Answers to questions we don’t need to answer about human origins

For many years I have been arguing that there isn’t a specific genetic variant associated with “modern humanity.” If most selection is on standing variation in the form of soft sweeps, then what distinguishes our “modern” lineage from older hominin lineages which flourished 200,000 years ago is more a matter of degree than kind. The reason that our lineage, which we label “modern humans,” has ancestry from various “archaic” lineages is that they were recognizable as human too. And, their genetic differences were not that great from us.

If Denisovans and Neanderthals were discovered in a remote part of the Altai today, they would be given human rights, not put in a zoo.

Of course, how we understand the emergence of what we term modern humans, the mode and tempo of the population substructure that we see across our species, has evolved over the past generation. It is no surprise to anyone who reads this weblog that ancient DNA helped reshape our understanding. But, it has to be said that some of the proponents of multi-regionalism in the late 20th-century were not entirely wrong in the process, even if they were very wrong in the nature of the phenomenon over the last 50,000 years.

The old debate between the multi-regionalists and proponents of “out of Africa” was framed in part as one between continuity and rupture. As it happens, the “out of Africa” model got something big right insofar as 50,000 years ago there was a massive expansion from a small founding population which contributes to the overwhelming majority of the ancestry of all living hominins. A subset of anatomically modern humans.

There is an important nuance here in that outside of Africa the vast majority of ancestry derives from a small founding population. Within Africa, the ancestry is more complex. Some groups, like the San Bushmen of the Kalahari, have strands of ancestry which diverged from other human lineages on the order of 200,000 years ago. Other Sub-Saharan African groups are closer to non-Africans, possibly due to admixture (gene flow between Africa and non-Africa in either direction) or ancient population structure (i.e., the pro-non-African group was more closely related to some proto-African groups than others).

A punctuated demographic origin for non-African humanity makes some sense. But it is less clear it makes sense within Africa, especially before the Holocene, when agricultural and pastoral populations expanded across most of the continent, marginalizing the hunter-gatherer populations. This is why “African multi-regionalism” is a thing. With very little ancient DNA to go on and researchers unsure about the inferences one can make into deep time from modern variation, genetics can’t easily adjudicate the “original homeland.” And now, neither can archaeology.

The remaining African hunter-gatherers, in particular, the San Bushmen, exhibit evidence in their DNA that they did not undergo a significant period of being within a very small breeding population, as can be seen in the case of all non-Africans, and to a lesser extent in agricultural Africans. This is not to say that 150,000 years ago most of the people alive on earth were San Bushmen. Not only were there Neanderthals and Denisovans, but there were many other African populations. Unlike the ancestors of most modern humans the ancestors of the San Bushmen did not experience a near-extinction event during the Pleistocene, nor did they undergo a transition to agriculture, which favored a few “early adopters” at the expanse of most humans.

Such a complex landscape and model has many lacunae, which ancient DNA is attempting to fill. There are obvious technical limitations (Africa is hot, and it isn’t as if > 100,000-year-old remains are copious even in cold Eurasia).

But let’s go forward and backward in time for a moment. In 2006 a paper was published, Genetic evidence for complex speciation of humans and chimpanzees, which argued that the emergence of our human (hominin) lineage was subject to periods of reciprocal gene flow with the ancestors of chimpanzees. Though this thesis is still somewhat controversial, that is due to the arguments around the limitations of the resolution of statistical genetic power, not the idea of “complex speciation.” Second, we now know that the genetic characteristics which are clear and evident in modern samples as “European” have a relatively late Holocene origin, threaded together from very distinct ancestral populations.

What both of these phenomena have in common is admixture, reticulation, and an “edge” in the abstract, rather than a “tree.”

The “out of Africa” model ascendent in public imagination, and to a lesser extent among human evolutionary biologists (yes, I am aware that there were savvy geneticists who were always skeptical of some details), presented a simple model of a diversifying tree of modern humans expanding across the world. In contrast, multi-regionalists posited deep regional continuities, with the human species tied together through gene flow. It turns out that multi-regionalism was wrong in suggesting that as a null hypothesis we should assume continuity. Turnover is common. Ubiquitous even. But, “out of Africa” made us dismiss the importance of admixture.

