Category: Human Evolutionary Genomics

How the worm turns the genic world

By Razib Khan | November 26, 2011 12:25 am

In the middle years of the last decade there were many papers which came out which reported many ‘hard’ selective sweeps reshaping the human genome. By this, I mean that you had a novel mutation arise against the genetic background, and positive selection rapidly increased the frequency of that mutation. Because of the power and rapidity of the sweep many of the flanking regions of the genome would “hitchhike” along, generating long homogenized regions of linkage disequilibrium. If that’s a little dense for you, just understand that very strong selective events tend to result in disorder and distinctiveness in the local genomic region.

But the late aughts and the early years of the teens are shaping up give us a more subtle picture. Instead of classic hard sweeps, researchers are suggesting that there may also be many ‘soft’ sweeps, where selection draws upon the well of standing genic variation. Instead of a novel trait becoming prominent, one tail of the distribution would rise in frequency. The ‘problem’ with this model is that it’s not as tractable as the earlier one of hard sweeps, and selection on quantitative traits with many loci of small effect is more difficult to detect. Its effect on the genome is more subtle and understated, which means that statistical tests often lack the power to grasp onto the underlying dynamics. Naturally this means that there is an extension of statistical techniques to ever greater degrees of sophistication. A new paper in PLoS Genetics attempting to tease apart the various potential selective pressures in the human genome is reflective of that tendency. Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution:

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How Archimedes' lever explains human evolution

By Razib Khan | November 5, 2011 6:38 pm

Last August I had a post up, The point mutation which made humanity, which suggested that it may be wrong to conceive of the difference between Neanderthals and the African humans which absorbed and replaced them ~35,000 years ago as a matter of extreme differences at specific genes. I was prompted to this line of thinking by Svante Pääbo‘s admission that he and his colleagues were searching for locations in the modern human genome which differed a great deal from Neanderthals as a way through which we might understand what makes us distinctively human. This sort of method has a long pedigree. Much of the past generation of chimpanzee genetics and now genomics has focused on finding the magic essence which differentiates us from our closest living relatives. Because of our perception of massive phenotypic differences between H. sapiens and Pan troglodytes the 95-99% sequence level identity is thought by some to be perplexing. Therefore models have emerged which appeal to gene regulation and expression, or perhaps other forms of variation such as copy number, to clear up how it can be that chimpanzees and humans differ so much. Setting aside that the perception of difference probably has some anthropocentric bias (i.e., would an alien think that chimpanzees and humans are actually surprisingly different in light of their phylogenetic similarities? I’m not so sure), it doesn’t seem to be unreasonable on the face of it to plumb the depths of the genomes of hominids so as to ascertain the source of their phenotypic differentiation.

But can this model work for differentiating different hominin lineages? Obviously there’s going to be a quantitative difference. The separation between chimpanzees and modern humans is on the order of 5 million years. The separation between Neanderthals and modern humans (or at least the African ancestors of modern humans ~50,000 years B.P.) is on the order of 500,000 years. An order of magnitude difference should make us reconsider, I think, the plausibility of fixed differences between two populations explaining phenotypic differences.


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The perils of human genomics

By Razib Khan | October 25, 2011 1:45 pm

A friend pointed me to the heated comment section of this article in Nature, Rebuilding the genome of a hidden ethnicity. The issue is that Nature originally stated that the Taino, the native people of Puerto Rico, were extinct. That resulted in an avalanche of angry comments, which one of the researchers, Carlos Bustamante, felt he had to address. Eventually Nature updated their text:

CORRECTED: This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

Here’s Wikipedia on the Taino today:

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Australia on fire

By Razib Khan | October 13, 2011 8:22 pm

Fascinating, Orbital cycles, Australian lake levels, and the arrival of aborigines:

But the other big feature is that the lake-filling events that occurred after 50,000 years ago were much smaller than those which occurred before. Climactically, the conditions 10,000 years ago should have been the same as the conditions 115,000 years ago. But the lake was only a fraction of the size. The authors find no natural causes which can explain this. So they suggest that the aridity starting around 50,000 years ago is related to the reduction in forest and increase in grasslands which occurred at this time. This vegetation change was a result of a huge increase in the frequency of fire in central Australia, which allowed fire-adapted plants to prosper at the expense of moisture-retaining forest. The increase in fire at this time is generally associated with the arrival of the first people on the Australian continent. It is known that of Australia’s megafauna went extinct at this time, but Magee et al. (2004) show that even the tropical rains were effected by human migration, with drastic changes to the continent’s largest river basin.

