“Who We Are: #7 Africa.

The African story is complicated, and getting steadily more so. But some of the big picture – involving relatively recent events – is fairly simple.

The biggest African language family is Niger-Kordofanian, which was probably spoken by most people in west Africa at least 5,000 years ago – a mark of an early expansion. One subgroup near the border between Nigeria and Cameroons seems to have had a set of crops that was less specialized for high-rainfall areas like west Africa – probably including some cereals like millet, as well as wet-country yams and bananas. This allowed the Bantus to expand out into dryer areas of Africa, which at the time were occupied by various hunter-gatherer groups. You could think of the Bantu as a bit like marcher lords, but at first more advantaged by their crops than their military technology. From genomics, it looks as if the Bantu first moved south and only later expanded into East Africa. They didn’t have iron-working in the beginning, but picked it up perhaps 500 to 1,000 years later. Iron-working led to better tools and weapons, which made displacement of hunter-gatherers even easier.

A few of the hunter-gatherer peoples are still around, but most have been replaced. The replacement was in some cases near-total, while other encounters sometimes led to substantial admixture between the Bantu and the previous hunter-gatherers. For example the Xhosa, a major tribe in South Africa, have about 25% Bushman ancestry. Look at Mandela. A similar group, one that only persists as an admixture component, account for about 20% of the ancestry in Mozambique. On the other hand, there’s no sign of hunter-gather admixture in some populations, like Malawi.

The remaining hunter-gatherers also have had varying amounts of Bantu admixture. The Ju/’hoansi, the population that Henry Harpending studied, have the least (about 10%). Pygmies also have substantial amounts of Bantu ancestry. Interestingly, the more Bantu ancestry, the taller the Pygmy (on average).

The Bantu expansion was the largest in Africa, but there were others. The Nilotic people, tall cattle-herders, expanded into East Africa, leaving tribes like the Masai and Tutsi.

Farmers from the Middle East settled Egypt and North Africa a long time ago, which strongly suggest that the Afroasiatic languages (traditionally known as Hamito-Semitic) originated in the Near East. A following pulse in the Bronze Age brought a later version of Middle Eastern genes (with an added eastern component) into Ethiopia and Somalia, which likely explains the origin of the Cushitic branch.

A fourth branch, the Khoe-Kwadi languages of southern Africa, are spoken by people also called Hottentots. They appear to be the result of an admixture between cattle-herders from the north and local hunter-gather populations (similar to the Bushmen). Those cattle-herders derive from an ancient West Eurasian population – so you see some Middle Eastern alleles in the Hottentots, a surprisingly result due to Joe Pickrell.

One thing to remember: although some of the hunter-gatherer groups are very interesting and tell us things about really deep prehistory – Bushmen, for example, apparently split off from the rest of the human race about 300,000 years ago – they make up a very small fraction of Africa’s population today. There are roughly 50,000 Bushmen, 1,000 Hadza (descendants of East African hunter-gatherers) and perhaps a million Pygmies.

These small remnant populations can be informative. It looks as if some of the hunter-gatherer populations mixed with unknown archaics about 50,000 years ago. Maybe not that surprising, since skeletons with archaic features have been found (in Africa) that are relatively recent, as recent as 11,000 years ago. Or consider homo naledi, a very different population (many skeletons found in a cave in South Africa), something like humans but with a very small brain, that seems to have lived in South Africa 200,000 years ago. Or recent analysis that suggests West Africans carry significant admixture (~10%) from a pop that split off after Neanderthals [ 600 k years] , but well before the Bushmen.

Another question: how did the Bushmen ( and apparently other populations) manage to stay so genetically isolated over hundreds of thousands of years? We’ve recently learned a bit more about their history, from sequencing Bushmen skeletons found in South Africa – skeletons that are only a couple of thousand years old, but date from before the Bantu arrived. Ur-Bushmen – which showed us how different they were before Bantu admixture.

Reich mentions some work by Peter Ralph and Graham Coop on the multiple origins of the sickle-cell mutation in different parts of Africa, which suggests very low rates of gene flow, since otherwise such a favorable mutation would spread rapidly, without the required wait for multiple occurrences. Alas, it turns out that HbS really does have a single origin, probably in West Africa about 7000 years ago – a nearby recombination hotspot confused the Issue. Which is what some people expected a long time ago – multiple origins never squared with the fact that there is no sickle-cell at all in South East Asia or New Guinea, even though there’s plenty of malaria.. However the point – very low gene flow – is still valid, since we see several different mutations that cause lactase persistence in cattle-herding populations in Northeast Africa. That implies very low gene flow from the parts of Eurasia that had the common European lactase mutation, as well as low gene flow within Africa. Or, possibly, it may suggest that these different mutations have different effects, so that they work better in some environments than others…

In some ways, on some questions, learning more from genetics has left us less certain. At this point we really don’t know where anatomically humans originated. Greater genetic variety in sub-Saharan African has been traditionally considered a sign that AMH originated there, but it possible that we originated elsewhere, perhaps in North Africa or the Middle East, and gained extra genetic variation when we moved into sub-Saharan Africa and mixed with various archaic groups that already existed. One consideration is that finding recent archaic admixture in a population may well be a sign that modern humans didn’t arise in that region ( like language substrates) – which makes South Africa and West Africa look less likely. The long-continued existence of homo naledi in South Africa suggests that modern humans may not have been there for all that long – if we had co-existed with homo naledi, they probably wouldn’t lasted long. The oldest known skull that is (probably) AMh was recently found in Morocco, while modern humans remains, already known from about 100,000 years ago in Israel, have recently been found in northern Saudi Arabia.

While work by Nick Patterson suggests that modern humans were formed by a fusion between two long-isolated populations, a bit less than half a million years ago.

So: genomics had made recent history Africa pretty clear. Bantu agriculuralists expanded and replaced hunter-gatherers, farmers and herders from the Middle East settled North Africa, Egypt and northeaat Africa, while Nilotic herdsmen expanded south from the Sudan. There are traces of earlier patterns and peoples, but today, only traces. As for questions back further in time, such as the origins of modern humans – we thought we knew, and now we know we don’t. But that’s progress.

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“Who We Are: #6 The Americas

In the Pre-Columbian settling of the Americas, there were early layers and late layers. Let’s talk first about the early layers. Some of this is from archaeology, some from genetics (including ancient genetics), a little from linguistics. The Reich lab has played a major role in the genetic work.

The population that accounts for the vast majority of Native American ancestry, which we will call Amerinds, came into existence somewhere in northern Asia. It was formed from a mix of Ancient North Eurasians and a population related to the Han Chinese – about 40% ANE and 60% proto-Chinese. Is looks as if most of the paternal ancestry was from the ANE, while almost all of the maternal ancestry was from the proto-Han. [Aryan-Transpacific ?!?] This formation story – ANE boys, East-end girls – is similar to the formation story for the Indo-Europeans.
This new population ended up in Beringia, a land that is today the shallow Bering Sea between Alaska and Siberia, then exposed because of the low sea levels of the Ice Age. It wasn’t easy to proceed further into North America, since the path was blocked by ice sheets, and apparently the Beringians hung out there for thousands of years.

But then the ice began to retreat. The Beringians managed to get past the glaciers – probably by following a path from one unglaciated patch to the next along the Canadian west coast. The idea that they waited until an inland ice-free corridor opened up seems to be mistaken: we keep finding remains that are too old to fit that scenario.

Those early Amerindians split into two close but distinguishable populations: one that occupied parts of eastern North America (Algonquians), the other now occupying central and South America. Those Amerinds spread rapidly through the two continents, and, for the most part, they’re still where they landed. There were some regional expansions, but nothing like the vast population/language expansions in the Old World – nothing like the Bantu or Indo-European or Hamitic-Semitic expansions. In many area, the Amerindian populations today are largely descended from the people that lived there 8,000 or more years ago.

This resulted in a pattern of many deeply diverged languages, rather than a few very wide-spread language families, as seen in the Old World. Reich thinks this vindicates Joseph Greenberg’s work on classifying the native languages of the Americas. Greenberg thought the many languages in the Americas split into only three families: Eskimo-Aleut, Na-Dene (spoken along the northern Pacific coast of the US, interior northern Canada, and the American Southwest ( Navajo) – a later migration – and Amerind (everyone else). This scheme fits what we find in the genes: just three migrations and three language families. Greenberg’s method, “mass comparison” works. Another point: Greenberg thought that there was a very distant relationship between Amerind and Indo-European. If correct, that suggests that Indo-European primarily originated from a language of the eastern mostly-ANE hunters, not from a population in the Caucasus or or northern Iran. Which also accords with work suggesting Kartvelian influences on PIE, rather than origins – also with PIE having a sister relationship with Uralic. Just saying.

Back to the new world. This picture was nice and simple, but there was a fly in the ointment. Isn’t there always? A Brazilian anthropologist, Walter Neves, had studied a number of old skeletons in Brazil that looked different. The most famous of these was Luzia Woman, about 11.500 years old. Neves and others thought that she ( and other similar skeletons) looked more like Australo-Melanesians than Amerindians. Reich is dismissive of Neves’ scientific credentials – ” If I don’ know it, it’s not knowledge” – but Neves was on to something important. One of Reich’s students, Pontus Skoglund, looked more closely at native American genetic data to look for traces of a different ancestral group. He found them. Parenthetically, I’ve heard that other people had seen something weird in those Amazonian genetic samples even earlier, but seem to have thought it was too weird to publish

Some populations of Brazilian Indians were genetically closer to Australasians than to other world populations – the general group that Neves and other anthropologists had said the old Brazilian skeletons resembled. The population with the greatest affinity were the Andaman islanders, short dark people that live on islands between India and Burma.

Several of the Amazonian tribes they looked at had this admixture, at a few-percent level: the Surui, Karitiana, and Xavante. It has since been found in some other groups in or near the Amazonian basin.

Some obvious attempts at an explanation don’t work. That genetic trace isn’t from Polynesians – not a good genetic match, and the admixture is old, while the Polynesian expansion into the Pacific is recent.

The pattern of the populations that don’t have this pseudo-Andamanese admixture is illuminating. You don’t see it in the eastern branch of Amerindians, You don’t see it most of the current southern branch ( i.e. central America and South America west of the Andes). You don’t see it in ancient members of the southern branch (The Clovis-complex Anzick-1 skeleton from Montana, about 12.6k years old). You don’t see it in a Beringian that was left behind in Alaska (about 11k years old).

How can you see it in Brazil if it wasn’t already there in Beringia? Or in the early expansion out of Beringia? Or in Central America?

