March 2026 has seen plenty of research papers published regarding hominins! This post will look into another introgression paper, that found not one, but two separate admixture events with archaics. One took place within Africa before Modern Humans set out on their Out of Africa migration, the second one affected people in Melanesia and Papua New Guinea, Oceanians.
This is the article: Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, Priya Moorja, (2026). Recovering signatures of archaic introgression using ancestral recombination graphs, nioRxiv 2026.03.03.709416; doi: https://doi.org/10.64898/2026.03.03.709416
Introgression Inside of Africa
They detected a first admixture with a ghost (unknown population) that added genes from a "super-archaic lineage" into the ancestors of all humans (Africans and Non-Africans), because it took place before the Out-Of-Africa event, in Africa.
"The ghost lineage, with a divergence time similar to Neanderthals, could plausibly correspond to Middle Pleistocene Homo groups or African Homo heidelbergensis populations that directly admixed with modern human ancestors before the OOA dispersal. For the super-archaic lineage, one potential candidate —compatible with the split time of approximately 1.8 Mya— is Homo erectus, as suggested by earlier studies."
The authors admit that it could have been one, single event, or there could have been more: "additional episodes of gene flow among structured African populations may have occurred but remain difficult to resolve with present data."
They noticed that the introgressed alleles could have been modified due to the action of natural selection perhaps because they provided adaptative benefits.
The paper says that their software (TRACE) found the following archaic ancestry in contemporary people from different regions, where N is Neanderthal, and D, Denisovan:
- Europeans. N: 0.99%; D: 0.03%.
- East Asians. N: 0.97%; D: 0.10%.
- South East Asians. N: 0.78%; D: 0.10%.
- Oceanians. N: 0.73%; D: 0.66%.
But, apart from Neanderthal and Denisovan alleles they also detected an introgression from a "ghost" source distantly related to Neanderthals and Denisovans: "Ghost segments exhibit deep divergence in marginal trees and show nearly identical genetic affinity to both sequenced Neanderthal and Denisovan genomes, indicating that they originated from an unsequenced lineage equally related to both archaic groups."
It was found in all modern humans at frequencies that ranged from 0.49 to 1.1%. This includes Sub-Saharan Africans.
Africans have more unique segments
The interesting part is that although non-Africans and Africans share alleles of the ghost introgression, "...both East and West Africans harbor a greater diversity of unique ghost segments." The authors don't attribute this enrichment and divergence to a recent or ancient admixture with archaics after the OOA event. Instead, they attribute it to the bottleneck caused by the OOA that led to the loss of these variants, now only found in East and West Africans.
Dates
The calculated "coalescence time" between human and ghost genes is, on average, 830,000 years (95% CI: 0.61–1.27 Mya).
This data leads the team to conclude that "an unknown archaic population, which diverged over 500,000 years ago, introgressed into the common ancestors of all modern humans prior to the OOA migration, resulting in similar patterns of ghost ancestry in non-Africans and Africans."
Denisovans injected super-archaic ancestry in Oceanians
Then they found a second introgression!
Previous studies have suggested that Denisovans may have mated with a super-archaic hominin (possibly Homo erectus), and as Papuans, Melanesians, and Southeast Asians have the highest level of Denisovan ancestry (they admixed when humans reached Sundaland, and the Philippines), the researchers wondered if the admixing led to a flow of super-archaic genes from Denisovans to humans.
They looked for super-archaic alleles contained within the Denisovan segments found in modern Oceanians. Their analysis revealed the 0.73% of Neanderthal and 0.66% of Denisovan ancestry mentioned further up, and also, a 0.33% introgression of super-archaic "ghost" ancestry.
"we infer that the super-archaic segments embedded within Denisovan ancestry tracts contributed almost 0.3% of the total detected Denisovan ancestry in Oceanians. This estimate constitutes a very conservative lower bound on the true fraction of super-archaic ancestry, as our analysis is restricted to Denisovan-introgressed regions in modern humans, requires segments longer than 20 kbp, and excludes loci where the sequenced Denisovan carries super-archaic ancestry. Using the marginal trees in SINGER, we estimate the coalescence time between these super-archaic segments and modern human lineages to be approximately 1.77 Mya (95% CI: 1.13–3.98 Mya), consistent with earlier reports."
The age given above points at Homo erectus, who was present in Eurasia 1.77 Mya.
I prepared the map above to show what the paper says: An archaic ghost population in Africa (red circle) admixes with Modern Humans prior to the OOA (blue circle). These introgressed modern humans go into Eurasia (losing some of the archaic alleles due to founder effects and bottlenecks, and also spread across Africa (violet arrows) where the archaic signal remains stronger, one group heads towards SE Asia, Sunda and Melanesia, where Denisovans (green) live. These Denisovans had previously admixed with a Super-Archaic (yellow) somewhere in Asia (dashed yellow line). (2) is the Denisovan-Oceanian admixture, and (1) is the admixture within Africa. The red population is linked distantly to Denisovans and Neanderthals.
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