If you read some of the academic literature on fire ecology you have a hard time not coming to the conclusion that modern humans terraformed the planet Earth! The hallmark of modern H. sapiens seems to be extinction of large organisms, a propensity to go where no hominin has gone before, and copious utilization of the “red flower.”

MORE ABOUT: Anthropology

The Australian Aborigines may not be just descendants of first settlers

By Razib Khan | September 22, 2011 5:52 pm

Just realized. The Science paper has some interesting dates which allows us to make the above inference.

- Separation between Europeans and East Asians 25-38 thousand years before present.

- Gene flow between proto-East Asians and proto-Australians before the Native Americans diverged from the former 15 thousand years before the present.

- A conservative first landing in Australia 40-45 thousand years before the present.

The Native American result, where they share some derived variants unique to East Eurasians (mutations which emerged after the separation from West Eurasians) with Aborigines, pegs a minimum date of admixture ~15,000 years ago. But, obviously the admixture had to occur after the divergence of West and East Eurasians. Let’s say ~30,000 years ago. Even assuming that the gene flow between East Eurasians and proto-Australians occurred immediately after the separation 38,000 ago, there were anatomically modern humans in Australia for thousands of years already! The implication is that the first Australians by necessity can not have contributed in totality the ancestry of modern Aborigines. The AJHG paper gives a 50:50 estimate for the ratio of proto-Australian and the Andaman Islander/Malaysian-Negrito related population. We don’t need to be certain of the exact value to assume that numbers like this imply considerable admixture above trace levels.

Of all the dates I’m probably most confident about the archaeological ones about the settlement of Australia by anatomically modern humans. 46,000 years ago the megafauna started going extinct. That’s an immediate tell that humans have been let into the garden.

Out of Africa onward to Wallacea

By Razib Khan | September 22, 2011 1:56 pm

There are two interesting and related papers out today which I want to review really quickly, in particular in relation to the results (as opposed to the guts of the methods). Taken together they do change our perception of how the world was settled by anatomically modern humans, and if the findings are found to be valid via replication (I think this is likely, in at least some parts) I was clearly wrong and misled others in assertions I made earlier on this weblog (more on that later). The first paper is somewhat easier to parse because it is in some ways a follow up on the paper from 2010 which documented admixture into Near Oceanian (Melanesian + Australian Aboriginal) populations from a distant hominin lineage, the Denisovans.

In this paper in The American Journal of Human Genetics they extend their geographic coverage. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania:

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

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Out of Africa's end?

By Razib Khan | September 17, 2011 12:54 pm

The BBC has a news report up gathering reactions to a new PLoS ONE paper, The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology. This paper reports on remains found in Nigeria which date to ~13,000 years B.P. that exhibit a very archaic morphology. In other words, they may not be anatomically modern humans. A few years ago this would have been laughed out of the room, but science moves. Here is Chris Stringer in the BBC piece:

“[The skull] has got a much more primitive appearance, even though it is only 13,000 years old,” said Chris Stringer, from London’s Natural History Museum, who was part of the team of researchers.

“This suggests that human evolution in Africa was more complex… the transition to modern humans was not a straight transition and then a cut off.”

Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.

They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought.

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When all probable things can not be right

By Razib Khan | September 14, 2011 8:35 pm

I’ve been chewing on the modern human range expansion into Neandertal territory paper for a few days now. But I haven’t been able to bring myself to say much. There are two reasons. First, it’s a simulation paper, and I don’t exactly know what I can say besides being skeptical of the plausibility of some of their results and their assumptions, unless I bother to replicate their simulations. There’s something of a “black-box” aspect from the outside operationally in the case of these sorts of research. Second, Ed Yong has boiled down the paper to its essence rather well, while John Hawks and Dienekes have offered their critiques. Dienekes and John get at one of my gnawing worries about all these sorts of models about deep history. Here’s John:

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Personal genomics & rare populations notes

By Razib Khan | September 14, 2011 12:32 pm

I’m going to address two points in this post. The next possible target for getting an undersampled population, and the Malagasy results.