Because these pseudo-Andamanese were there first, before the Amerindians ever got south of the glaciers. And were then seriously stomped by Amerindians, as has happened so often in prehistory.

If you go back 18,000 years or earlier, South America was a much more appetizing target for settlement than North America, which was was glaciated and cold. Taiga all the way down to the Gulf of Mexico. While the Amazon basin was reasonably warm and far less of a Green Hell than it is today – lots of savanna.

Although likely, that’s a bad explanation, because some people won’t like it. In addition, it’s too simple. People in the soft sciences routinely use Occam’s butterknife – entities should be multiplied out the wazoo.

I’ve seen an alternative scenario : as the southern branch of Amerindians was moving south, perhaps along the west coast, a single canoe or raft full of pseudo-Andamanese landed and merged peacefully. This has to happen at exactly the right time and place – at the wavefront of people moving south. Peaceful merger wasn’t any too likely either.

On the other hand, if you assume that the pseudo-Andamanese simply arrived before the Amerindians, hat could have occurred at any time over thousands of years, and instead of having to land near the front of that wave, they merely have to hit the west coast of South America – a big target. I figure that the early-arrival scenario is thousands of times more likely than the complex-population-structure model.

There were later, smaller migrations. First, perhaps 6000 years ago, another from east Siberia that led to the Paleo-Eskimos and the Na-Dene. We’ve actually traced a clear language connection between the Na-Dene languages and a Siberian tribe, the Ket. The Neo-Eskimos arrived yet more recently and rapidly replaced the Paleo-Eskimos. Both the Na-Dene and Neo-Eskimos picked up a lot of ancestry from Amerindians.


We found that Siberian and East Asian populations shared 38% of their ancestry
with a 45,000-yr-old Ust’-Ishim individual who was previously believed to have no modern-day descendants. Western
Siberians trace 57% of their ancestry to ancient North Eurasians, represented by the 24,000-yr-old Siberian Mal’t

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Live Not By Lies

The Genomics of Race and Identity

Reich starts out strong, telling the story of his work on identifying African-origin alleles that drive increased prostate cancer risk in African-Americans – and the dumbshit responses he got from his colleagues. He mentions an anthropologist that questioned his mention of “African” and ” European” DNA segments: he was flirting with racism. What a fool. By the way, there’s something odd and interesting in that early result: why would most of the risk variants all land in one small segment of the genome? But back to the fools: Reich talks about the anthropologists [ Montagu] , geneticists [Lewontin] , and sociologists that have argued that ‘race’ has no biological reality, that there are not really any significant biological differences between races, that research into such differences should be banned ( why is this necessary if differences don’t exist?), etc. All liars, of course. Although I can think of a few people saying similar things that are not liars: they’re just not very bright.

Speaking of such differences, here’s one Reich elucidated a few years back. The white count (white blood cells, neutrophils) is about a standard deviation lower in people of African descent than it is in Europeans? Why? Turns out it is innate, biological and quite simple: there’s a variant of the DARC gene that has a frequency > 99% in West Africans and < 1% in Europeans: that variant causes the lower white count. That African DARC variant is an almost perfect defense against vivax malaria, which is surely why it became so common.

Reich explains how recent genetic analysis shows that people’s genes cluster in ways that correspond pretty well with old-fashioned notions of ‘race’. He prefers to talk about 'ancestry', because (in his view) the word 'race' is too ill-defined and loaded with historical baggage. Whatever.

He goes on to say that people that deny the possibility of substantial differences between populations just can't do it anymore: they're putting themselves in an indefensible position. He is wrong: sure, their position is logically indefensible, the facts are against it, but what does that matter? The significantly crazier idea that there are no differences between the sexes – that sexual dimorphism itself is a myth promulgated by the Gnomes of Zurich or the orbital mind-control lasers – has become very powerful in much of the Western world: barking-mad craziness apparently doesn't need to defend itself.

He says that geneticists have tended to 'obfuscate' on this topic, mentioning Richard Lewontin. I'd put it a bit differently: they lie.

Reich mentions independent genome bloggers, some of them skilled analysts, who are on the whole less inclined to go along with the usual falsehoods. He thinks that means you can’t keep up the charade: again, he’s very likely wrong, not least because those skilled genome bloggers have a tiny audience. More important, Reich himself doesn’t want to keep up the charade. That may matter.

Reich goes on to demolish some fairly common false arguments about how different human races – excuse me, ‘ ancestral populations ‘ – really can’t be very different, at least not in any traits that would upset people. You know, for the same reasons that dog breeds can’t really be very different.

First, an argument that somehow it’s very hard, or takes forever, for natural selection to change traits that are influenced by many genes. I have no idea where this piece of nonsense originated – we’ve been selecting on highly polygenic quantitative traits forever and a day without any special problems. In the standard formulation for estimating the effects of selection, the number of genes influencing the trait drops out of the equation entirely. It just doesn’t matter. Reich understands this, not least because he’s done analysis of selection for height in Europeans.

Some might say that genetic influences in height are one thing, but surely genetic influences on cognition and behavior are mystically unknowable. Reich knows better: he knows that recent studies are finding those influences. Reich weasels a little, suggesting that these variants may influence educational achievement by influencing timing of childbirth – but probably not, since the pro-educational alleles also result in larger brains.

