A weakly structured stem for human origins in Africa:
While it is now broadly accepted that Homo sapiens originated within Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent. Progress is hampered by a paucity of fossil and genomic data, as well as variability in prior divergence time estimates. Here we use linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference to discriminate among such models. We infer detailed demographic models for populations across Africa, including representatives from eastern and western groups, as well as 44 newly whole-genome sequenced individuals from the Nama (Khoe-San). Despite the complexity of African population history, contemporary population structure dates back to Marine Isotope Stage (MIS) 5. The earliest population divergence among contemporary populations occurs 120-135ka, between the Khoe-San and other groups. Prior to the divergence of contemporary African groups, we infer long-lasting structure between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years (i.e. a weakly structured stem). We find that weakly structured stem models provide more likely explanations of polymorphism that had previously been attributed to contributions from archaic hominins in Africa. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be morphologically similar. Despite genetic similarity between these populations, an inferred 1–4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains variation in previous divergence time estimates and argue that studying a suite of models is key to robust inferences about deep history.
Privately some people have been grumbling about models of deep structure between very differentiated populations for a while. They claim this is just a bias in the model specifications because it’s so easy to think of gene flow happening in periodic pulse admixtures. But the reality is that Africa doesn’t seem to have had the same barriers as across Eurasia or between Eurasia and Africa, so how are these deep lineages persisting?
The preprint here shows that the data can fit a different model, one that they find more biologically and paleoanthropologically more reasonable. The discussion has an “out of Africa with total replacement” flavor, but here it is within Africa:
Multiple studies have shown a correspondence between phenotypic differentiation, usually assessed with measurements of the cranium, and genetic differentiation among human populations and between humans and Neanderthals 36,37,38 (see also Section 5.3). This correspondence allows predictions of our model to be related to the fossil record. The fossil record of Africa is sparse during the time period of the stems, but of the available fossils, some are very similar in morphology to contemporary humans (e.g., from Omo Kibish, Ethiopia 39,40), others are similar in some morphological features but not others (e.g., from Jebel Irhoud, Morocco 1,41), and others are very different in morphology (e.g., from Dinaledi, South Africa 42,43). If, as our model predicts, the genetic differences between the stems were comparable to those among contemporary human populations, the most morphologically divergent fossils are unlikely to represent branches that contributed appreciably to contemporary human ancestries.
This result would recenter Omo Kibish from what I can tell.
“We find that weakly structured stem models provide more likely explanations of polymorphism that had previously been attributed to contributions from archaic hominins in Africa. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be morphologically similar.”
So does Africa lack ghost populations of archaic hominins after all? That is a replicated finding that would be quite notable to abandon, especially in light of super-archaic Y-DNA in Western Africa.
@ohwilleke
The A00 Y-lineage in Cameroon (west central Africa), if that’s what your referring to, would not be super archaic (and it’s fairly rare even there). It could be modern, early modern/sapiens (or at most transitional/proto-sapiens) A00 dates to around 250,000 BC-300,000 BC, which is within the time of homo sapiens, e.g.: Jebel Irhoud (Morocco) is from ca 300kya, the Florisbad skull (South Africa) is from 259kya, the Guomde remains (Kenya – discussed, I believe, in Stringer 2016) are from ca. 270-300kya, and the Omo Kibbish remains (Ethiopia) were recently redated to around 233kya (https://www.nature.com/articles/s41586-021-04275-8)
Correction: *”what you’re referring to…”
Minor edit:
Stringer 2016 describes the Guomde femur as seemingly modern and compares the partial skull found at Guomde to the modern/sapiens/AMH remains Omo I and II
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920294/). But a more recent study (which also places the development of sapiens in Africa around 260-350kya) dates Guomde to about 270-300kya (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736881/)
Clarifying edit: “Stringer 2016 describes the Guomde femur….and partial skull (etc.)…but dates it vaguely to only 180 kya or earlier. But it was a more recent study that dates Guomde to about 270-300kya.”
Off topic but related to previous post: https://www.science.org/doi/10.1126/science.abk1534 – “Bronze and Iron Age population movements underlie Xinjiang population history“
The bit related to previous topic is as described by the press release (https://phys.org/news/2022-03-year-population-history-xinjiang-brought.html): Phenotypic analysis of several remains, the first reported for ancient Xinjiang, gave depth to the genetic results. The majority of individuals investigated had dark brown to black hair and brown eye color throughout Bronze Age, Iron Age, and HE. Corresponding with the appearance of Andronovo Steppe ancestry, a small proportion of the Iron Age individuals are marked by blond hair, blue eyes and lighter skin tone in the west and north of Xinjiang. Two Early Bronze Age Tarim Basin mummies in east Xinjiang were found likely to have had dark brown to black hair and darker skin, despite their archeologically-identified “western” features, and a more recent third mummy from the Late Bronze Age was likely to have had a more intermediate skin tone.
The early samples include contributions from four ancestries; Tarim Basin mummies who are almost purely North Eurasian (this seems not found in high proportion of unadmixed form in any new samples), the early Steppe (Yamnaya/Afanasievo), Chemurchek with ancestry from the Bactria-Margiana complex and an Inner East Asian group.
Blonde hair, blue eyes and lighter skin enter in with the Andronovo (the frequency looks decent from the supplement). The Tarim Mummies – who were previously sequenced for Zhang’s paper (samples L6103, L5209 and XHM135) – were checked with Hirisplex and are apparently dark skinned like WHG, which fits with them being from a remarkably isolated group that probably didn’t get the major variants, perhaps like Western WHG.
So it’s more consistent with derived light pigmentation post 16kya than with the meme of “super blonde/blue eyed/etc North Eurasians”. (I think I mentioned before that the one female Tarim Mummy I could find info on who fit in with the ANE cluster seemed to be fairly short, comparable in height to EEF and WHG.). The blonde(r) blue(r)-eyed folk seem like they’re the ones derived from the CWC complex, with 30%ish EEF ancestry and 70% Yamnaya (or probably 40% if we normalize to the pre-Yamnaya steppe).
Paper is paywalled but the supplements are open.
Not to disrupt from the Africa deep structure topic with too much ever-present Yamnaya chatter.
@Matt
Since you posted this, and also not meaning to distract from the African paper, but what’s interesting here is how the ANE mummies appear relatively depigmented to what you would expect based on the Hirisplex results above.
If individuals such as the Xiaohe princess are really ANE-derived, perhaps they had other variants related to lighter skin color or their appearance was a result of the mummification process.
I definitively do not believe in the blond etc North Eurasians but I don’t believe they would be as dark as WHG considering the pigmentation of related groups.
PS. East Asian ancestry was present in low amounts in these ANE, this possibly was the cause of their apparent depigmentation if that is indeed a real thing.
@James, yes, without getting too into it because this is not the thread, if the mummies surviving skin colour is representative (I don’t know!), that’s an interesting check. Perhaps this group is just too remote for the predictions to work. Or like you say maybe their minor East Asian geneflow gave them some variant we still don’t know about.