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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