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