Asia some 280 kya. This introgression took place in Malaysia or Borneo.
5. This group split: those heading into the Philippines mixed with yet another group of Denisovans and the hunter-gatherers living there nowadays carry this genetic imprint.
6. The group heading south towards Australia met some humans which were not Homo erectus, or Neaderthal or Denisovan, they were not the Flores "Hobbit" either. The genetic signals of this archaic group has been found int he short-statured people living on Flores nowadays.

Nobody seems to have admixed with the other known species of that region: the Homo luzonensis (from the Philippines) and the Flores Island hobbits.

The following images are from this paper:

 

 

These unknown hominins are indeed a very interesting find! We will have to await for further studies to learn more about them.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall ©