179 | David Reich on Genetics and Ancient Humanity

0:00:00.1 Sean Carroll: Hello everyone, welcome to The Mindscape Podcast. I'm your host, Sean Carroll. We talked about DNA and genomes, here on the podcast quite a bit, there's a lot of information locked up in our DNA and both information about how we as organisms or other organisms function right in the here and now, but also there's information about our history. Remember a few months ago we talked with Betül Kaçar about Paleogenomics, learning about very, very early life by looking at the current genomes of different organisms and seeing what they have in common, but if you wanna look at human history, you're talking about thousands or hundreds of thousands of years ago, not billions of years ago, and that gives you a different thing that you can do, you can look at the actual DNA of the actual humans from tens of thousands or hundreds of thousands of years ago. Can't do that, if you're looking at billion years ago, there's no DNA left from a billion years ago, so this is a new field of signs that has really exploded in the past decade or two, learning about ancient human history by looking at the actual genomes from skeletons and fossils of real human beings who lived back then. And today's guest, David Reich, is one of the world's leaders in this field.

0:01:14.5 SC: He's made many discoveries along these lines in his lab, perhaps most provocatively, he's one of the people who discovered the fact that there is Neanderthal DNA in most human beings today, other than Africans, other than people whose ancestors had been in Africa the whole time. Most other human beings have a tiny amount of Neanderthal DNA mixed in. So this tells you something since Neanderthal were Europeans and Asians predominantly and human beings homo sapiens came out of Africa. What this means is that when the humans came out of Africa, they got it on with some Neanderthals, they mixed up the gene pools a little bit, and that kind of analysis can be done at many layers in many different times, and we learn a lot, a lot of surprising discoveries have been made. I don't wanna give away all the surprising discoveries, David will tell us about them, but there's this idea that has come about of ghost populations, you find some archeological find and look, so there's some civilization or some settling. Maybe it's not really civilization, but some group of human beings, they use certain tools or they hunted or they gathered or whatever, but how are they related to other groups of human beings.

0:02:28.4 SC: The DNA is telling us this. And so the ghost populations are populations of people who no longer exist, but there's little genomic remnants, little trace of signals in the DNA of other human beings that lets us indicate that they were there and think about how they related historically to other populations. We can use this DNA evidence in conjunction with evidence from archaeology and language and even written history to put together a much more nuanced and complex view of how human beings have developed ever since human beings came on the scene roughly 160,000 years ago. So again, this is one of those areas which we like to do on Mindscape where it's kind of brand new, anything that didn't exist when I was a graduate student, as far as I'm concerned, is completely brand new, and that means that we're just at the beginning of figuring out what we're learning, but David has interesting things to say about human behavior and history in Africa, Europe, Asia, the Americas, the whole bit. Lots of surprises along the way. So let's go.

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0:03:52.8 SC: David Reich, welcome to Mindscape Podcast.

0:03:55.0 David Reich: Hi.

0:03:55.1 SC: I have to start with one amusing anecdote, because I get many people in the podcast in many different areas, and without trying, I keep noticing that a lot of people, even though they're doing neuroscience or philosophy, they had some physics in their background, and I promise, I'm not trying to do that, but indeed I notice on Wikipedia or somewhere that you have a little bit of physics in your background?

0:04:14.8 DR: Yeah, I got an undergraduate degree, and so that means that I studied Physics formally for a few years, but I didn't go on to get a graduate degree or to develop a real expertise in any particular area.

0:04:27.6 SC: But you actually not just took courses, but got a degree in Physics?

0:04:30.2 DR: Sure. My bachelor's degree is in Physics.

0:04:32.1 SC: Did you have the hopes to become particle physicist or astrophysicist.

0:04:36.1 DR: I applied to grad school in atomic optical and molecular physics, and I was gonna go to Berkley, but I deferred it and I ended up getting distracted.

0:04:46.4 SC: Distracted in a good way, clearly. Is the physics education color how you do your DNA research these days?

0:04:54.4 DR: I think so, I think that a lot of my work relies on trying to be sophisticated about quantitative thinking about the data that we produce, and that the laboratory is a kind of hybrid laboratory that both generates data, but very much also develops methodology that's data-driven in order to be able to analyze the data in new ways, and that's always been central to our laboratory, in fact, even the primary thing, and I think I'm able to do that because I have this quantitative background.

0:05:26.3 SC: That's very nice. And there's a revolution going on. But let's explain, because I think that we've talked on the podcast before about Paleogenomics, about learning about early life from modern genomes, given that there's a certain diversity of life and they have certain things in common, you can say things about the past, but that's not exactly what you're doing, you're actually taking advantage of digging up bones of human beings and looking at their DNA.

0:05:50.9 DR: Yeah, that's right. And so, if your interest is in deep, deep time and trying to understand the history of life, the time scales you're interested in are millions, tens of millions, and hundreds of millions, maybe even in some cases, thousands of millions years, but ancient DNA, DNA doesn't really preserve more than a million years, and mostly doesn't preserve more than hundreds of thousands of years. So if your question is to try to understand events, for example, associated with mammalian radiations and dispersals, it's not gonna help you very much, but what it does do is it actively and powerfully interrogates the last tens of thousands and maybe hundreds of thousands of years.

0:06:28.3 DR: And so modern humans descend largely from a common ancestral population in the last 200,000 years, and so what we can do with ancient DNA is sample DNA from all around the world from known times and places and archeological sites and see how the people whose DNA we obtain is related to each other, the other sites and also to people today, and that allows us to understand how the diversity of the world got to be the way it is today, and what's actually quite interesting is that when one does this, when you look at the DNA from ancient archeological sites and see test how it's related to other archaeological sites and people today is consistently surprising. And so the reconstructions one makes from populations living today are often quite different from the reconstructions you make when you actually looked at DNA from known times and places, and that's telling you that people have moved around too much, such that the present day diversity around the world has obscured what was there before.

0:07:23.8 SC: And is your team actually going out there and digging up bones or do you partner with the archaeologists who are digging of the bones?

0:07:30.6 DR: It's almost all partnership with hundreds of archeologists around the world, we work with on a variety of projects.

0:07:36.4 SC: So they'll throw you a bone quite literally, and you will take out its DNA, is this something that we've known how to do for a long time, or is that actually, part of what is new and fun?

0:07:45.2 DR: So the ancient DNA field has been around for maybe 40 years, but it's only become really serious in the last 10 years, and it was been around with a little 40 years because people, for the first time, were convincingly getting snippets of DNA out of old samples, but really until 10 years ago, the only substantial amounts of DNA people were getting were from the mitochondrial sequences, mitochondrial sequences are the energy factories of cells. It's about 16000 DNA units, DNA letters long, and that's about 200,000 of the Human Genome in size, it's only a small fraction of our genome, and it contains the record of our mother's mother's mother's mother's mother and entirely maternal lineage, which is of course fascinating. Important, but it's limited in terms of its statistical information it provides about the past, 'cause it's only a single statistical instantiation of the evolutionary process recorded in mitochondrial DNA. But of course, the whole genome records not just one's mother's mother's mother's mother, but one's mother's mother's father and mother's, fathers, mothers, all over on genealogical ancestors at least, possibly in practice, tens or hundreds of thousands, and with all that data, one could obtain precise information about how people are related to each other.

0:09:00.1 SC: And maybe good background, distinguishing between mitochondrial DNA and nuclear DNA. What do we call the rest of the DNA in the human genome?

0:09:07.1 DR: So your DNA is packaged into 47 units in your cells, in the great majority of your cells, 23 pairs of chromosomes, and your mitochondrial sequence. Your mitochondrial sequence is carried in the eggs that your mother's egg is fertilized and it occurs in several thousand copies, typically per cell but each cell also has one copy each of those 46 DNA packets, the chromosomes that come in 23 pairs, so the copy number of them is much lower than that of the mitochondrial DNA, but there's much, much more information and then 200,000 times more of your DNA is in them, and that's where almost all the genetic information is encoded. It used to be that people study in mitochondrial DNA because it occurred in thousands of times more copies...

0:09:50.8 SC: I was gonna ask, good, yeah.

0:09:51.8 DR: Given how degraded the material it is, maybe that's where you start, because you have a better shot of pulling it out if you have several orders of magnitude more material to start with, but with the new techniques, we can actually work with everything.

0:10:03.7 SC: The new techniques just cheaper, is that the real... Well, effectively, for your purposes, is the reason why there's been a revolution a last 10 years, just because it's easier to reliably sequence to the ancient DNA, or have we learned something sort of qualitatively different about how to analyze it?

0:10:23.1 DR: I think it's all of those things, but it's technically driven as many of these things are, and we're probably getting DNA out with maybe eight or nine orders of magnitude more efficiency than we were 13 years ago.

0:10:36.7 SC: Efficiency in this case means...

0:10:38.5 DR: Costs, say.

0:10:40.4 SC: Okay.

0:10:41.4 DR: And the reasons are number one, short-read sequencing, which is the DNA sequencing revolution, which made sequencing literally 10 to the 5th, 10 to the sixth times more cheaper than it used to be, and that happened in the late 2000s. And another reason is that the only way it was possible before to study DNA was to use Polymerase Chain Reaction, PCR, which required pulling out segments of DNA by putting unique primers down on top of the DNA, and that would end up sacrificing maybe 30 or 40 DNA letters, just in order to pull out the sequence, but the typical fragments of ancient DNA are only about 40 or 50 bases, so if you sacrifice almost everything just in order to pull it out, there's almost nothing left. [chuckle] And so what was happening is it was incredibly expensive to sequence, and the only way people were able to pull it out was by Polymerase Chain Reaction, which lost almost all of the target.

0:11:37.7 DR: And so there was almost nothing left. There have been major technical biochemical improvements that have massively increased the efficiency of the extraction, the purity of the extraction, so all of those are improvements as well, and the result has been, was that beginning in 2009, 2010, it began possible to generate whole sequence data from human remains thousands, tens of thousands, in some cases, hundreds of thousands of years old.

0:12:00.4 SC: But when you say whole genome, are we only getting 30 or 40 base pairs?

0:12:04.0 DR: The DNA is naturally fragmented by the degradation process into fragments that are rarely more than 70 or 60 bases long, and the typical length that we get from sequencing is maybe 30 or 40 or 50 bases. But there are billions and billions of molecules even in a degraded DNA extract and by brute-forcing it or using various tricks, we can get many hundreds of millions of independent DNA fragments and puzzle together, genome scales worth of data.

0:12:34.5 SC: Good, that's what we need for background for the DNA. How about background for the evolution of human beings, 'cause it's always very confusing to me, there's a lot of names of different species and sub-species. What is the big picture story, let's say, from when humans and other primates split, which was a few million years ago?

0:12:55.5 DR: So our closest living relatives are the chimpanzees and bonobos, and slightly more distant to that is gorillas. The chimpanzees and bonobo lineage split from ours probably somewhere between five to seven million, maybe 8 million years ago. It's not even completely clear where that occurred.

0:13:18.3 SC: And where geographically.

0:13:18.5 DR: Where geographically that occurred. And the gorillas are a couple of million years earlier than that. In the intervening time, the lineage leading to modern humans was certainly at sometimes, almost certainly was in parts of Africa, although not necessarily during the whole time, leaving skeletons like the astrolopithecenes, and the artipithecenes and the early Homo human lineages like Homo habilis and Homo erectus, which also dispersed to diverse places in Eurasia already about 2 million years ago. At which point, the thread is not clear anymore, where the ancestors of people, of humans, primary humans, we lived, but beginning maybe 500,000 or 400,000 years ago, it's absolutely clear that the modern game in lineage giving rise to the great majority of people today is again in Africa, and the earliest skeletal remains of people whose skeletons look anatomically modern are 200,000 to 300,000 years ago in different parts of Africa. And then there is an explosion of anatomically modern humans out of Africa and the Near East between 50,000 and 100,000 years ago, that disperses around Eurasia and eventually, and very quickly also to Australia and New Guinea, and then after 15,000 years ago into the Americas, and then in the last couple of thousand years to the last habitable places on earth.

0:14:38.6 SC: And that means we're very young, the species was. We split off from chimps and bonobos millions of years ago, but modern humans only came into existence maybe 200,000 years ago?

0:14:49.3 DR: Or maybe 300,000 or 400,000 years ago, not clear, and only 70,000 years ago, there were at least five groups living around the world that we know about today, through a combination of skeletal analysis and DNA data that were each as different from each other, much more different from each other than any groups living today, the most diverse living groups living today. But within a few tens of thousands of years, we were alone on the planet, these groups were subsumed within, mixed with or displaced by the expansion of modern humans or at the same time as modern humans were expanding. So it's not clear how young we are, comparatively. To me, it's not... I think it's sometimes exaggerated how young we are or how non-diverse we are. If you look, for example, compared to chimpanzees, today, chimpanzees, western chimpanzees, if I remember right, have about as much diversity as humans do, but there are also some other chimpanzees groups like central chimpanzees and Eastern chimpanzees and Nigerian chimpanzees, and together all of those chimpanzees are more diverse than modern humans are, but perhaps they would not have been more diverse than humans, were 70,000 years ago.

0:16:00.0 SC: So it is an interesting thing, we are taught about evolution of various species and you see speciation in different branches and so forth, but this human story reminds us that it's hard to draw fast lines between species and what counts as species, like you say, there was a lot of... I shouldn't put words in your mouth 100,000 years ago, there were organisms that were sort of close to human, that were all over the place, but were they different species or were they sort of different subspecies. How would we describe it?

0:16:34.5 DR: I think that's a philosophical question, and as a biologist and as a geneticist, I'm actually not so interested in philosophy and... What is a species? It's not particularly important to me. I thought about that topic a lot, a lot of people are interested in that topic, and in fact, our collaborative team has thought about that topic and we punted on it, we did not... We refuse to engage with it, so in 2010, I was lucky to be part of a team that was able to sequence DNA from a tip of a finger bone from a cave in Siberia, and we obtained incredibly high quality DNA from this type of a finger bomb and it turned out not to be from any known human group, it was from a group that was almost as different from Neanderthals as Neanderthals were from human. It was separated by many hundreds of thousands of years, maybe 400,000 years from anything we had seen before, so it was incredibly exciting, we didn't have any archaeology that had pointed there to be in a different group living in this region, and so it was incredibly exciting to have this data. And some of the people on our team wanted to call this a new species name, that's one of the ambitions of many paleoanthropologist to have a paper which coins in new species name.

0:17:47.5 DR: The name was gonna be Homo [0:17:48.5] ____, human from the Altai. And we had a long debate and discussion in our team, and we decided to just call it by a common colloquial name, Denisovans, and the reason we decided to do this was that it was completely unclear to us what a species is the classic biological definition, philosophically, as determined by maybe the biological species concept, originally suggested by the biologist Ernst Mayr who argued that species are groups of organisms that do not in practice interbreed with each other, and what we had seen in our genetic data is that these groups were interbreeding with each other, and we're able to form successful mixed groups, like all of non-Africans today who are the descendants of mixtures between Neanderthals and modern humans, or like people in New Guinea today who are descendants of mixtures between Neanderthals, Denisovans and modern humans. So if the definition is that mixtures of groups do not occur and do not lead to successful populations, if they do occur, then our situation did not qualify.

0:18:51.7 DR: On the other hand, the physical anthropologists have argued to us quite often and said, Well, the Neanderthals must be a different species, not by the biological species concept, but by the morphological species concept, they're so different from each other in terms of their forms, they need to be considered a different species. They're very specialized. I don't have an opinion, it feels very philosophical to me, and I'm not so interested in philosophy.

0:19:15.8 SC: I love philosophy, but I get that there are good philosophical questions and less useful ones, but is there a way of, from a more scientific perspective, at least saying that there was a greater diversity of human forms 100,000 years ago than there is today or is even that a bit of an exaggeration?

0:19:31.1 DR: That's absolutely correct. So if you actually... You can imagine some kind of measure of variation amongst populations living around the world, maybe that measure of variation is that if you take two random individuals from geographically around the world, what is their average genetic differentiation from each other, and how much larger is that compared to the differentiation within the population? That's known as FST, it's a measure of how the variation is partitioned, and it would have been larger 70,000 years ago or 100,000 years ago than it is today. Today, that number is maybe 0.1, and that mean... Or it depends on how you compute it. But on average, the amount of genetic difference between two individuals or two genomes within a population is six times greater than the average across two populations. So only a small amount of the variation existing within humans today is a cross-population variation. But amongst chimpanzees today and amongst humans, many tens of thousands of years ago, that would have been a relatively higher proportion.

0:20:38.3 SC: Okay, that makes sense. And let's zoom in on this because there's a famous and incredibly fascinating example of the humans, the predecessors of modern humans fan out from Africa 50,000 years ago, and one of the places they go is to Europe or Eurasia maybe and they meet the Neanderthals. So one question is, is it Neanderthals or Neandertals? Is there an H in there? I've seen it either way. [chuckle]

0:21:05.0 DR: They're both correct in the English language.

0:21:07.2 SC: That's too bad. [chuckle]

0:21:11.0 DR: In our papers, we've used both depending on journal style.

0:21:11.8 SC: Fair enough. I grew up with Neanderthals, so that's probably what I'm gonna try to stick with. But Neanderthals, again, they can clearly interbreed 'cause that's what they did, right? And so, how recent is this understanding and what exactly did we learn?

0:21:23.7 DR: Yeah, So Neanderthals from archaeology are an incredibly impressive group of humans that lived in Western Eurasia, not just Europe, but also in places like Central Asia, and even to parts of East Asia probably. There's a debate about how far east they ranged. Neanderthals appear clearly in the skeletal record a few hundred thousand years ago, and late Neanderthals persist in Europe until about 40,000 years ago, at which point they seem to disappear from the skeletal record as a distinct group of humans. Neanderthals in Europe, late Neanderthals, as well as earlier Neanderthals were large. They were as big or bigger than modern humans. Their brain capacities were as large or larger than those of modern humans, even though their skulls were differently distributed.

0:22:12.5 SC: You said as large... Or as larger.

0:22:16.5 DR: Or larger. So if you do allometrically scaled brain capacity, it's just as large or larger. And they're also larger individuals. And they made complex tools that must require a rich amount of learning and skill in order to create, and had been doing so for hundreds of thousands of years prior to the time they disappeared. So these humans occupied Western Eurasia, and we know they encountered modern humans as modern humans expanded out of Africa and the Near East. We know that because we can see the archeological and skeletal remains of modern humans as they expand out of Africa and the Near East between 150,000 years ago. And we can also see sites, for example, in parts of France where there are Neanderthals and modern humans living side by side and altering, alternating occupations at the same caves.

0:23:10.4 DR: We can see that less sharply in the Near East, in places like present-day Israel and the Mt. Carmel region, where you can again also see Neanderthals and modern humans, but not clearly at the same time the way you can see them in Europe, but in fact, it seems likely they were living there at the same time and interbred, 'cause that's the most likely location where the interbreeding probably occurred. And so a question has always been, as modern humans expanded out of Africa and the Near East, to how did they interact with these other impressive humans who they encountered who were using at least initially similarly complex and sophisticated economic and life history strategies? And the genetic data beginning in the '80s seemed to be suggesting that modern humans, people living all around the world today shared no DNA that was plausibly derived from a group like Neanderthals. All modern humans, for example, on the mitochondrial DNA, the maternally inherited DNA, or also on the paternal DNA, on the Y chromosome, all seem to descend from a common ancestor in the last couple of hundred thousand years, which was highly unlikely to come from a group like Neanderthals which would minimally have diverged many hundreds of thousands of years or even a million years ago, people thought at the time. And so...

0:24:18.6 SC: I'm sorry. Had that been true, would we have thought that that's because the modern humans wiped them out or just couldn't interbreed with them, or was there even a theory?

0:24:27.1 DR: Multiple possible explanations. Some population geneticists, people in my field, argued that there could not have been very much interbreeding because we know from studies in ecology of lots of different species that if there's even a little bit of interbreeding, when a small pioneer group even with advantage spreads into a region occupied by a group that's more well-established and larger in population, as you might imagine modern humans might do as they expanded into a territory previously occupied by Neanderthals, if this occurs, even with a low rate of interbreeding, they'll eventually be swapping of the nuclear genome by the genetic material coming in from the larger group if the process is not instantaneous. And so again and again in different types of animals, you see this nuclear swapping effect during the range expansion, such that even though the population that migrates out is successful ecologically, genetically, the existing population somehow leaves a major imprint. There was no evidence of that, and so it's suggested that maybe there was very, very little interbreeding, or if there was interbreeding, there were some kinds of incompatibilities, either as they call... Either socially or biologically and causing these groups to interbreed.

0:25:43.0 DR: So when I went to grad school, that was the orthodoxy, that was the situation, we thought there was no evidence amongst modern humans of divergent ancestry that might be consistent with substantial interbreeding with a group like Neanderthals.

0:25:55.5 SC: Okay, but... [chuckle]

0:26:00.1 DR: So I mean I think that one of the questions that we were interested in once we knew that we could obtain genome-scale data from Neanderthals, once Svante Pääbo group working in Leipzig made it clear that they would be able to get genome-scale data from Neanderthals which happened in the last years of the 2000s, and they pulled together a consortium, which I was lucky to be involved with, once it became clear that that was gonna be possible, there were a number of questions and one of them is, what is the relationship of Neanderthals to modern humans? One of those questions is, did they interbreed with with people they encountered like non-Africans? The top candidate would have been the ancestors of Europeans.

0:26:35.6 DR: And there were other questions like, when did this lineage split from that of modern humans? Would it have been a few hundred thousand years ago? Would it have been a million years ago? So these were the types of questions we were after. And so when we looked at the data, that was my job to study the relationship amongst these groups along with other people we were working with. One of the questions we asked, of course, was, are they more closely related to some humans than to others living today, because that would be perhaps a sign of interbreeding, if there was interbreeding with some humans more than others, and then you might expect the descendants of those humans to be more closely related.

0:27:09.6 DR: And when we looked at the data, we saw such a signal, and we were actually quite incredulous at that signal because I certainly came from a background which thought there was no such signal, and so I was very skeptical. And also some features of the signal were surprising. There was no excess signal in Europeans. In fact, the signal in East Asians was just as strong. And so that was surprising too, because East Asians, there were no Neanderthals in East Asia, and so this really seemed to be a sharp divide between some Sub-Saharan Africa and Eurasia and the rest of the non-African populations. So that was surprising too. So what we did over the next couple of years is we really wrestled with this observation. We thought maybe this is an artifact of our dirty data of various problems with our data that might occur contamination which had afflicted our field. And so we tested the data in various ways, and stratified the data in various ways, looked at various types of this type data, looked at various types of modern human data, looked at various technical processing of the data computationally and developed several different statistical techniques which would independently look at different types of information that is recorded in genetic data about how populations are related to each other. And they were all pointing very clearly and consistently at a history of interbreeding.

[chuckle]

0:28:30.5 SC: So essentially, every population of people here on Earth does have some Neanderthal DNA in them other than the ones who stayed in Africa.

0:28:41.8 DR: That's close to true, although Sub-Saharan Africans today, many Sub-Saharan Africans today have some degree of Neanderthal ancestry, possibly due to small amounts of back-to Africa gene flows over the last tens of thousands of years. And we can't currently rule out some persistent Neanderthal exchange, but it's a much, much lower level, if at all.

0:29:06.9 SC: So what does this teach us? What are we then thinking about the relationship between the early humans and the Neanderthals? Were they friends? Or did they go to war and capture some slaves? Is that something that we can even hope to answer?

0:29:21.6 DR: I think we could probably hope or we should try to learn more than we currently know, but currently, there's a number of alternative scenarios that are consistent with the data. I'm not trying to mince words at all, but what is clearly the case based on the archaeology, not based on the genetics, is that when Neanderthals and modern humans encountered each other, there was a period of co-existence, but that the co-existence in any one geographic region was limited in time, at most a couple of thousand years in the parts of Western Europe where it's been looked at most carefully, and then Neanderthals quickly disappear. However, it's also true that a lot of the modern human groups that they co-existed with also disappear. So it's not obvious that the Neanderthals were out-competed by modern humans. In fact, there's some archaeological evidence that some of the Neanderthals even picked up modern human technology and learned from them, and especially in France where there is some archaeological evidence from this. But after about 39,000 years ago, many of the early modern human archaeological cultures that are evident in Europe before that time, as well as Neanderthals, disappear and are replaced by a relatively homogeneous archaeological care that potentially re-expands from one place, maybe even the Near East.

0:30:32.0 DR: So it's not just that the Neanderthals disappear, it's that there's many group human groups disappearing, one of them or multiple of them are Neanderthals. And whether that's because modern humans displaced Neanderthals because they had a more different psychology that sort of was incompatible with co-existence or a different life history strategy or whether there was active conflict over limited resources, or whether there were just more modern humans because they had a different economic strategy that allowed them to exploit the environment more intensively and the Neanderthals just got absorbed through mixture, we don't know.

0:31:07.2 SC: Okay, okay. 'Cause I was gonna ask, but I think you just answered it, should we broadly think of the... If we were drawing these diagrams of species coming up on a tree through time, should we think of Neanderthals ending or being absorbed back into the rest of humanity, and maybe the answer is we just don't know.

0:31:25.7 DR: Well, I think that's a philosophical question, which is probably interesting.

[chuckle]

0:31:29.2 SC: Okay, good. We could at least delineate which philosophical questions are interesting or not. Okay, so that was... And this was a revolutionary discovery. This is not what people really thought, like you just said. This is something that we've learned very recently about the genomic history of modern humans.

0:31:46.8 DR: That's right. This and many, many other findings from the application of this technology have been shocking and surprising.

0:31:53.8 SC: And again, all within the last 10 years, it's safe to say, roughly speaking. You have a graph at some point, of the number of genomes that have been sequenced, it's sort of like single digits for a long time, and then just explodes.

0:32:05.4 DR: Yeah, that's right. And so, for example, in 2009, it was zero, and in 2010, it was five, and maybe in 2014, it was maybe 40 or so, and now it's well over 7,000.

0:32:18.1 SC: Okay, so we're learning a lot. And now we're at the point where it's just so many interesting things going on that I wanna hit some of the highlights and then feel free to chime in if I'm missing a highlight. But clearly, there was a lot of action in Europe post the intermingling of modern humans and Neanderthals, right? So I mean I have here in my notes, roughly between 4000 and 10,000 years ago, there were different populations in Europe. And so one question is, is it just... Do we think that there's all this diversity that we know about in Europe just because we've studied Europe more, or do you think that it's a reflection of the actual migration patterns and so forth?

