How non-Africans came to be….

Most of the history of the human species is in Africa, which is why I wrote a Substack trying to outline what I think are various alternative models about what’s happened. But the last 100,000 years has been defined by the migration out of Africa for many. The above chart is a simplified representation of what I think is a good model for what happened. For a more complex and thorough treatment, check out Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.

Also, new PNAS paper, The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa:

The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.

This “stand still” out of Africa has been identified for a few decades now in the genomic data. I’m not sure people necessarily believe it…but it’s clear that non-Africans are very homogeneous and closely related to each other compared to various diverse African groups. That indicates a long period of isolation and homogeneity. The “Basal Eurasians” were part of this.

But earlier “modern” or “para-stem” populations may not have been. The Altai Neanderthal samples that date to 100,000 years ago have some “modern” ancestry. How? The best assumption right now is that these were very early migrants out of the African ur-heimat that mixed with Neanderthals in their eastern range, likely coming up through East Asia? Possibly mixed with Denisovans?

The point here is that some elements of the “weakly structured model” probably applies to Eurasia too. Africa is a big continent and good habitat for humans. Pulses out of this continent probably happened all the time. It’s just that the last Eurasian expansion about 50,000 years ago erased everything earlier (or absorbed it). Though I still think if we get ancient DNA from Laos it may turn out that 1% or something of the ancestry of Andamanese may date to a population that diverged 85,000 years ago from the main out-of-Africa group, before their isolation in the Near East (since the divergence is not that great, I don’t think the models would have good power to detect this proportion).

Early Maghrebis are Eurasian back-migration


A new ancient DNA paper from Northwest Africa: Northwest African Neolithic initiated by migrants from Iberia and Levant:

In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1,2,3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

Basically, the ancestors of the Berbers seem to be a mix of indigenous people whose ancestors were Eurasians who arrived during the Last Glacial Maximum, Early European Farmers (Anatolian) and Levantine farmers/pastoralists, in that order of timing, but reverse order of contribution. To me it is interesting that there is no Sub-Saharan African ancestry in the earliest populations, indicating that the Sahara was really not habitable for humans for much of the Ice Age.

Moderate population structure out-of-Africa

A few weeks ago I wrote on my Substack about a new model of African H. sapiens genesis that assumes recurrent gene flow between deeply divergent populations within the continent. In contrast, the out-of-Africa movement was defined by a rapid expansion from a small ancestral founding group that diversified over the last 50,000 years. But there is a twist to this: the out-of-Africa event was presaged by many earlier expansions outward.. The Neandersovans were one clear example, about 600,000 years ago. But there were others. We know this because Neanderthal Y and mtDNA seems to be more closely related to modern humans than the whole genome, and the Altai Neanderthal shows clear evidence of modern human admixture as early as 100,000 years ago, far earlier than the primary out-of-Africa event 50,000 years ago.

Laos cave fossils prompt rethink of human migration map:

Archaeologists have uncovered two new bone fragments in a cave in northern Laos, suggesting that Homo sapiens wandered southeast Asia up to 86,000 years ago. The findings, published this week in Nature Communications1, indicate that humans migrated through the area earlier than previously thought.

Over more than a decade, excavations in the Tam Pà Ling cave have uncovered seven bone fragments sandwiched between layers of clay. Laura Shackelford, an anthropologist at the University of Illinois Urbana–Champaign, and her colleagues have regularly had to hike through sticky tropical heat to reach the mountain-top cave.

After digging 7 metres down, excavations have finally hit bedrock, and the team has been able to reconstruct a complete chronology of the cave, says Shackelford. Sediment and bones unearthed in the cave show that modern humans have inhabited the mountainous region for at least 68,000 years, and passed through even earlier.

These archaeological findings seem to solidify the idea of modern (African) humans in Southeast Asia. They don’t seem to have left an imprint, but that’s OK, the first modern Europeans didn’t either.

Ancient Africa may not have had as much deep structure as we think

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.

Recent human origins in 2021

I wrote three long pieces for my Substack:

  1. Yo mama’s mama’s mama’s mama… etc.
  2. Our African origins: the more we understand, the less we know ($).
  3. What happens in Denisova Cave stays in Denisova Cave… until now ($).

I’m thinking about where I’m going to go in relation to this topic, and i think it may be in the direction of Eurasian back-migration to African and what we know now.

Also, I’m at nearly 60 podcasts after more than a year of the Substack. Please remember to rate it positively.