First, lots of great submissions in regards to populations which are undersampled. Some of them are actually already in the data sets. For example, the Burusho and Kalash are in the HGDP. There has been a major dump of data from the Americans recently as well. Zack Ajmal at HAP has the most systematic description online about where to find these that I know of. Additionally, I’m looking for stuff which is interesting where N = 1 would make a difference. I think that was the case for the Tutsi sample, as well as the Malagasy. When you have no prior information, adding one data point is notable. Obviously I can’t afford the money, time, and energy, required to get a good representative sample from a given region. Though I hope researchers who have a gusher of grant money might look at the above thread for ideas.

I think the next population to look for is someone with Ainu ancestry. This is easier said that done, so I need to think about it (both because of dilution and the language barrier). But then again, the Tutsi and Malagasy requests had a much more positive and faster turnaround than I had expected. So I’m not going to get all down about the likelihood.

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Neandertal introgression and admixture

By Razib Khan | September 12, 2011 3:11 pm

Ed Yong has a good good review of a new Neandertal introgression/admixture paper in PNAS. It’s not live on the web yet, so let me quote Ed:

Even if the odds of successful interbreeding were just 5 percent, Neanderthal genes would make up the majority of the human genome today. As it is, a lack of viable sex explains why none of the Neanderthals’ mitochondrial DNA made its way into modern humans, and why so little of their main genome did.

Currat and Excoffier suggest that either modern humans and Neanderthals didn’t have sex very often, or their hybrids weren’t very fit. They favour the first idea. According to their model, it would only have taken between 197 and 430 liaisons between ancient humans and Neanderthals to fill 1-3 percent of modern Eurasian genomes with Neanderthal DNA. Considering that they two groups probably interacted for 10,000 years or so, it would have been enough for one human to sleep with one Neanderthal every 23 to 50 years.

From what I gather in the comments this is due to the fact that if there was a wave of advance very small levels of admixture per unit of advance can build up rather rapidly. I think this is easy to express in temporal rather than spatial terms.

For example, let’s imagine a population of modern humans expanding into a population of Neandertals. The original source population doesn’t receive any more contributions after the initial push, so you have a series of admixture events over time. Assuming 5% admixture per generation, this is the dilution of the “original ancestry” which would occur over 30 generations, or 750 years:

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The gift of the gopi

By Razib Khan | September 8, 2011 2:12 pm

Krishna with milk-maids

Unlike in some Asian societies dairy products are relatively well known in South Asia. Apparently at some point my paternal grandmother’s family operated a milk production business. This is notable because Bengal is not quite the land of pastoralists. In much of North India milk and milk-products loom larger, in particular ghee. People don’t tend to consume what makes them ill, and even accounting for some processing in the form of butter, most researchers have assumed a substantial number of South Asians must be lactase persistent. That is, they can extract nutritive value out of the lactose sugar present in milk (in addition to fat and protein). Additionally, many South Asians have the well known -13910 C>T common in Western Eurasia. How do I know this? Because I share my genetic information with lots of South Asians, and some of them, especially Punjabis, come up as “lactose tolerant” on that allele.

A new paper in Molecular Biology and Evolution confirms this with a larger data set, over 2000 samples from South Asia. The geographical pattern is exactly what you’d expect:

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Racism, what about speciesism?

By Razib Khan | September 8, 2011 12:49 pm

One thing that came to the fore in late 2008 was the worry that a financial regulatory regime which had been exceeding lax was now more conscious of the excesses of the previous era. The problem being that one will not necessarily be prepared for the next crisis. Similarly, terrorist actions such as those of the 9/11 hijackers are probably unlikely in their specific details, because the element of surprise is gone. That’s what makes much of the TSA “security” measures so frustrating for many people, there is a strong suspicion that the authorities are aiming to prevent the previous operation, when real terrorists will naturally alter tactics.