He also knows that the plus alleles, the ones that increase intelligence, are getting rarer at a scary pace, decreasing IQ at something like a point a generation. This illustrates a pattern with Reich: this was roughly understood a long time ago, just from looking at demography and fertility patterns. It was known before genomic analysis existed. Cyril Kornbluth knew about it back in the 1950s – thus his short story “The Marching Morons”. Reich could have known this when he was twelve, but I doubt if he did. Reich often seems to think that if a result wasn’t proved using powerful contemporary genomic methods (what he uses), it wasn’t really known at all. If I don’t know it, it’s not knowledge: that’s a wrong way of thinking.

next fallacy: human populations just haven’t been separated long enough to have changed much due to selection. He knows that’s not correct. He points out that in many cases populations have been separated for 50,000 years, while some African groups appear to have been separated far longer, perhaps 200,000 years. A recent study showed that there has been noticeable evolutionary change in the English over the past 2000 years: selection for increased height, infant head circumference, blondness, etc etc. If it can happen there in 2000 years, it can happen anywhere.

And he expects that more such racial differences will be found – but now he has to weasel again. He says that nobody knows what those differences will be! So we might find that, in terms of fundamental biological potentials, Koreans are dumb while Pygmies are tall. Suuuuuuuuuuuuuure. That could happen.

Next he slams people that suspect that upcoming genetic genetic analysis will, in most cases, confirm traditional stereotypes about race – the way the world actually looks.

The people Reich dumps on are saying perfectly reasonable things. He criticizes Henry Harpending for saying that he’d never seen an African with a hobby. Of course, Henry had actually spent time in Africa, and that’s what he’d seen. The implication is that people in Malthusian farming societies – which Africa was not – were selected to want to work, even where there was no immediate necessity to do so. Thus hobbies, something like a gerbil running in an exercise wheel.

He criticized Nicholas Wade, for saying that different races have different dispositions. Wade’s book wasn’t very good, but of course personality varies by race: Darwin certainly thought so. You can see differences at birth. Cover a baby’s nose with a cloth: Chinese and Navajo babies quietly breathe through their mouth, European and African babies fuss and fight.

Then he attacks Watson, for asking when Reich was going to look at Jewish genetics – the kind that has led to greater-than-average intelligence. Watson was undoubtedly trying to get a rise out of Reich, but it’s a perfectly reasonable question. Ashkenazi Jews are smarter than the average bear and everybody knows it. Selection is the only possible explanation, and the conditions in the Middle ages – white-collar job specialization and a high degree of endogamy, were just what the doctor ordered.

Watson’s a prick, but he’s a great prick, and what he said was correct. Henry was a prince among men, and Nick Wade is a decent guy as well. Reich is totally out of line here: he’s being a dick.

Now Reich may be trying to burnish his anti-racist credentials, which surely need some renewal after having pointing out that race as colloquially used is pretty reasonable, there’s no reason pops can’t be different, people that said otherwise ( like Lewontin, Gould, Montagu, etc. ) were lying, Aryans conquered Europe and India, while we’re tied to the train tracks with scary genetic results coming straight at us. I don’t care: he’s being a weasel, slandering the dead and abusing the obnoxious old genius who laid the foundations of his field. Reich will also get old someday: perhaps he too will someday lose track of all the nonsense he’s supposed to say, or just stop caring. Maybe he already has… I’m pretty sure that Reich does not like lying – which is why he wrote this section of the book (not at all logically necessary for his exposition of the ancient DNA work) but the required complex juggling of lies and truth required to get past the demented gatekeepers of our society may not be his forte. It has been said that if it was discovered that someone in the business was secretly an android, David Reich would be the prime suspect. No Talleyrand he.

He doesn’t just slander, he lies. He says “most stereotypes will be disproved.” Want to bet? Most stereotypes are true – true everywhere. In what country do the Chinese disproportionately fill up the special ed classes? If we we’re talking cognition and personality, the behavioral geneticists keep finding that A. genetics matters, and B. The usual suspects, like family environment, don’t matter much.

There may be a few exceptions to ” what you see is what you get”, and understanding them might be very valuable: if some pop appeared to have a lot on the ball ( genetically) but isn’t doing well, there might be another cheap, simple solution, like iodine supplementation. And there will be differences that are fairly subtle and not much noticed, say in liver enzymes or the immune system, that might be highly relevant to disease prevention and treatment.

Reich’s position is that we don’t know anything until someone (him !) has analyzed it with modern genomic techniques. That’s ridiculous. Reich found that on average, given similar diets, northern Europeans are about a standard deviation taller than southern Europeans. But I already knew that, well before Reich was born. Seneca knew it: Tacitus knew it. There’s a reason the Byzantines hired plenty of Scandihoovians (including 7-footer Harold Hardrada) into the Varangian Guard. Mark Twain knew that Ashkenazi Jews were smart: he didn’t need IQ tests or GWAS for that.

If he thinks that the genetics typically push in a way that is the opposite of the patterns we actually observe, he must believe that environmental influences are very powerful, so much so that there’s not much point in even knowing genetic influence – and therefore not much impact from discovering them . But clearly he does worry. Why?

When he says that we don’t have any idea what we’ll find, he’s lying again.

But don’t think that deliberate deception rules out occasional confusion. Reich talks about the success of West Africans (and their diaspora) in track: all the male finalists in the Olympic 100-meter race since 1980 have had West African ancestry. Every men’s world record at every commonly-run track distance belongs to a runner of African descent.