The admixture with deeply diverged lineages, such as Neanderthals and Denisovans, did happen. But arguably even more important has been admixture between more closely related lineages. This is how West Africans, Europeans, West Asians, and South Asians came about, through the admixture of lineages which have diverged only in the last 20,000 to 200,000 years.

All this is to set the stage for the reaction to this paper in Nature, Human origins in a southern African palaeo-wetland and first migrations:

Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1,2,3,4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1’2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi–Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240–165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast–southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to sustained effective population size (L0k), whereas wet–dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1’2), as supported by extensive south-coastal archaeological evidence8,9,10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.

Ed Yong reports on some of the negative comments, as well as the defenses from the authors themselves. Twitter pretty much exploded.

In light of what I have stated above, a paper like this answers questions that are not really asked because they are not seen as relevant. The question of the “original home” of “modern humans” within Africa is not totally a sensical query in light of what we know now (i.e., the likely polycentric character of anatomically modern humans within Africa). What this paper likely discovered, with the deeply diverged branches of mtDNA haplogroup L0, is to confirm that the San Bushmen of southern Africa have a unique history in comparison to other modern humans. It’s not that they are particularly ancient. They aren’t. It’s that they did not undergo the demographic trauma of the Pleistocene that left its mark in the genomes of non-Africans, and they are not predominantly descended from a small group of founding populations which underwent rapid expansion due to adoption of agriculture and pastoralism.

I believe that this paper would have benefited greatly from being a preprint first because the feedback would have been immediate. The reviewers that Nature selected also clearly were either not skeptical or aware of the literature in human evolutionary genetics because there would have been some immediate comments that they should have made (I suppose the editor could have overruled them). Because of the high visibility in Nature and the claims, you have pieces like this on the BBC now: Origin of modern humans ‘traced to Botswana’.

At this point I think most researchers in this field would say that such an assertion is “not even wrong.”


10 thoughts on “Answers to questions we don’t need to answer about human origins

  1. Outstanding piece. I’m recommending it as a ‘must read’ to anyone I know who is interested in modern human origins.

  2. Shouldn’t project on to others, Walter. I knew in primary school that Africa is a huge continent.

    What is worth studying and thinking about are paleo-climate and environments.

  3. Where did these reviewers come from? Even a casual reader of this blog would detect the flaws in this paper.

  4. This proves once more that peer Review is oftentimes rather like a bouncer or censorship it isnt that old anyway. But when real scientific criticism and input would be needed, all to often it doesnt appear in peer review.

    Its common sense that where an old isolated lineage survived is not necessarily the place of origin of all. It can be, but its no conclusive proof.

  5. Question: Why are they restricting this to Africa?

    Answer: Because this is a religious dogma.

    Way back when the Communists and the Rising Tide of Color fixated on Africa in order to humble the white man and Christianity in one mighty blow. Unfortunately for them, it isn’t true. If there is a homeland for modern humans (ie not bushmen and pygmies) it is the Middle East which acted as a hub of tricontinental gene flow, put together a winning package and then proceeded to sweep through much of the world, picking up presumably but not certainly helpful bits of DNA from others along the way. Only the farthest, most hostile, and most remote areas have delayed this total replacement for the time being (ie the jungles of Africa).

    There is no magical barrier at the Red Sea or even Gibraltar for that matter. If globetrotting erectus could do it, there is no way “modern” humans would be bottled up in Africa from 200,000 to 70,000 ya. Modernity didn’t begin until 75+-25 kya. But that would be racist, no?

    The religious impulse is masquerading as science in this supposedly secular age. This wont end well.

  6. Well articulated, Afterthought.
    Bonehead ideas like mitochondrial Eve and out of Africa just look silly now.
    Can any of these so-called anthropology types even locate for us here the points in the L0 mtDNA where it differes from the standard ref sequence?

  7. Great stuff. Well articulated, Afterthought.
    Bonehead ideas like mitochondrial Eve and out of Africa just look silly now.
    Can any of these so-called anthropology types even locate for us here the points in the L0 mtDNA where it differes from the standard ref sequence?


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