There is a hominin named Homo naledi whose remains have been found in a cave in South Africa, dated to around 300,000 years ago (300 ky). It is very primitive and its small skull size and archaic shape is not shared by modern humans or our ancestors like Homo erectus, Neanderthals, Denisovans, and us, humans. Yet, their age places them in Africa at the time our species is said to have appeared there, 300 ky ago! We are supposed to have co-existed with naledi in South Africa before bursting out on our Out of Africa migration.
Those who have studied naledi argue that it has contributed genes to our species and is much more advanced than its primitive appearance may lead us to think. These scholars argue that naledi created rock art, and that it buried its dead (a recent paper published in Cell on June 24th, 2026, reports that all twenty specimens from the cave are female, so they suggest selective gender burial there, it also mentions a protein found in teeth, which I will discuss further down).
Other scientists are not so conviced, like Chris Stringer, who argues that they are not members of the homo group: "I use human as equivalent to genus Homo, while acknowledging that future phylogenetic or proteomics research may show that things like rudolfensis, habilis, floresiensis, luzonensis and naledi don’t really belong in the genus…"
A post on X, formerly Twitter, by @HighlyCitedX (June 28, 2026) raised the question of how could both modern humans and archaic naledi share the same territory, and provides a thought provoking answer: "John Hawks raised this problem before: How could Naledi co-exist with large brained hominins for a million years? Most likely they were not co-existing because there were no large brained hominins in East Africa until late. https://bbc.com/news/science-environment-39842975."
The BBC link is a 2017 article which includes comments by John Hawks, one of the leading researchers of the Naledi site in Africa, I will quote it at length below:
"The fact that Homo naledi was alive at the same time and in the same region of Africa as early representatives of Homo sapiens gives us an insight into the huge diversity of different human forms in existence during the Pleistocene.
"Here in southern Africa, in this time range, you have the Florisbad skull, which may be an ancestor or close relative of modern humans; you've got the Kabwe skull, which is some kind of archaic human and possibly quite divergent; you've got evidence from modern people's genomes that archaic lineages have been contributing to modern populations and may have existed until quite recently," said Prof Hawks.
"You have this very primitive form of Homo [naledi] that has survived alongside these other species for a million years or more. It is amazing the diversity that we are now seeing that we had missed before."
As to how H. naledi held on to its distinctive characteristics while living cheek-by-jowl with other human species, Prof Hawks said: "It's hard to say it was geographic isolation because there's no boundary - no barrier. It's the same landscape from here to Tanzania; we're in one continuous savannah, woodland-type habitat.
He added that the human-sized teeth probably reflected a diet like that of modern humans. In addition, H. naledi had limb proportions just like ours and there is no apparent reason why it could not have used stone tools.
"It doesn't look like they're in a different ecological niche. That's weird; it's a problem. This is not a situation where we can point to them and say: 'They co-existed because they're using resources differently'," Prof Hawks told BBC News."
Hawks tries to explain the pacific overlap and co-existence as a consequence of exploiting different ecological niches. He also notes that there was a vast savannah from South Africa into Tanzania, all the way to the south of Ethiopia. No geographic barriers, only different niches. I tend to agree with @HighlyCitedX, there was no overlap because there were no humans (or close ancestors) in Africa at that time.
The odd non-homo amino acid in the Naledi teeth
Interestingly, John Hawks reports that an ancient hominin known as Paranthropus robustus, that lived in South Africa 2.3 to 0.9 Million years ago, a member of the australopithecine group, and therefore not a homo, had a variant of an amino acid in its teeth, that was quite unique.
The amino acid in question, forms part of a protein known as COL17A1, that together with enamelin play a critical role in the formation and development of teeth. The COL17A1 variant found among Paranthropus is the original, or ancestral version. Modern humans, Neanderthals, and Denisovans carry a mutation, the later, derived variant. So it shows that we, and our homo relatives are in a different lineage when compared to the Paranthropus. The Homo naledi aligns with the primitive non-homo group because it carries the ancestral variant. Hawks writes: "This confirms earlier work showing that naledi is likely an outgroup to modern humans, Neanderthals, and Denisovans". But, I don't know why, tries to argue that naledi and Paranthropus are not closely related: "Because this is an ancestral variant, shared with other primates, it does not support a close relationship between P. robustus and H. naledi." In fact, all primates sampled (except one lemur species) carry the ancestral variant found in naledi and P. robustus, African apes from which our most distant ancestors came from also carry the archaic variant. But somewhere down the line, when the homo genus appeared, they carried a mutated variant that we share with Denisovans and Neanderthals, but not with the primitive naledi or the non-homo Paranthropus.
Hawks adds two interesting facts about the ancestral variant: "So far there is no reporting on this variant in H. antecessor or H. erectus data. One interesting possibility for Homo naledi is that the species may have contributed genes to modern humans. The ancestral COL17A1 variant has not yet been seen in the genomes of living people, which at least suggests that this part of the genome did not have a naledi origin." (See the study on the CO17A1 in Madupe et al., 2017 who mention that Homo erectus and Homo antecessor were not sampled for this amino acid.
The paper published in Cell by Madupe, Hawks, et al., on June 24, 2026 still supports a homo affiliation for naldedi: "... the archaic COL17A1 P635 variant we observe in 5 H. naledi individuals is derived in Denisovans, Neanderthals, and modern humans, and it has not been covered in H. erectus, from either Dmanisi (Georgia) or China, and Homo antecessor.17,29 Interestingly, though, it has been observed in two P. robustus specimens, namely SK835 and SK14132. Determining which variant is present in this and other informative positions, in other extinct hominin species, such as H. erectus and Australopithecus africanus, will help clarify the phylogenetic position of H. naledi."
I have posted about the possibility that Homo habilis is not a homo (more likely an australopithecine), and related to Homo naledi. Today's post adds more evidence to this possibility.
It is intriguing though, to imagine an evolution of homo genus in Eurasia, with australopiths evolving in Africa, (see my post about this), and a much later entry "into Africa" "Out of Asia" of more advanced hominins 300 kya, modern humans.
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