He says that A. there could have been an upward shift in West African sprinting ability due to natural selection, which could easily lead to vast over-representation at the top level of competition, or B. West Africans might just have greater genetic variation, which would (he thinks) lead to a wider spread of abilities. And maybe that greater variation applies to cognitive traits, where Reich expects a higher proportion of sub-Saharan Africans with extreme genetically predicted abilities.

None of this is correct. First, we known damn well that the West African edge in track is due to systematic racial differences, not greater phenotypic variability. We know that blacks have shorter torsos and longer legs, more fast-twitch muscles, narrower hips, lighter calves. Those same characteristics are disadvantages in some other events, like swimming. The relatively more mesomorphic build of Europeans pays off in swimming, weightlifting, wrestling and field events. This kind of specialization is what you expect from systematic racial differences: you’d see a different pattern from significantly greater variability in one group.

The ‘greater variability” theory’s biggest problem is that none of its obvious implications actually happen. People of African descent just aren’t in general more variable in phenotype. I checked out the population variability in height in a number of African countries: it’s generally about the same as in the US or Europe. I checked out black variability in IQ (in the US) : it’s noticeably smaller than that in whites – about 12 or 13 points, instead of 15 – combined with a significantly lower average (about 85) If this “greater variability” idea were correct, blacks would be greatly over-represented at the very highest scores on cognitive tests – instead, they are greatly under-represented. If African-American success in track were due to greater variability, you’d see them dominate at the highest level of competition, but far less so in a typical high school. But you do see it in low-level competition, to the point where white kids increasingly don’t even bother to compete in black-dominated events.

Or you could look at domesticated animals, which always have less genetic variation their wild ancestors. Is the smallest wolf smaller than a Chihuahua – is the largest wolf larger than a Great Dane? No. Selection dominates. Or look at the results of breeding experiments: the general trend is that increasing heterozygosity leads to lower phenotypic variability.

I am surprised that Reich, who is a smart guy, would fall for this notion.

Posted in Ashkenazi Jews, Book Reviews, Genetics | 179 Comments

Who We Are: #4 Denisovans

In Chapter 3, Reich talks about the discovery of the Denisovans, a sister archaic group to the Neanderthals that lived in eastern Asia. It all started out with a pinky bone found in a cave in southern Siberia. The DNA in the little bone was very well preserved – they got better info from that one bone than all previous Neanderthal DNA work. It’s an odd situation – we now know a lot about Denisovan genetics, but we don’t have a skeleton and have no idea what they looked like.

The Denisovans were closer to the Neanderthals than they were to AMH, but not by much. Apparently modern humans split with the common ancestors of Denisovans and Neanderthals about 700,000 years ago, while Neanderthals and Denisovans separated not much later. Almost a trichotomy. Something similar happened when AMH spread into Eurasia: quite early, maybe 50,000 years ago, we split into eastern and western branches. Probably it’s all geography.

With a high-quality Denisovan genome to work with, they tested whether any population seemed to be especially close. To their surprise, people from New Guinea were indeed significantly closer: they must have some Denisovan ancestry, somewhat surprising because New Guinea is a long way from Siberia. Although, since the Denisovans had hundreds of thousands of years to differentiate and spread over eastern Eurasia, far more time than we have had, it’s not really that odd.

In a sense, Reich’s team already knew this, although it sounds as if they didn’t know that they knew it. That same year, they had put out their big Neanderthal paper. Deep in the supplements, there was a table that showed genetic distance between a number of populations, including the Bushmen. Since the Bushmen had split off before other modern humans moved out of sub-Saharan Africa and settled the rest of the world, everybody in Eurasia should have been the same distance from Bushmen. And almost all were – except for people from New Guinea, who were noticeably more distant. Which mean that they had extra admixture from some archaic group, probably not Neanderthals, since there’s never been any sign of them that far east. My guess was Denisovan.

Sarah Phillips-Garcia, at the University of New Mexico, saw a sign of archaic admixture in people from New Guinea even earlier: she saw that something had introduced new variation in STRs (short tandem repeats) in New Guinea, variation you didn’t see in the rest of humanity.

Meanwhile Reich’s team were analyzing that Denisovan genome. They found that something like 5% of New Guinea ancestry is Denisovan, on top of the usual Neanderthal ~2% in Eurasians. This Denisovan admixure came from a Denisovan population that was fairly divergent from the genome found in Siberia. Some people in New Guinea have considered taking advantage of this high level of archaic ancestry: when facing potential criticism from the UN Human Rights Commission for some kind of intertribal strife, they were going to argue that it didn’t apply to them, because they weren’t human. I never saw that one coming. Similar amounts of Denisovan admixture are found in Australian Aboriginals, people in the Solomon Islands, and some Philippine Negritos.

You might think that this suggests that this major admixture maybe happened in Southeast Asia or nearby islands, but Reich accepted the argument of Yousuke Kaifu, an anthropologists who pointed to the lack of archaeological artifacts in the region that would support the notion of big-brained hominins in that region. But that’s silly. Bamboo. Probably it did happen in that region, likely in Sundaland. Very recent work suggests that there may have been two separate Denisovan admixture events: the first one contributing to Melanesians, the second to the much smaller amount of Denisovan admixture found in mainland Asia.

Linkage analysis showed that the main Denisovan admixture occurred a bit more recently than Neanderthal admixture, around 50,000 years ago. The possible second admixture seems to have happened more recently.