0:32:58.0 DR: I think that everyone who thinks about this data should think about the data from Europe, not as indicating that Europe is in any way a special place, but just as a reflection of what's possible to do when one has a lot of data. And the reason we have so much data from Europe is for several reasons; one is that it's in European laboratories, that the technology for doing this work developed first, and it's also European archaeologists who have been pretty consistent over the last century and a half at assembling skeletal material and keeping it in museums and other collections. And so... And there's also resources in Europe and the United States, and for doing this kind of work, and the field's so young that people are now only reporting the DNA that they started working on, even though it's rapidly expanding to other parts of the world. So Europe's not more important than other places of the world, but it's a place that you can use almost as a kind of laboratory to understand what's possible with applying this type of technology to learn about the past. And what we now have is many, many thousands of whole genome datasets published, and many, many more unpublished more than we have published, that provide a nearly gap-less record of European population history in space and time over the last 10,000 years with a more gap-y record between about 50,000 and 10,000 years.

0:34:21.0 DR: And that's an incredibly powerful resource. We are locked in two dimensions today in terms of our understanding of human variation, but we now have a third, and in Europe, it goes back to even time and it's dense and it's possible to do things that we couldn't do before.

0:34:36.5 SC: And there's a sense in which if you apply this sort of logic to or this sort of way of thinking to Europeans today, they're all one population in a way that there were different populations in the near past.

0:34:49.0 DR: That's right. I mean, I think that Europeans today are not one population. There are substantial variation amongst Europeans, and more broadly, Western Eurasians, or people who are called Caucasians or white on the US census. But there's actually pretty substantial differences amongst these groups, but they're genetically much more similar to each other, everybody in that category usually, than for example, Europeans or East Asians today. And it wasn't always so. So if you look in the places where 400 years ago, people of that US census category would have have lived, the level of differentiation amongst those groups a few hundred years ago would have been similar to what it is now, but roll back 8000 years and there would be many groups in that region is different from each other as European and East Asians are. So when... This was one of the many senses in which people's intuitions, including mine, were wrong about the past. If you had asked me in, I don't know, 2002, what would be the level of differentiation within Europe 10,000 years ago, I would have guessed that it would have been relatively modest, that this region like today would have been a region of relative genetic homogeneity, but in fact, you look at the data, that's completely not the case.

0:35:54.6 DR: And if you were to assign census categories in the past, they would have broken down along completely different fault lines from the way you break them down today. So the past is not really well-described by the present and that's very important to keep that in mind. And one of the things we see again and again with ancient DNA data is when one goes and collects DNA from archaeological context that have never been interrogated before with this technology and makes a guess beforehand about how these people would be related to people living afterward and people living today, almost always that guess is wrong, and often profoundly wrong. And we know this now not just in Europe, but in many, many places in East Africa, multiple places in East Africa, in South Central Africa, places like Malawi, in Cameroon, in India, in Pakistan, in Central Asia, in East Asia, in Japan, in multiple parts of the Americas, essentially everywhere we look almost, we see patterns like this, where again and again, you see that groups in the South Pacific that are not directly ancestral or primarily ancestral to people living today.

0:37:01.6 SC: I like the way you put it that there were populations in what we think of as Europe 8000 years ago that were as different from each other as modern Europeans are different from East Asians. That's something we can visualize a little bit. How much do we know about these populations? And in particular, there's this wonderful idea of a ghost population, like a whole group of people that we don't even... Wouldn't even think existed just on the basis of looking at who exists today and moving backwards. Only through looking at DNA do we realize, "Oh, there's this whole kind of person that we didn't know existed."

0:37:33.0 DR: Right, so ghost populations are groups that emerge out of models, so when you write down a statistical model, a mathematical model for trying to understand how you derive the ancestry of present-day populations from previous populations, models are never perfect, but you write down a model and you can do a goodness of fit test to the data, and you could say, "Oh, this population is a mixture of two, three, four ancestral populations at different times in the past." And when you do such a model, for example, for present day European populations, the first approximation in many European populations today can be relatively well described as a mixture of three ancestral populations. We knew that already in 2014, and you can ask, "What do those three ancestor populations look like?" In order to fit the data, and in fact, none of those populations exist today. The one that's closest to existing today are groups like present day Sardinians, but even Sardinians are not a perfect proxy for one of those three ancestral populations. What happened is that these three ingredients... Source populations for present day Europeans are predicted based on the genetic data of people today, but they're not present anymore because they got mixed together and they exist in different mixed proportions in people living today.

0:38:45.1 DR: So what often happens is when you look at modern data or a mixture of modern and ancient data, you can see that there probably was or there must have been or there parsimonious was an earlier population that now no longer exists in mixed form, but contributed substantially to one or more populations living today. That's what we call a ghost population, a population we reconstruct statistically from groups living today, but we don't have samples from today, and what we find again and again with DNA is we predict these populations and then we see them once we obtain DNA from the right time in place.

0:39:16.6 SC: So we see them in the archeological data... In the bones, in the DNA from the bones that we were actually digging.

0:39:21.2 DR: Correct.

0:39:23.5 SC: Yeah. Okay, and are the Yamnaya one of these? Am I pronouncing it correctly?

0:39:28.7 DR: That's right.

0:39:28.8 SC: That's a ghost population?

0:39:30.5 DR: That's right. So the Yamnaya are a group of people who... Or archaeologically were... Expand about 5000 years ago, across the steppes north of the Black and Caspian seas. The earliest Yamnaya are probably north of the Black and Caspian Sea somewhere, maybe in the Don or the Dnieper River valleys or in the Volga River valleys, but they develop a new economy that is based on at least two major inventions that didn't exist prior to the time that they expanded, that weren't used in those regions before. One of them is the invention of the wheel, which was invented around that time, and we don't even know who invented it first because once it was invented, it spread like wildfire.

0:40:17.7 SC: But plausibly it was the Yamnaya?

0:40:19.9 DR: It's not obviously not the Yamnaya, but it's not obviously them either, and they certainly picked it up pretty fast, and the other was the domestication of the horse, and it was probably not fully domesticated yet, but they were using domesticated horse and domesticated herds, and they took their wagons and they hitched them to domesticated animals, and they moved them out into the open steppe lands, which had been previously uninhabitable because they were far away from water, but they were able to take their supplies out into these regions and graze much larger herds than was possible before on the large biological resources, for example, the grasslands of the steppe, and these people expanded very dramatically, so instead of... Prior to this time, there were many diverse archeological cultures making different types of ceramics and pots, but after the Yamnaya expand, there's a monoculture and homogeneity across a vast region, all the way from central Europe, Hungary, all the way to Mongolia, as these people expand very rapidly.

0:41:15.6 DR: It was not known how this impacted the populations of places that had been previously and continued to be densely settled, like Europe, but we now know from the genetic data that this was a massive impact, so in Northern Europe, more than half the ancestry of many northern parts of Europe today descends from this expansion.

0:41:35.1 SC: And it's not necessarily like an empire, right? With a central rule or anything like that, but the culture of these people, like you said, spread from Europe to East... To Central Asia?

0:41:47.1 DR: That's right, yeah. So I think that the... And the DNA from these people spreads from all of these places, and so I think that many archaeologists would tell you, "Do not confuse this with an invasion," and they'd be right to emphasize that. I mean, maybe... And this is about the time of the earliest Egyptian civilization, so maybe there there would be capacity for an invasion and for organized state society, but up on the steppes, there would not have been that type of organized state society in the same way. We do not know to what extent this was systematic raiding or exploitation, some people argue it might have been, some people argue it might not have been, but in any case, this group was very effective, in terms of expanding, and there's a number of arguments about whether this was related to economic exploitation of niches that were not previously exploited related to grazing or use of new technologies, or to what extent this was active and involuntary displacement.

0:42:43.5 SC: Since there's so much that we don't know, is it a responsible speculation to wonder whether they might have been more centrally organized than we give them credit for? I mean, there might have been a 5000 or 8000-year-old empire that really did answer to a single government?

0:43:00.8 DR: So this is not my expertise, but I'm almost certain the answer is very powerfully that that would be extremely unlikely.

0:43:07.5 SC: Okay.

0:43:08.5 DR: So these people were highly decentralized, there's no evidence of... And there's a lot of archaeology, there's no evidence of centers of power or central settlements, there's no evidence of large congregations of individuals, there's no evidence of systematic war-like events, even though there is evidence, perhaps, or there could be evidence maybe of raiding, and certainly tons of evidence of violence. I think people, if they were interested in violence as a kind of mechanism for these groups expanding, would be more interested in ideas like cattle raiding or resource raiding or raids on other communities to take... By men after women or various things like that, but not organized in a large way. People argue that mythology spoke in Europe and India today associated with Indo-European language speaking cultures has shared traits that might descend from a population that spread these languages and some of that shared mythology, and people try to reconstruct some of the shared values in these ancestral Indo-European language speakers and people argue based on this, that this would have been a society that was focused on practices like cattle raiding or various male-centered expansion practices. They are seen in kind of distorted reflected form in Indic mythology and Nordic mythology and Greek mythology and so on.

0:44:40.1 SC: Well, and the application of gender to these questions is not purely hypothetical, right? Because we can separately look at the DNA from the patrilineal line and the matrilineal line by looking at Y chromosomes and mitochondrial DNA.

0:44:53.3 DR: And X chromosomes, and the rest of the genome, because X chromosome is a kind of female-colored chromosome, because two-thirds of the X chromosomes running around in the world today are in women compared to only one-third in men, whereas for the rest of the nuclear DNA, it's half and half. And so you can kind of... The X chromosome's huge compared to the other parts of mitochondrial DNA and Y chromosome, which are only one instantiation of the evolutionary process, whereas the X chromosome is thousands, and so it actually contains quite a lot of information, so even though the information is in some sense not as crisp is that of the Y chromosome and mitochondrial DNA, it's arguably, in some cases, maybe usually balanced out by the many, many independent flips of the evolutionary coin, allowing one to learn more precisely how groups are related to each other. And so by looking at the X chromosome and solving the system of equations where in one case it's two-thirds, one-third, and for the rest of the genome, it's one-half, one-half, one can extrapolate out what the male and female contribution to different events would have been. And so we have that tool available to us too, to understand the process of sex bias and mixture processes of different populations.

0:45:56.7 SC: And presumably unsurprisingly, one's guess is correct that there are certain men out there who are very good at spreading their seed all over the world. [chuckle] That we have... Our most recent common male ancestor is probably more recent than our most recent common female ancestor.

0:46:11.6 DR: The opposite is true, actually.

0:46:13.6 SC: Oops, got it wrong. Sorry.

