Planet Earth

Of beasts and men

Gene ExpressionBy Razib KhanSep 6, 2011 1:23 AM

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"There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown."

- Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn't that much I can add at this point. A lot of the guts were pushed into the supplements, which aren't on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean? First, let's stipulate that this is a model which infers the past from the variation we have on hand. In this way it is qualitatively a different method than that used to ascertain the Neandertal or Denisovan admixture events, which derived from comparisons of moderns with the concrete genome of these ancient lineages. The authors in the PNAS paper observe that the likelihood of ever replicating the non-African results within Africa is low because of the nature of fossil preservation. The likely region of admixture, central Africa, is simply not conducive to the preservation of fossils, let alone genetic material. Now, I have stated before that I am cautious of results from computational models because they regularly reported no admixture as well, further confirming "Out of Africa" with 100% replacement. The change here is that our expectations have been shifted by the possibility of admixture outside of Africa. By testing the power of their models on the Eurasian findings they firmed up their credibility in the absence of ancient DNA. These authors used 61 non-coding genomic regions to reach their conclusions. One presumes that these findings should become more compelling once researchers start performing full genome analyses. If not, then they may be spurious. With that out of the way, let's review the results and what they mean on the assumption that they're valid. The PNAS paper supports a model where a subset of descendants of anatomically modern humans (AMH), and an unnamed archaic group, population X, hybridized relatively recently. Within the last ~40,000 years or so. It seems that this post-dates the "Out of Africa" migration. This should not be shocking, and hopefully will dispel the strange notion that Africa remained static after the emergence of AMH (which leads to some reconstructions of early Eurasians as looking like modern Africans!).

It also hints at the possibility that contemporary Pygmies and Bushmen are not the ur-humans, the oldest of old, but rather novel morphs which derive from a recent hybridization event

(just like non-Africans). This brings us to why Pygmies and especially Bushmen were assumed to be ur-humans, the best exemplars of early AMH:

they're basal to other human populations, AMH fossils are found in eastern and southern Africa at a very early date, and they are the most genetically diverse.

If this admixture event holds up my intuition tells me that both of these findings are in part derived from this component of the ancestry of these populations. The separation between population X and AMH occured ~700,000 years ago. If I recall my human evolution chronology correctly this is about two hundred thousand years greater than the divergence between AMH and the Neanderthal-Denisovan clade! Depending on the population genetics of the X group, they may significantly reshape a phylogenetic tree which does not incorporate the correct model of divergence and admixture (reticulation). I assumed that the Mbuti would be special even before seeing the paper because physical anthropologists have long observed that there's a greater phenotypic difference between them and their Bantu neighbors than the Biaka and their Bantu neighbors. Playing around with public data sets (HGDP) it's also clear that the Mbuti are more distinctive than the Biaka from other Africans. Additionally, to my great surprise there is a "hunter-gatherer clade," where the Pygmies and the Khoisan seem to form a cluster against other African populations. It seems implausible to me that these patterns are due purely to admixture from population X. But I think it must play a role. It may also explain the finding from some full genome analyses that West Africans are closer to non-Africans than they are to Pygmies or Khoisan. This may be a function of their lack of population X (and/or, possible back-migration from Eurasia). At this point I feel a little strange referring to "population X." It was nice that "X-woman" eventually become the Denisovans. What should we call these potential additions to the human family album? Greg Cochran suggested to me the term 'Mangani', by analogy with the use of 'Hobbit' for H. floresiensis. Don't remember who the Mangani were? Here's Wikipedia on the Mangani:

As described by Burroughs, Mangani are organized in tribal bands ruled by dominant males, or "kings," which subsist by foraging for fruit, grubs, insects, and sometimes meat, in localized territories. Tribes are generally identified by the names of their kings. Burroughs portrays the Mangani (and indeed most jungle animals) as susceptible to occasional bouts of madness in which they will lash out violently and unpredictably at other living creatures in their vicinity. Tarzan is raised in the tribe of Kerchak, based in the coastal jungle of equatorial Africa, as shown in Tarzan of the Apes and Jungle Tales of Tarzan. As an adult he comes to lead this tribe; later, he becomes accepted in other tribes of Mangani, such as the tribe of Molak in The Beasts of Tarzan. Tarzan continued to associate occasionally with his original tribe until cast out in Tarzan and the Golden Lion, as the result of a Tarzan impersonator having murdered one of its members.

From what I recall in the films and television shows the Mangani are portrayed as rather more bestial, and ape-like, than the description above. It also made the story of Tarzan extremely implausible, more in the vein of Romulus and Remus or Mowgli. But Edgar Rice Burroughs original conception was clearly less fantastic, as the Mangani were intelligent, if profoundly different. If modern humans are the 'third chimpanzee,' the Mangani may have been another chimp tribe (H. floresiensis, Neandertals, and Denisovans would also be distinct tribes in this model).

