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 © 

Did Humans admix with Neanderthals? Paper in Nature says NO

Research published in Nature on Dec. 13, 2024 suggests, as its title says, that some models used by scientsts may lead to assume the existence of false introgressions. The word spurious used in the title means "based on false reasoning or information that is not true, and therefore not to be trusted". The paper can be found online: Tournebize, R., Chikhi, L. Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events. Nat Ecol Evol 9, 225–236 (2025). https://doi.org/10.1038/s41559-024-02591-6🔒

A preprint free version is available on line in Biorxiv 🔓

The paper's Abstract is quoted below:

"Abstract
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation."

Notice how the authors criticise the models used ("mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure [but, ignoring] population structure can lead to the inference of spurious demographic events ").

The authors assumed that there were two population groups. One named metapopulation M_A tht generated a second one, M_B between 9 Million years ago and 500 ky. This created two populations (Bipartite structure) within Africa. Then, some individuals from the M_B group left to colonize Europe and Asia splitting some 650 ky ago from the remaining populations that stayed in Africa. Those who went to Eurasia became the metapopulation M_N, originating the Neanderthals or Hn population. The African metapopulations M_A and M_B evolved into Homo sapiens (Hs). Later Hs left Africa and colonized Eurasia forming an M_C metapopulation there. The paper states that "the new Hs Eurasian metapopulation M_C with the African Hs metapopulation M_B (itself connected to the Hs metapopulation M_A). Note however that none of the Hs metapopulations (M_A, M_B and M_C) ever exchanged gene flow with the Hn metapopulation (M_N). In brief, our model does not allow admixture between Hs and Hn."

Therefore this study suggests that instead of actual mating between Homo sapiens and Neanderthals, as a means by which genetic material was shared by both groups, the common fragments of genetic material may have originated in ancestral populations that split and carried them with them through time with no need for admixtwure.

Below is Fig. 1 from the paper, and the original caption is the following: "Simplifed representation of the 1D structured model considered in this study. Time flows from top (past) to bottom (present), with an initial metapopulation M_A consisting of nA (=10) demes exchanging migrants with their neighbours. At some point in the past, the rightmost deme of M_A founds a new metapopulation M_B of nB (=10) demes, with which it will continue exchanging migrants till the present. Later, the rightmost deme of M_B founds the metapopulation M_N of nN (=10) demes which will become Neanderthals. The MN metapopulation will never exchange migrants with any other deme from the other metapopulations. Closer towards the present, the rightmost deme of M_B founds M_C which corresponds to the expansion of H. sapiens towards Eurasia. White feet represent the sampled populations (not the specific demes) for respective sampling times. The location of the sampled demes (within the corresponding metapopulations) is a random variable... Fifty individuals are sampled in M_A and in M_C to represent modern-day YRI and CEU samples respectively. For the Neanderthals (M_N), one individual is sampled at 50 kya."

Fig. 1 in the Biorxiv preprint. Source

Comments

Interesting indeed! Could these admixture events be mere artifacts of these black-box statistical models used by scholars? I have posted some critical comments on these models in the past (See: Some thoughts about the tools used in genetic admixture analysis, Biases in Genetic Models that are generally overlooked). I favor admixture, yet, I also consider that the software used by scientists may not accurately reflect the real population dynamics of our ancestors.

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

Archaic humans admixed with modern humans in Africa

News published on the Internet these last few days mentioned that scientists had discovered large strands of ancient DNA (i.e. Neanderthal and other even older archaic hominin) lurking in the "Dark Heart" of the human genome. I was intrigued after reading these laymen articles.

But the news is old, the original publication dates back to July 30, 2018, almost 11 months ago ( Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA, Sasha A. Langley, Karen Miga, Gary Karpen, Charles H. Langley, doi: https://doi.org/10.1101/351569).

Their paper is interesting; they looked into "centromeres", specialized portions of DNA located more or less in the middle of chromosomes, that bind or link the two arms that text books typically show as a chromosome: one is the original chromosome, the other is its copy, they are called "sister chromatids" and form an "X" shaped structure. The centromer is where each part meets the other, in the "waist" of the "X".

Centromers serve to anchor fibers that pull the arms apart again when the cells divide, so each cell has one and only one chromosome.

The paper by Langley et al, reports "large-scale haplotypes (cenhaps) in humans" spanning the centromer region with "surprisingly deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans".

They found that "Despite being fairly common among Africans today, a distinctly diverged chrX cenhap (cenhap 1, highlighted in purple, Fig. 1b,c) is rare outside of Africa. Examination of the haplotypic clustering (...) yields a parallel relationship among the three major cenhaps and an estimated Time of the Most Recent Common Ancestor (TMRCA) of ≈700 KYA (Fig. 1d) for this most diverged example.".

What is interesting is that they wonder about this very diverged cenhap: "It is unclear if this cenhap represents an introgression from a distinct archaic hominin in Africa or a surviving ancient lineage within the population that gave rise to AMHs". The ancient hominin admixing with modern humans is something that we have mentioned in other posts as a reason for the "greater diversity" of humans in Africa: they got a dose of very ancient DNA which increased their diversity, but this took place recently.

The paper states that it is old, but (as we highlighted in bold) it is consistent with a recent admixture:

"The most diverged, basal clade on chr12 (Fig. 2c, indicated in brown) is common in Africa, but, like the most diverged chrX cenhap, is not represented among the descendants of the out-ofAfrica migrations (26). The great depth of the lineage of this cenhap is further supported by comparison to homologous archaic sequences (21,22,23).
Consistent with the hypothesis that this branch split off before that of Neanderthals/Denisovans, members of this cenhap share fewer matches with derived SNPs on the Neanderthal and Denisovan lineages (DM) and exhibit strikingly more ancestral non-matches (AN) than other chr12 cenhaps (see Fig. 2b).
This putatively archaic chr12 cenhap represents a large and obvious example of the genome-wide introgressions into African populations inferred from model-based analyses of the distributions of sequence divergence (16,17).
(...) This bolsters the conclusion that the basal African cenhap represents a distinct, older and likely introgressed archaic lineage.
Unfortunately, there are too few coding bases in this region to support confident estimation of the TMRCAs of these ancient chr12 cenhaps. Based on the numbers of SNPs underlying the cenhaps, this basal cenhap is twice as diverged as the apparent introgressed Neanderthal cenhap, placing the TMRCA at ~1.1 MYA, assuming the Neanderthal TMRCA was 575KYA(23). While there is no direct evidence of recent introgression, the large genomic scale of this most diverged cenhap (relative to apparent exchanges in other cenhaps) is consistent with recent admixture with an extinct archaic in Africa, although, again, suppression of crossing over is an alternative explanation."

The finding is interesting, and it supports the idea of an enhanced modern African diversity due to the archaic admixture event with modern Africans.

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