I thought of that when forwarded a link to a new book by a friend, Race and the Genetic Revolution: Science, Myth, and Culture. Here’s the summary:

Do advances in genomic biology create a scientific rationale for long-discredited racial categories? Leading scholars in law, medicine, biology, sociology, history, anthropology, and psychology examine the impact of modern genetics on the concept of race. Contributors trace the interplay between genetics and race in forensic DNA databanks, the biology of intelligence, DNA ancestry markers, and racialized medicine. Each essay explores commonly held and unexamined assumptions and misperceptions about race in science and popular culture.

This collection begins with the historical origins and current uses of the concept of “race” in science. It follows with an analysis of the role of race in DNA databanks and racial disparities in the criminal justice system. Essays then consider the rise of recreational genetics in the form of for-profit testing of genetic ancestry and the introduction of racialized medicine, specifically through an FDA-approved heart drug called BiDil, marketed to African American men. Concluding sections discuss the contradictions between our scientific and cultural understandings of race and the continuing significance of race in educational and criminal justice policy.

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Of beasts and men

By Razib Khan | September 5, 2011 9:23 pm

“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?

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Africans aren't pure humans either

By Razib Khan | September 5, 2011 3:38 pm

Last year when discussing the possible admixture of Neandertals with the ancestors of modern non-Africans I joked that Sub-Saharan Africans were “pure humans.” This was tongue-in-cheek in part because the results from the Neandertal genome shifted my assessment of the probability of archaic admixture within Africa as well. In other words, there may never have been a pure “human” type which expanded and assimilated archaic ancestry on the margins of its range. Species Platonism may be very misleading for our particular lineage. Rather, what it means to be human has always been in flux, a compromise between extremely different ancestral components.

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Tutsi probably differ genetically from the Hutu

By Razib Khan | August 29, 2011 11:04 pm

Paul Kagame with Barack and Michelle Obama

I first heard about Rwanda in the 1980s in relation to Dian Fossey’s work with mountain gorillas. The details around this were tragic enough, but obviously what happened in 1994 washed away the events dramatized in Gorillas in the Mist in terms of their scale and magnitude. That period was a time when the idea of “ancient hatreds” leading to internecine conflict was in the air. It was highlighted by the series of wars in the former Yugoslavia, and the Tutsi-Hutu civil wars in Rwanda, Burundi, and Congo. Of the latter the events in 1994 in Rwanda were only the most prominent and well known.

After having read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa I am relatively conscious of the broader canvas of what occurred in Central and East Africa in the 1990s. Not only was there a conflict between Tutsi and Hutu in Rwanda, but a similar dynamic also flared up in Burundi. The tensions are more complex in Congo and Uganda, in large part because there are many ethnic players, and the Hutu role as the antagonists with the Tutsi is divided among many different populations. In trying to distill the complex ethnography of this region in setting the structural parameters of the landscape into which the violence of the late 20th century emerged many pundits have pointed to the role of the Belgian colonial authorities in crystallizing, sharpening, and perhaps even originating the distinction between Tutsis and Hutus. This is not totally unreasonable if you don’t know much. A quick “look up” will confirm that there is no linguistic or religious distinction between the two groups; they share a common culture in many ways. Rather, the differences seem more of class and ecology. The Tutsi minority had a much stronger pastoral element to their economy. The Hutus were conventional farmers, clear legacies of the Bantu expansion which swept from West-Central Africa east and south, all the way to the Cape of Good Hope and the Indian Ocean. As is not uncommon in the history of humankind the pastoral Tutsi tended to dominate the Hutu peasant. This is where the class dimensions are clearest, as the modest Hutu were traditionally ruled by the wealthier Tutsi aristocracy.

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Deleterious drag as a side effect of adaptation

By Razib Khan | August 26, 2011 12:04 am

The Pith: Evolution is a sloppy artist. Upon the focal zone of creative energy adaptation can sculpt with precision, but on the margins of the genetic landscape frightening phenomena may erupt due to inattention. In other words, there are often downsides to adaptation.

A few weeks ago I reviewed a paper which suggests that Crohn’s disease may be a side effect of a selective sweep. The sweep itself was possibly driven by adaptation to nutrient deficiencies incurred by European farmers switching to a grain based diet. The reason for this is a contingent genomic reality: the positively selected genetic variant was flanked by a Crohn’s disease risk allele. The increment of fitness gain of the former happens to have been greater than the decrement entailed by the latter, resulting in the simultaneous increase in the frequency of both the fit and unfit variants. You can’t always have one without the other.