At this point some of you might be alarmed. When evidence for Neandertal admixture surfaced in 2010 message boards had discussion threads with titles such as 'White People Aren't Human'. Whether you find this sort of joke amusing or not, it's at least marginally acceptable to make light of scientific findings to poke fun at what is the dominant ethnic group in the developed world (e.g., see also 'white people are mutants'). Substitute in black people, and the valence is entirely different. But these findings don't actually imply this. Many African populations may have the highest quantum of AMH ancestry of all human groups. Rather, this new archaic element is found in Pygmies and Khoisan in particular. The ethnography is rather rich in documenting the dehumanization of these two populations at the hands of their Bantu neighbors. If you have tracked the conflict in the Democratic Republic of Congo you are also probably aware that the Pygmies in particular are targeted in the most grotesque fashion because they are perceived to be less than human.

But don't these results suggest that Pygmies are less than human?

I think on a deep level we may have to start putting this question into the "not even answerable" category. Recently I had an exchange with John Farrell in regards to how Christians, and in particular Catholics, are handling modifications to the "Out of Africa" model. I'm not expert on this obviously, but from what I can gather it seems that some Christian thinkers have taken succor in the romantic narrative of "mitochondrial Eve" and "Y chromosomal Adam" as scientific vindication of at least the general outlines of Genesis. For Roman Catholics, who otherwise can accept evolution without much qualification, the existence of these two individuals is necessary for ensoulment and the fall. Apparently some Catholics are discomfited by the opening toward polygenism implicit in the new model of admixture with archaics. Since I don't give much though to the religious implications of science, not being religious, I view the whole discussion with curiosity more than concern. But I think the Christian arguments about the implications of science still have something to teach secular people, because I believe we need to reconceptualize what it means to be human. The "Out of Africa" model, which is classical monogenesis on steroids, does not perturb our intuitions about ideal types and kinds. Rather, it reinforces a Platonic model of what it means to be human, as humans are all kith and kin, descendants in totality and universally from a small group of Africans who flourished ~100,000 years ago. This idea is so pervasive that it even pops up in the series finales of science fiction shows. I now believe that those of us without religious presuppositions should abandon more vigorously this model of humanity.* In a deep sense we already do, in that many of us accept without much controversy that we're simply the product of material processes. There is nothing which makes us ineffably human. This is why many of us do not consider abortion the murder of a person. At some point the fetus becomes human in all the ways we understand to be human. The zygote's putative descent from two individuals created in the image of God is not sufficient for us to grant it status as a person. We don't accept the reality of this descent in the first place. I don't think we should be too terrified of this leap. Many of us have already abandoned a deep belief in the idea of 'free will,' religious and secular, and yet life goes on. For all practical purposes of decency all human populations present today are basically equivalent as humans. Whatever results we may uncover via science aren't going to change that, because our intuitions about right or wrong don't derive from our understanding of the latest science.

Tansey Coetzee

But let's end on a fun note, because science is fun. To the left is an image of Miss South Africa 2007, Tansey Coetzee. Ms. Coetzee has an Indian mother, and a father who is Cape Coloured

. So let's assess her ancestry. Her mother is Indian, so she is half-Indian. But what about her father? The genetics seems to indicate that the Afrikaans speaking Coloured population has ancestry from Western Europe, India, the Khoisan, the Bantu, and from Southeast Asia. From the Khoisan there will be a dollop of archaic admixture from this new population X. From the Eurasian ancestors there will be Neandertal. The Southeast Asian ancestry of the Cape Colony generally derives from what is today Indonesia (then a Dutch colony). Therefore it is not impossible that Ms. Coetzee has some Melanesian ancestry, and therefore some Denisovan! Yes, the last is a stretch, but work with me. It seems then that Ms. Coetzee may have fractions of ancestry not only from diverse modern populations, but slivers from all the known "other humans!" Above I appealed to your intuition in simply discarding the model whereby humanity is contingent on pure descent from AMH. Individuals such as Ms. Coetzee, and Desmond Tutu, Nelson Mandela, and most of the readers of this weblog, are a refutation of the Platonic model of a human essence made concrete. I know I'm human despite my Neandertal blood. You know in your heart I'm right, so let us accept the finding of science with as much equanimity as we can muster. Our understanding of the details of the human past does not alter our humanity. Just because God is dead does not mean that everything is permissible. * I generally hold to the position that artificial general intelligence, if it ever arises, should be given the same due consideration, rights, and respect, as organic intelligence. For all practical purposes, they should be treated as we would treat humans. So this isn't a big leap for me personally.

Image credit: Jose Rosengurtt

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