Tales of Human History Told by Neandertal and Denisovan DNA That Persist in Modern Humans

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(click) (inspirational piano music) - We are the paradoxical ape. Bipedal, naked, large-brained. Long the master of fire, tools and language, but still trying to understand ourselves. Aware that death is inevitable, yet filled with optimism. We grow up slowly. We hand down knowledge. We empathize and deceive. We shape the future from our shared understanding of the past. CARTA brings together experts from diverse disciplines to exchange insights on who we are and how we got here. An exploration made possible by the generosity of humans like you. (upbeat music) (upbeat music) - Good afternoon. I think I have the longest title talk of today. So that's something. (audience laughs) Thank you very much to the organizers for inviting me to come and speak. Hope you feel better soon, Sarah. So, we've heard throughout the afternoon that modern humans overlapped in time and space with multiple hominin lineages. In one topic that has been of enduring interest is, was there any admixture that happened between modern humans and these other groups of humans? And for a long time, the answer was well maybe yes and maybe no, and people debated it pretty vociferously. And that was largely because the data to answer that question didn't exist. And it wasn't until more recently that Svante Paabo's group in Leipzig on developed and pioneered tools for studying ancient DNA, and they produced the first Neanderthal Genome Sequence. And we finally had the tools to be able to say definitively whether admixture occurred or not. And indeed, as Sriram talked about earlier, all non Africans derive about 2% of their ancestry from Neanderthals. And what was even more interesting is a few years later, this same group published another paper where they sequenced ancient DNA isolated from a small fragment of a pinky bone, thinking that it was perhaps Neanderthal or maybe modern human, and it turned out to be this entire new branch of humanity that we now call the Denisovans. And this is in fact, the first species to be entirely described by DNA. And so ancient DNA has transformed our understanding of human history over the past decade. And we've learned many things, like what the distribution of Neanderthal ancestry is in populations across the world. And again, we saw this this morning, but we can see that on average, individuals outside of Africa can trace about 2% of their genomes back to Neanderthal ancestors. And strikingly, we find a very different picture for Denisovan ancestry. So here, we really only find Denisovan ancestry in parts of the world down here. Oops, that's not working. So I'll just talk. In populations of Melanesian and Australian Aboriginal origin. So we have a very different geographic pattern of surviving ancestry. And that's great, we can describe global ancestry proportions. But studying ancient DNA is still hard. So my interest in this area can be traced back to a few years ago, where we had this idea that, well, if modern individuals interbred with Neanderthals and Denisovans, then maybe we don't have to excavate ancient DNA directly from fossils, but we could indirectly isolate Neanderthal and Denisovan sequences from the genomes of modern humans. And so we call this molecular excavations. And I borrowed this slide from a CARTA meeting a few years ago, which I think is a really beautiful representation of this idea of molecular excavations. And so, literally what we're trying to do, is develop computational or statistical models and walk along somebody's genome and pull out the bits that were inherited from the Neanderthals or Denisovans. And molecular excavations are really powerful because they enable us to identify the specific DNA sequences that were inherited from Neanderthal or Denisovan ancestors. So it's one thing to say something about a proportion, but when you can actually identify the sequences, you can do a lot of interesting things with it. So you can test evolutionary hypotheses. And you can even start thinking about, well, what's the influence of Neanderthal and Denisovan sequences on traits and diseases in present day populations? And I'll try to touch on all of this in my talk. So we've discovered methods to identify Neanderthals and Denisovan sequences, and we've applied them to geographically diverse populations. We've largely looked at around 2,500 genomes that are part of a publicly available project called the Thousand Genomes Project. But we've also worked with colleagues in some cases, to sample populations from particular regions of the world. For instance, Melanesia, where we expect Denisovan ancestry to be the highest. And so how much of the Neanderthal and Denisovan genome persists in modern individuals? So if we just represent the Neanderthal genome as this circle, when we look across all 2500 people, we actually recover about 41% of the Neanderthal genome. And that's pretty striking, right? That we're not actually sequencing a Neanderthal, but we're stringing together these bits and pieces that survive in modern individuals. And by doing that, we can find almost half of the Neanderthal genome. And that might seem surprising, especially in light that each of us only carries a little bit of Neanderthal ancestry. But the reason this works is that the 2% of Neanderthal sequence that I have might be a little bit different than the 2% that you have, and when we look collectively across large numbers of individuals, we can recover a substantial amount of the Neanderthal genome. And on an individual basis, non-African individuals have about 55 million base pairs of Neanderthal sequence per individual. And this is pretty similar across populations. So East Asians, South Asians, Europeans and American individuals, there's a little variation, but it's fairly consistent. And incidentally, if you get your 23andMe report, and they tell you, you either have the most Neanderthal ancestry or the least Neanderthal ancestry, what it's really saying is that if you have the least amount, you have about 40 megabases of sequence, and if you have the most, you have 60 megabases of sequence and whether that's interesting or not, that's entirely up to you. (audience laughs) So we can do the same thing for Denisovan sequences, again, represent the Denisovan genome as this circle. And here, we don't do quite as well, so, but we still recover 10% of the genome, which is a substantial amount. And the reason we don't recover quite as much is that Denisovan ancestry is largely confined to Melanesian populations. So in fact, Melanesians have about 40 megabases of Denisovan sequence per individual, and you find very little Denisovan sequence in other populations. And in fact, this 10% number is actually pretty good because we only have a sample size of 35 individuals, compared to the 2,500 individuals that we're looking for Neanderthal sequence in. So in fact, there's a lot more of the Denisovan genome to be found. So that's interesting, we can identify introgress sequence, but really what we're interested in is understanding whether admixture was just an interesting side note to human history, or was it something more significant. And in particular, did the sequences that we inherited from Neanderthals and Denisovans, did they have negative fitness consequences? That means were some of these sequences deleterious, were some of the sequences advantageous and confer an advantage to our ancestors. And then ultimately, we'd like to know, what are the phenotypic consequences of hybridization? I'm going to focus mainly on these two issues today. So this is an overwhelming slide showing the distribution of Neanderthal sequence that we can find in modern individuals. In European individuals in blue and East Asian individuals in red. And each place we find Neanderthal sequence in one of these populations, we put a tick mark on the chromosome. The gray regions are just parts of the genome that are too structurally complex to analyze, so we just ignore them, and the black circles are centromeres. And one thing that you might be able to see if you stare at this long enough, and we stare at it for long times, is that there's a non-uniform distribution of surviving Neanderthal lineages. For example, this region, also highlighted by Sriram this morning, is about a 10 megabase region on chromosome seven that's significantly depleted of Neanderthal sequence. It's also significantly depleted of Denisovan sequence. And what this suggests is that there once probably was Neanderthal and Denisovan sequence in this region, but it was deleterious in modern humans and eliminated by natural selection. And as Sriram pointed out, right in the middle of this region is the gene FOXP2, that's been implicated in speech and language. So if we're interested in the genetic substrates of uniquely modern human's phenotypes, these deserts of archaic sequence, I think, are a really, a good starting point. But not all sequences that we inherited from Neanderthals or Denisovans were deleterious. Some, in fact, were advantageous. And we know that there's somewhere on the order of 50 to 100 places in the genome, where there's examples of adaptive introgression. That is, Neanderthal and Denisovan sequences were beneficial and rose to high frequency in the population. We can find examples of this in all of the populations that we look at. And this is pretty fascinating, because as modern humans are dispersing into these new environments, they're admixing and picking up beneficial copies of genes from species or group of populations that have been there for hundreds of thousands of years before them. And so this is a pretty efficient way to adapt to new environmental conditions. And you can sort of generally say that the phenotypes that we're likely influenced by adaptive introgression tend to fall into a couple categories. So things that influence our ability to adapt to new environments like high altitude, for example. Vast majority of adaptive introgression genes are involved in pathogen defense. We know that pathogens are of the strongest selective pressures in humans. And then there's a set of genes that we don't really fully understand that are involved in skin and hair biology, and they too