But that’s just focusing on one gene, though the authors did indicate that this may be a genome-wide feature. A new paper in PLoS Genetics argues that that is the case, at least to some extent. Evidence for Hitchhiking of Deleterious Mutations within the Human Genome:

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The divisibility of human ancestry

By Razib Khan | August 25, 2011 6:05 pm

The class human or H. sapiens refers to a set of individuals. On the grand scale it’s really not all that clear and distinct. When do “archaic” humans become “modern” humans? Taking into account human variation, what is a “human universal”? A set of organisms are given a name which denotes the reality that they may share common ancestry, and interact behaviorally, and are potential mates. But many of these phenomenon are fuzzy on the margins. Many of the same issues which emerge in the “species concept” debates are rather general up and down the scales of natural complexity. A similar problem crops up when we conflate the history of genes with the history of populations. Such a conflation has value and utility to a first approximation. The story of mitochondrial Eve was actually the history of one particular locus, the mitochondrial genome. But it did tell us quite a bit about the history of the human species, even if in hindsight it looks as if some scientists overinterpreted those findings. One of the major issues I’ve noticed over the past year, with the heightened likelihood of archaic admixture in the modern human genome, is that people regularly get confused by the difference between total genome ancestry, and the evolutionary history of one particular gene.

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The HGDP made less racist!

By Razib Khan | August 17, 2011 10:30 pm

Back in the 1990s there was a lot of controversy around the Human Genome Diversity Project. In fact there were whole books devoted to the sociology of the project. Though on some of the details critics of the project may have had a point, their overall aim of stalling scientific inquiry in this area failed in totality. A few years ago a team out of the University of Chicago even produced a web browser so you can explore the data yourself. To my knowledge this hasn’t resulted in massive genocidal action against indigenous peoples; the human race doesn’t seem to need any scientific backing for that, alas.

But, if I was a Lefty the-man-is-racist type I think I might assert that the chips which were used to generate the 600,000 markers for the HGDP public data set are racist! I’m not one of those types, so what I really am concerned about is ascertainment bias. From what I have heard many of the SNP chips floating around today are looking for variants found in Europeans most often. That’s because so many study populations in medical genetics are of European descent. This is not a total deal breaker, a lot of European variation is useful in understanding world wide patterns of variation. But ultimately it’s not optimal.

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Platonism is useful only when it's useful

By Razib Khan | August 16, 2011 10:44 pm

Below John Farrell posted an amusing comment:

Razib, are you implying there was no clearly defined ‘ontological leap’ from the animal to the human??? I’m going to have to clear this with the CDF in Rome.

The figure to left illustrates the simultaneous encephalization of diverse hominin lineages over the past few million years. When I first saw this result it kind of blew me away. I had known that Neandertals had the largest cranial capacities of any hominins to walk the earth, but to see how many diverse groups exhibited a secular increase in volume over time is still something to behold. It also reminds us that our own conception of “us” vs. “them” in a deep and substantive manner may be somewhat illusory. This element of fiction doesn’t negate the utility of the concepts. There are constructs and ideas which are highly valuable in generating inferences and scaffolding models, which nevertheless collapse under closer scrutiny. But we shouldn’t forget that our concepts are only approximations on the real order of things.

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The point mutation which made humanity

By Razib Khan | August 16, 2011 1:30 am

Steve Hsu points me to a piece in The New Yorker on the science and personality of Svante Pääbo. The personality part includes references to Pääbo’s bisexuality, which to me seemed to be literally dropped into the prose to spice it up. Of course it was the science which I found interesting. There are many more bisexuals than there are heterodox scientists. And yet like many researchers of yore it seems that Pääbo is out to find the genes which make humanity distinctive as we understand it (if the reporting is accurate, which I don’t take as a given). There are some interesting tantalizing clues littered about; some genes implicated in autism seem to exhibit Neandertal vs. modern human differences (with the Neandertals carrying the autism-implicated variants).

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