Reich talks briefly about some of the advantageous genes we picked up from Neanderthals and Denisovans. It was predictable [ John Hawks and I predicted it] that at least some of their gene variants would be useful – after all, they’d lived in Eurasia for hundreds of thousands of years and ought to be well-adapted to local conditions. Reich mentions the high frequency of Neanderthal-origin keratin gene variants in Eurasians, variants that affect hair and skin. He also mentions a particular Denisovan variant of the EPAS1 gene that has become common in Tibetans and helps them deal with life at high altitude. Since Tibetan adaptations to high altitude are considerably more effective than those of Andean Indians, more like those of species that had spent a long time at high altitude, there was an obvious possibility that Tibetans had picked up variants from archaic populations that had spent hundreds of of thousands of years in that environment. And lo, it was so.

The oldest-found human DNA is from ancient fossils at the Sima de Los Huesos caves in Spain, more than 400,000 years old. These skeletons looks like ancestors of Neanderthals, but they carry mtDNA that is much closer to that found in the Denisovan sample. There is an idea that Neanderthals may have mixed a bit with the ancestors of modern humans, say a quarter of a million years ago, and picked up a new form of mtDNA. Which they may have needed: Neanderthal population was small enough to potentially cause trouble in the long run ( because of inefficient selection) but that’s even more true for mtDNA, whose effective population size is four times smaller.

It also looks as if the Denisovans may have mixed with an unknown but very archaic population in East Asia, possibly descendants of homo erectus, which goes back 2 million years in Eeurasia.

One growing suspicion, originating from ancient DNA work and recent fossil finds, is that anatomically modern humans may not necessarily have originated in sub-Saharan Africa. The oldest probably-modern skeleton we have was recently found in Morocco. There is evidence that African populations, too, mixed with unknown archaic hominids (evidence for Pygmies, Bushmen, and also more typical West Africans such as the Yoruba, which implies that at least some parts of sub-Saharan Africa were occupied relatively recently by non-AMH populations. Homo Naledi, a small-brained homonin identified from recently discovered fossils in South Africa, appears to have hung around way later that you’d expect (up to 200,000 years ago, maybe later) than would be the case if modern humans had occupied that area back then. To be blunt, we would have eaten them.

Deep prehistory was always complicated: we just didn’t know much about it before. Ancient DNA analysis is the path forward.

Posted in Archaic humans, Book Reviews, Denisovans | 63 Comments

“Who We Are: #3 Neanderthals

In Chapter 2, Encounters With Neanderthals, David Reich talks about his work in analyzing the first successfully sequenced Neanderthal genomes, and the discoveries that led to.

Reich’s team, with Nick Patterson making an especially important contribution, found that Neanderthals were about equally [genetically] close to Europeans, East Asians, and people from New Guinea, but closer to all non-Africans than to sub-Saharan Africans. This was what you would expect if the ancestors of non-Africans had interbred with Neanderthals, while sub-Saharan Africans had not.

Even thought these results were statistically very strong, Reich was skeptical because it went against the scientific consensus of the time – that there had been no admixture between anatomically modern humans and archaics such as Neanderthals as AMH expanded out of Africa. This was a question that I and John Hawks were interested in. We had concluded that the “scientific consensus” was based on nothing and put no stock in it. We had predicted that such admixture would be found, and that sometimes Neanderthal alleles would have conferred selective advantages and become common. Our reasoning went as follows:

The evidence for zero mixing was weak. It was clear that modern humans did not carry Neanderthal Y-chromosomes or mtDNA, but that could have occurred because they reduced fitness (a slight reduction have been enough to eliminate them, over tens of thousands of years) or because they were never common and were later lost by chance. Y-chromosomes and mtDNA are only two loci. We had checked what was known about successful hybridization in mammals: it turned out that after two species separated, it usually took a couple of million years for serious genetic incompatibility to develop. But we knew, from the fossil record, the Neanderthals split off around a half million years ago. Hybridization should have been possible. Moreover, if it happened, even at a low level, it would be an efficient means of transmitting new favorable alleles to modern humans, some of which might be common today.

One reason [ we think] for that bogus scientific consensus was a confusion of terms. Paleontologists call two sets of fossils separate species if they look sufficiently different [morphological species] while biologists usually define separate species as populations that can’t interbreed. Those aren’t equivalent definitions: we can distinguish the skeletons of Labrador retrievers and poodles, yet labradoodles happen.

Another reason: Ernst Mayr, a prominent figure in biology had opined that hybridization was an unimportant factor in evolution, as far as I can tell for no particular reason at all. For equally mysterious reasons, people paid attention to him.

Anyhow, Reich’s skepticism led to even better evidence for mixing with Neanderthals, which is the way it’s supposed to work in science. By looking at the average length of Neanderthal-derived segments of the genome, they were able to make a rough estimate of the time of mixing. Later work, using ancient DNA from a modern human that lived and died in Siberia about 45,000 years ago, gave a more accurate of 50-60 thousand years ago for Neanderthal admixture. The fact that the amount of Neanderthal admixture was not very different in widely separated populations in Eurasia suggested that admixture occurred in the Middle East, an inevitable first step in expanding out of Africa.

Later work showed something very interesting: the amount of Neanderthal ancestry ( in regions that actually do anything) has been slowly declining over time. In certain regions you see no Neanderthal ancestry at all – Neanderthal gene deserts – bu the trend is general. Not universal, since some Neanderthal genes appear to have been useful and have become common, but the general trend is the gradual shedding of the minority genome.