Through northern Arabia

Multiple hominin dispersals into Southwest Asia over the past 400,000 years:

We have identified at least five pulses of human dispersal into northern Arabia, each associated with a phase of decreased aridity. The differences in material culture between these phases—with two phases of Acheulean technology and then three distinct forms of Middle Palaeolithic—suggests that diverse hominin populations, and probably even species, were expanding into the region at different times…

From the supplements:

Little is known of the Pleistocene fauna of southern and eastern Arabia, but the repeatedly distinctive, localised, character of material culture suggests that crossing the Red Sea at the Bab al Mandeb was not a primarily dispersal route and that instead populations filtered through northern Arabia. In northern Arabia the growing fossil record suggests repeated connections to Africa across a contiguous grassland zone through the southern Levant which formed during repeated humid episodes (discussed in SI 10). To that we can add significant aspects of material culture which we have reported in this paper. The absence of Acheulo-Yabrudian assemblages in northern Arabia, and the southern Levant, suggests that the Late Acheulean in this area relates more to Africa than to areas to the north. Likewise, with the early Middle Palaeolithic at KAM-4 (Assemblage C of the Northwest Lake) both technological features (such as the methods of Levallois surface preparation, see SI 7) and quantitative characteristics in terms of PCA of Levallois flake shape situate the assemblage between the Levantine Early Middle Palaeolithic the early Middle Stone Age in East Africa (SI 9)…

…The possible MIS 3 presence of Neanderthals in Arabia may suggest that they expanded further south than previously thought, and highlights that there is currently little clarity on where the main pulse of admixture between Homo sapiens and Neanderthals occurred, beyond probably Southwest Asia broadly.

As a closing note, we emphasise that as well as our results being consistent with repeated pulses of hominin dispersal out of Africa into Southwest Asia, the possibility of movement in the reverse direction should be kept in mind. Given factors such as current uncertainty on the background to the earliest known Homo sapiens in Africae, and discussions on the possible
involvement of a hominin closely related to Homo antecessor as an ancestor of our species, currently only known from Eurasia, as a precursor to Homo sapiens, building reliable records for the later Quaternary in Southwest Asia is not only important for understanding ‘out of Africa’ dispersals, but also for ‘into Africa’ dispersals.

Was H. luzonensis Denisovan?

Philippine Ayta possess the highest level of Denisovan ancestry in the world:

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

T: The Story of Testosterone, the Hormone that Dominates and Divides Us

Carole Hooven has a new book, T: The Story of Testosterone, the Hormone that Dominates and Divides Us. I’ll be honest and admit I was only vaguely aware of the book until yesterday when a social media controversy erupted over her “transphobic comments” on Fox & Friends. You can watch the clip yourself, and see that she’s not transphobic at all.

I assume though the accusation will be enough to open some Title IX complaints. Unless her colleagues step up I assume she’ll be hounded out by the bureaucracy, though I hope I’m wrong.

Hooven has been all over the media, just see what she’s RTed on her Twitter account. She makes it pretty clear she’s not going to back down on the scientific questions and answers. Which is how it should be, but that sort of stance is far less common than groveling obeisance before the new red guards.

More and more evidence for ‘complex demography’ in archaic ancestry

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes:

We note that our estimated TMRCA to Neanderthal within Neanderthal-introgressed segments in all non-African populations is recent, ~74 ka ago, and implies therefore that little genetic drift separates admixed humans from sequenced Neanderthals in these segments. This recent TMRCA suggests that the majority of Neanderthal ancestry in modern humans originated from Neanderthal gene flow into the ancestors of all non-Africans before populations diversified. It also suggests that at least one of the Neanderthal genomes used here is closely related to the Neanderthal(s) involved in this admixture event. The slightly elevated Neanderthal ancestry that others have described in Central and East Asian populations also appears to have originated in this first pulse, as Central and East Asian Neanderthal haplotypes are mostly shared with other, geographically distant populations. This observation favors the hypothesis that the increased Neanderthal ancestry in these populations relative to others is due to weaker selection against alleles that may be mildly deleterious (32), made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events (22). Our evidence of many small-scale, population-specific admixture events, however, together with a simulation study that found a single-pulse admixture model followed by drift unable to explain the discrepancies in admixture proportions in European and Asian genomes (49), hints at a complex history of admixture throughout Eurasia not fully captured by either of these two hypotheses.

I don’t think that it’s weaker selection in East Asians. I think it’s complex demography.

Complex admixture of “Denisovans” in Southeast Asia and Sahul


A new paper, Genomic insights into population history and biological adaptation in Oceania, is worth reading. Read it along with Multiple migrations to the Philippines during the last 50,000 years and Multiple Deeply Divergent Denisovan Ancestries in Papuans.

I’m going to sidestep the new inference that Austronesian expansion may predate the movement out of Taiwan. I’ll revisit. Rather, let’s reflect on the Denisovans. There is strong evidence of more than one admixture from this lineage into modern humans. And, multiple papers now support a model where various Southeast Asian groups have several different pulses. Finally, the “Denisovans” have really deep divergence. Way deeper than anything in modern humans.  Some of them split right after the west-east Eurasian hominin split.

All this is curious in light of small hominins in the Philippines and Flores, as well as late ‘erectus.’ I think it is likely that some of the Denisovan lineages have ‘super-archaic’ admixture, while some of the gene flow is mediated by highly admixed moderns with high Denisovan load.