This article supports the highly plausible theory that all humans share pre-Out of Africa admixture with "ghost" archaic hominin populations, but the methodology used is fairly new and untested.
Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations.
We introduce TRACE, a reference- and outgroup-free approach that uses features of ancestral recombination graphs to identify archaic ancestry. Simulations show TRACE has high precision and low false discovery rates.
Applied to 1000 Genomes, TRACE recovers known Neanderthal and Denisovan introgression and uncovers ghost admixture from uncharacterized hominins in both Africans and non-Africans. Ghost ancestry persists in Neanderthal and Denisovan ancestry deserts, challenging their interpretation as Homo sapiens–specific regions. In Oceanians, TRACE finds deep lineages are enriched in Denisovan compared to Neanderthal regions, supporting super-archaic introgression. TRACE enables mapping archaic introgression without archaic genomes.
Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, and Priya Moorjani, "Recovering signatures of archaic hominin introgression using ancestral recombination graphs" Science (July 30, 2026) (open access) DOI: 10.1126/science.aef887
10 comments:
H. heidelbergensis Kabwe is obvious candidate
OT Jomon fat burning https://phys.org/news/2026-08-ancient-jomon-dna-reveals-hidden.html
@DDeden Thanks for the pointer.
@neo That is certainly one possibility. Given poor preservation in tropical areas it is also possible that the ghost is an undescribed archaic hominin for which we have no remains.
The Kabwe skull is Estimated to be roughly 300,000 years old, it is traditionally classified as Homo heidelbergensis is too young to be a direct ancestor
Anthropologist Proposes Folding Australopithecus and Paranthropus into Genus Homo
“Recent discoveries are eroding the usefulness and accuracy of current classification, including the current species in our own genus Homo, but also in Australopithecus and Paranthropus, who all lived within the past 5 million years,” Dr. Towle said.
“Discoveries and advances in evolutionary and genetic analysis make this an ideal time to reconsider whether our traditional taxonomy still accurately reflects human evolution.”
“These groups do not necessarily represent distinct evolutionary branches, or clades, and differences in behavior and ecology once used to distinguish them have also become increasingly difficult to maintain.”
“I propose expanding Homo to include these other groups to provide a more accurate and stable way to represent the complex evolutionary relationships revealed by the growing fossil record.”
Dr. Towle argues that the current three-genus system taught in textbooks and museums no longer reflects what the fossil evidence actually shows.
He contends that Australopithecus in particular functions as a taxonomic wastebasket, a grouping repeatedly shown by phylogenetic studies to be non-monophyletic, meaning it doesn’t consist of a single ancestor and all its descendants, the standard modern biology uses to define a valid group.
He also traces how traits once considered defining features of Homo, such as brain size or tool use, have been undermined by discoveries like Homo naledi and Homo floresiensis, both small-brained species that nonetheless get grouped with humans.
https://www.sci.news/othersciences/anthropology/pan-homo-genus-15003.html
My thoughts: gorillas and chimps were never Homo but hominins. Extant gorillas are the only survivors of A robustus & P boisei (Western forest refuge from Homo spp., later developed knucklewalking ), extant chimps-bonobos are the only survivors of A afarensis (Lucy & Selam had laryngeal airsacs unlike all fossil Homo) (Central forest refuge from Homo spp., later independently developed knucklewalking), Homo maintained upright lateral arboreal bipedalism (cf pairbonded gibbons) during terrestrial transition, modified arboreal nightly ape bowl nest into transportable tandem forage basket/cradle carried between pairbonded mates (so minor sexual dimorphism) on foraging treks, inverted at night into shared quiet dome shell thus hair loss + no advantage in enlarged airsacs + obligate orthograde posture/locomotion with each having a free hand for tool/weapon at all times, very altricial infant, yet able toddler perched on father's shoulders as lookout.
@neo re "Anthropologist Proposes Folding Australopithecus and Paranthropus into Genus Homo"
Ultimately this is just the classic splitter v. lumper debate. In academia, there are incentives to favor the splitters, as discovering a new genus is more prestigious than discovering a new species, and discovering a new species is more prestigious than discovering a new subspecies.
I favor treating Neanderthals as a species rather than a subspecies, because there is strongly suggestive evidence that Haldane's law, which applies to separate species in the same genus or family that can produce cross-species children (like mules), seems to apply to them (cross-species children are predominantly female).
Clearly, all of them are part of the great ape family, Hominidae. Clearly to me, they are closer to modern humans than gorillas, placing them in the "tribe" Hominini, that includes humans, australopithecus and paranthropus, and chimpanzees. Australopithecus and paranthropus probably not in the subtribe "Panina" that includes chimpanzees and not humans, and are instead in the subtribe level clade "Hominina", which is the conventional and current classification.
I don't think we have enough data (and we may never have it) to confidentially say that australopithecus and paranthropus are species of Homo rather than separate genus, and the definition of the difference between species that share a genus vis-a-vis species that share a subtribe is more art than science.
Given the lack of any clear and definitive evidence to go one way or the other, I'd favor the status quo simply due to back compatibility with prior scholarship, but I don't think that it is a very important debate in hominin evolution.
@Ddeden "Extant gorillas are the only survivors of A robustus & P boisei (Western forest refuge from Homo spp., later developed knucklewalking ), extant chimps-bonobos are the only survivors of A afarensis (Lucy & Selam had laryngeal airsacs unlike all fossil Homo) (Central forest refuge from Homo spp., later independently developed knucklewalking), Homo maintained upright lateral arboreal bipedalism (cf pairbonded gibbons)" Possible but speculative.
Speculative but parsimonious. Afaik, tails are very rare in humans, but we know they exist; not a single case of a human with bilateral laryngeal airsacs has ever been known, while 6 & 7 digit hands are comparatively common. Lucy displays pre-knucklewalking chimp morphology and continues the upright bipedal stance/locomotion seen in lesser apes.
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