There are a couple of explanations under consideration for this genetic rejection. One is that Neanderthals were messed up: because their long-term numbers were lower, particularly at glacial maxima, purifying selection would have been less efficient in Neanderthals, and slightly deleterious mutations would have accumulated to higher levels than in anatomically modern humans. We have more example: it looks as if most of the functional part the Denisovan genome is also being slowly rejected by Melanesians. But there’s more: West Africans seem to have have picked up genes from an archaic group in Africa that are slowly being rejected, while Altai Neanderthals seem to have picked some modern human ancestry ( possibly from the Qafzeh-Shkul population in the middle East around 100,000 years ago) and they were rejecting the modern human genome. I can’t see how Neanderthal genomes could simultaneously be both better than and worse than modern human genomes: I think it more looks like a kind of mild incompatibility, where every subspecies is rejecting minority DNA from any exterior source. If true that would be very interesting. But I could be wrong. Probably am.

Reich believes that moderns and Neanderthals were at the edge of biological compatibility, probably with reduced fertility. The evidence is that there is an especially low level of Neanderthal ancestry on the X chromosome, a known hotspot for fertility problems in crosses between related species. And that’s good evidence. But on the other hand, comparisons with other mammalian sister species indicates that it usually takes a considerably longer separation before real fertility problems show up – enough, say, to materially inhibit gene flow.

Probably we need to define terms. I think that a few-percent decrease in fertility in people with large amounts of Neanderthal ancestry might be enough to create those Neanderthal gene deserts on the X chromosome – but at the time, nobody would have noticed it. Smallish effects had something like 2000 generations to play out.

Posted in Archaic humans, Book Reviews, Neanderthals | 55 Comments

The Usual Suspects

David Reich’s book has stirred up a lot of the usual suspects. Most are non-geneticists, but there are a few geneticists among them. Sorta kinda. Here’s an interesting example – something by Dan Graur, a geneticist currently at the University of Houston.

Graur says: “For selection to operate and counteract the effects of random genetic drift, the effective population size should be large. Unfortunately, the long-term effective population size for all the humans in the world is barely 10,000—lower than that of chimpanzee. By necessity, the effective population size of each “race” separately is much smaller. So, the chances that 74** loci will experience significant changes in allele frequencies simultaneously in each of the four populations is zero. With one locus, a change in human allele frequency may occur, albeit very rarely, as evidenced by the case of lactase persistence in North European and the case of the EDAR allele in East Asians. To imagine that 74 alleles change frequency in concert and that the 74 alleles have successfully battled genetic drift and recombination in merely 2,000 generations requires an extremely naïve and unsophisticated view of the evolutionary process.

Moreover, according to Augustine Kong, whom David Reich quotes, educational attainment is a deleterious trait that is selected against. The selection against educational attainment, according to Kung, is extremely powerful, so much so that differences in allele frequencies are observable after merely 3-5 generations (100 years). If one believes these claims, one should explain how come there are so many university graduates in Iceland. With such huge purifying selection against education, it’s a miracle that any one in Iceland knows how to read and write.

Kong A. et al. 2017. Selection against variants in the genome associated with educational attainment. PNAS 114: E727-E732

Moore DS, Shenk D. 2017. The heritability fallacy. WIREs Cogn Sci, 8:e1400. doi: 10.1002/wcs.1400

Okbay A et al. 2016. Genome-wide association study identifies 74 loci associated with educational attainment. Nature 533:539–542 ”

The interesting thing about this is that Graur has had prestigious jobs in areas relating to evolution, while apparently understanding nothing about it. Graur served as associate editor of the journal of Molecular Biology and Evolution from 1995 to 2011. Since 2009, he serves as associate editor of the journal Genome Biology and Evolution. From 2009 to 2011 he has held the position of Councillor for the Society for Molecular Biology and Evolution, won the Humboldt prize in 2011, and was elected a fellow of AAAS in 2015. In spite of this, every single statement in this short note is incorrect.

Graur says “For selection to operate and counteract the effects of random genetic drift, the effective population size should be large.” Well, it would be nice if the effective population size were large, but that is by no means necessary. German Shepherds were created in the 1890s, by interbreeding several breeds of dogs ( and wolves !), followed by selection for desired traits. That didn’t require tens or hundreds of thousands of dogs. Thoroughbreds are the fastest horses in existence: their effective population size is around 100. Dachshunds are smaller than they were in the 1970s – but then everybody knows they’re contrary enough to violate the laws of genetics. Born that way, probably.

I could go on – and on, and on. Every example we have of selection on domesticates is a counterexample to what Grauer is saying here. No farmer he. Does he think that some ancient geneticist corralled a million aurochsen in order to breed the domesticated cow?

A large population size is nice, because it generates more favorable mutations, but that is not necessary. Selection, at least in the short run, does not require any new mutations at all. Nice, because a large population size reduces the strength of chance, so the probability of the change in the trait under selection stalling or reversing in a given generation is lower – the results of selection become more predictable, especially in the short run. Next, Grauer talks about the long-term effective population size (EPS) in humans being around 10,000 – which he seems to think is too low for selection to work. He’s wrong, but that number is also the wrong number. He’s talking about the neutral-theory effective population size, which is a function [ harmonic mean] of long-term population size over the last million years or so – and it’s the wrong ‘effective population size’ for selection questions. There are different values of EPS for different questions. The right one is the “Variance EPS, which tells you the theoretical population size that yields the same noise in allele frequency change, right now. It basically measures how little a population is susceptible to drift.” The correct value of EPS, for different continental branches of humanity, has been hundreds of thousands to millions for a long time, well before agriculture was developed.