show a very strong signature of adaptive introgression. So we'd like to continue to understand how hybridizing or mating with Neanderthals and Denisovans influenced the trajectory of human evolution. But in the last few minutes that I have, I want to tell you about some work that we published just a few weeks ago, actually, in which we developed a new method that reveals a new twist in our understanding of human history and mixing with Neanderthals. And one thing that you might have noticed earlier in my talk, is that when I talked about patterns of Neanderthal ancestry, I exclusively focused on non-African populations. So, I showed you how much Neanderthal sequence there were, there was in East Asians, South Asians, Europeans and American populations, but didn't say anything about individuals of African ancestry. And that's because all of the methods up until this point have assumed that Neanderthal ancestry in Africa was either very little or non-existent. And so we recently developed a new method that didn't make this assumption. And so we were excited to apply it to individuals of African ancestry. And to our surprise, we actually found substantial amounts of Neanderthal sequence in African individuals. And these were the five populations that were available for analysis from the 1000 Genomes Population or Project. Purple here represents African admixed individual, so largely African Americans, but even in these African populations from the 1000 Genomes Project, we find about 17 megabases of Neanderthal sequence per individual. And just as a comparison, when we look at sort of the same individuals and call Neanderthal sequence using previous methods that we developed that make this assumption that there's little Neanderthal ancestry in Africa, we only call maybe 500 kilobases, so, like, two orders of magnitude less. So this was a really strong signal, and it was very surprising. So we do see Neanderthal ancestry using this new method. But what explains the signal? Well, to make a long story short, there's really two primary explanations. So, the first is that there were migrations back to Africa. So people left Africa in the the major heart of Africa dispersal, hybridized, or admixed with Neanderthals, and some returned back to Africa carrying the Neanderthal sequence with them. And our results show that the amount of back migration has probably been much larger than we've previously thought. So that's one part of the signal. The second part actually is really fascinating and something that we really wasn't on our radar until we, we got this result. And that is that part of the signal of Neanderthal ancestry in Africa is due to an early out of Africa dispersal and gene flow from humans into Neanderthals. And so, let me unpack that a little bit for you. So this is a simple phylogeny, showing the relationship between Neanderthals and three modern human populations, so Africans, Europeans and East Asians, and so the bottom here represents the present and we go into the past as we go towards the top, and this hatch mark just is to indicate that the times aren't going to be drawn proportionally. So we know that Neanderthals and modern humans split around 600,000 years ago, and what our data shows is that not only was there this out of Africa dispersal that happened 80,000 years ago that resulted in the peopling of the world, but there was also a much earlier dispersal of humans out of Africa around 200,000 years ago, and they encountered Neanderthals and admix with them. So, in fact, some of the sequence that we call as Neanderthal, it's not Neanderthal sequence in modern humans, it's that Neanderthals have modern human's sequence. And so this adds a further twist to sort of this complex pattern of admixture, and gene flow and arrows pointing in every direction. So in conclusion, there is substantial amounts of the Neanderthal and Denisovan genome that remain in modern individuals. There were fitness consequences to hybridization, both good and bad. Humans, Neanderthals, and Denisovans have mixed multiple times likely in multiple places, and that there were multiple dispersals both in and out of Africa. And I think this last point is something that is really important in genetics is that we often have a simple models of how humans dispersed around the world, and that the more data we look at, the more complex these models become. And that it's important to take into account the dispersals both out of Africa and back into Africa to really understand patterns of Neanderthal ancestry. So I would like to acknowledge my lab, in particular, Ben Vernot who did a lot of the early work on finding Neanderthal sequence, my collaborators, and my two boys who I'm sure are not watching right now. Thank you very much. (chuckling) (clapping) (upbeat music)
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Channel: University of California Television (UCTV)
Views: 562,848
Rating: undefined out of 5
Keywords: CARTA, evolution, neanderthal, denisovan, homo sapiens
Id: 54zB8FOlFcE
Channel Id: undefined
Length: 18min 30sec (1110 seconds)
Published: Wed Apr 08 2020
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