Graur is making a very basic mistake: he is perfectly happy making an argument to which there are many counterexamples. They don’t bother him. Even one counterexample should bother you. As I said, every domesticate is a counterexample to what he’s saying. We know of many genetically caused differences between human populations, such as height, skin color, disease resistance, ability to efficiently utilize certain foods, tolerate high altitude, low temperatures, high levels of arsenic, etc etc. By ‘we’ I mean anyone who can read. Some of those genetic differences are caused by new forms of one or a few genes ( like sickle-cell), others by small shifts in the frequency of many alleles that influence the trait.

Graur notes, incredulously, Augustine Kong’s work showing that the frequencies of variants influencing educational attainment are changing rapidly – in a way that decreases potential for educational attainment. We’re getting dumber. He asks how there could be so many university graduates in Iceland. But this kind of strong selection against potential for educational attainment – selection against intelligence – has been predicted for many years by people that understood that A. intelligence is highly heritable and B. On the whole smarter people, especially smarter women, have significantly fewer kids than average in contemporary society. This is almost certainly a new phenomenon, less than a hundred years old, just as mass higher education and artificial birth control are new things. Although Kong showed this directly, through genetic analysis, the idea is hardly new. R.A. Fisher talked about it, in The Genetical Theory of Natural Selection [published in 1930]. Of course Fisher understood polygenic selection pretty well too, having been the main developer of the theory of quantitative selection. Demographers in the 1950s talked about it. Cyril Kornbluth understood it ( ‘The Marching Morons’ ): but to be fair, Kornbluth was no ordinary man.

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Rapid Change in Polygenic Traits

A few people have occasionally claimed that natural selection takes a long time to change any trait that might bother them – sometimes, they say this of polygenic traits, ones influenced by many genes, like height and intelligence. Kevin Mitchell has said this (“at least 100 millennia to evolve appreciably”), so has Brad Delong (an economist at Berkeley). David Reich mentions Joseph Graves, in a talk at Harvard, saying something similar in a lecture in 2016. They’re all 100% wrong: it is easy to select on polygenic quantitative traits, and we do it every day. Dogs vary a lot in height and most of the big differences are the result of fairly recent selection: nobody had Chihuahuas or Great Danes back in the Ice Age.

Human populations vary in height – not just from differences in nutrition. We know [work from the Reich lab] that northern Europeans are around a standard deviation taller than southern Europeans ( given adequate food), and we know some of the alleles behind that. Andaman islanders are four standard deviations shorter than the Dutch , Efe Pygmies almost five std shorter.
Probably the total range in humans, from the tallest (Dinaric Slavs, 6 1, to Efe Pgmies, 4 8) is six standard deviations. I’m sure that David Reich can explain to me how this is a small, even insignificant difference.

You may ask yourself why fairly prominent people manage to say instantly falsifiable things about human genetics. Good question. I might be partially protected from this error by preadaptation, having spent years and years walking past the Morrow Plots on my way to the main undergraduate library at the U of I. Delong has the excuse of not being any kind of biologist, but then again he ought to know that. A couple of us were trying to educate him on Twitter: he started accusing the mathematician involved of innumeracy, so the mathenaut called him “just another regression monkey”. Good times. As for Kevin Mitchell and Joseph Graves – well a lot of people in biology and medicine just don’t know much about selection. And of course in this context they don’t want to know.

Quantitative selection is a lot easier than people think. If I kidnapped a year’s worth of National Merit Scholars and dropped them on a deserted but fertile island, a new race with an average IQ around 130 would develop ( unless those little brainiacs escaped. You have to watch them all the time). If I dropped a lot of NBA and WNBA players, you’d see the tallest race, if we could just get them to reproduce.

But… there are some subtle points here. Great Danes exist and persist, but they have a bundle of health problems, and they don’t live too long (8-10 years). Wolves last around 15-16 years in captivity, with a record of 20. If you wanted to create a new race with an average adult height of 7 feet, I’m sure you could, but I’d bet money they’d have bad knees.

On the other hand, if they stayed 7 feet tall for a couple of million years, they would not be particularly prone to bad knees. There would be gradual selection for tougher knees: changes in development, changes in bones and tendons and cartilage, eventually perhaps fundamental changes in the architecture of the knee. There would be lots of little changes that made development among those giants more robust, changes that reduced the incidence of many problems that centers fall heir too.

Brain size in ancient and archaic humans was plenty big, but we don’t really see signs of rapid innovation, art, and decent fast food until fairly recently, 50,000 years or so. Some anthropologists says that humans were just as smart 100 or 150k years as they are today ( which may be true for some people) – but the notion that people managed to get smarter without showing any practical sign of it for 50 or 100k years is, in my opinion, just plain stupid.

So I think Kevin Mitchell ( not the other two) has a point. It’s possible, even likely, that the populations that have relatively high IQs today haven’t had them for very long, and that they’re not terrible well adapted to their new mental horsepower. Susceptible to various mental problems and illusions that would probably be a lot rarer if natural selection had had time to iron out the bugs.

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