0:46:16.4 DR: No, I think your argument is correct. The truth... The oldest common male ancestor is about twice as deep as that of the most recent common female ancestor, so we estimate based on counting mutations since a common ancestor, which serves as a molecular clock, and knowing what the mutation accumulation rate is, approximately. We estimate that the common female ancestor is roughly 150 to 180,000 years ago, approximately that, and until recently, we thought that that was about the same for the Y chromosome, but then a personal ancestry group studying African-Americans found a Y chromosome type that was twice as deep in African-Americans, and then surveys in Africa found a higher frequency of this type, specifically in Cameroon, where there's a number of groups that have a substantial frequency of this Y chromosome type, which has persisted, but in studies of many, many, many, many tens or even hundreds of thousands of people, nobody has found a mitochondrial sequence older than this this one.

0:47:13.3 DR: So it's actually quite interesting. The Y chromosome and mitochondrial dynamics spread around the world, mitochondrial differentiation across groups tends to be lower on a short geographic scale and potentially higher on a large geographic scale, whereas Y chromosomes are the opposite. So females and males migrate at different scales. So in a lot of communities, but this is not true exclusively, women are the ones who move between communities, so many communities, but not all communities, are patrilocal or virilocal, and so you'll have... Typically men will range less far from their homesteads than women, so you might have... I don't know, in a model... In a diffusion model, you might have in this community women on average diffusing 10 kilometers or 20 kilometers from their homestead and men maybe not as much, and so that type of process will result in mixing on the scale of tens or hundreds of kilometers, but long, long... So that... Mitochondrial sequences. But long, long range mitochondrial movements seem to be... Human movements seem often to be propelled to a larger extent by male movement, and so that would produce more homogenization... Y chromosome only on a large scale, so there's a scaling factor geographically that is not obvious.

0:48:33.8 SC: So women diffuse a little bit more quickly, but men either stay at home or go way far away.

0:48:37.4 DR: Maybe. On a scale of thousands of years.

0:48:39.5 SC: Sure.

0:48:41.7 DR: With exceptions.

0:48:42.9 SC: There's always gonna be exceptions. I think we can take that for granted here. I was gonna ask about how we should envision what is actually going on in these migrations, is it hundreds or thousands of people picking up stakes and moving from one place to another? Or is it a few explorers going out? Or do we have any idea about something like that?

0:49:01.4 DR: I think we have an increasing amount of information about that process, but that is one of the big open interesting questions that can be addressed in principle, and that we have a lot of possible technical ways to make progress in addressing through looking at this type of data, but I think that in different instances, there are different processes that one might imagine are occurring, so. Yeah.

0:49:30.5 SC: You mentioned something very provocative I wanted to get back to. If it's... Well, if we're talking 5000 years ago or even 8000 years ago, we have language, right? These people could talk to at least their friends. Is that fair? And maybe we can relate the spread of language and the fact that there's something called Indo-European as a precursor of many modern languages. Can we help understand that by understanding how these populations moved around? 'Cause it was always surprising to me that India, which seems pretty isolated from Europe in ancient history, in my brain, shared this sort of language family with us.

0:50:06.4 DR: That's been surprising to people for more than 200 years ever since it was noticed by people who learned Sanskrit and also had learned Latin and Greek, and noticed that these ancient languages were pretty similar to each other, as well as the languages derived from them or related to them. It's been a big mystery about why people across such a broad region all the way from India to the Atlantic shores of Europe spoke similar languages in places also like Armenia and actually, archeological work has since uncovered Indo-European speaking peoples in places where Indo-European languages are not commonly spoken today, including early divergent forms of them, for example, in Anatolia spoken by the Hittites several thousand years ago, and even in the Eastern deserts of the present day territory of China. And so it's been a big mystery how these languages got to spread so far, and we know from ethnographic studies that languages tend to spread through movements of people, and so large scale movements of people, although there are exceptions to that where there's a [0:51:07.5] ____ population... Conversions of the languages has occured, for example, in Hungary, but usually it's through large scale movements of people, so one is tempted to argue that there were movements of people that were vectors for spreads of these languages, and since the time scale over which languages are discernible related to each other, is really only shallow at some level.

0:51:26.5 DR: It's really not more than 10,000 years, and some people even think that's a stretch in terms of reconstruction of shared languages, that provides us information or hypotheses that we can test with genetic data about how particular language groups spread. Indo-European languages are an amazing instance, but by no means the only instance of amazing language spreads. One of the most amazing is the spread of Austronesian languages, these are the languages spoken throughout the Pacific and with the most diversity in the present... In aboriginal peoples of Taiwan, but spoken throughout the Pacific, from Easter Island and New Zealand and Hawaii, through many, many of the islands of the Pacific, through Indonesia. Almost all Indonesian languages are Austronesian, and even Madagascar, off the Eastern Coast of Africa, speak these languages. This expansion occurred just in the last three or 4000 years, and is geographically and humanly at least as dramatic as that of Indo-European, and there too, there's a question of the movements of people that spread these languages, but there's others as well. Everywhere in many, many places in the world. But Indo-European is an amazing example. And one of several were we have strong insights from the genetic data.

0:52:35.0 SC: Well, and for the Austronesians, what do we know? Is the genetic data helpful there, or is it just not there yet or we haven't figured it out?

0:52:42.1 DR: Yes, it's super helpful, maybe even more clarifying in some ways than the Indo-European language data at this point. So linguistically, the deepest roots of Austronesian languages are in Taiwan, as I mentioned. If you look at Aboriginal groups in Taiwan and study their languages and build a tree of how those languages are related to each other and to the ones spoken in this much vaster region, the deepest roots of that language tree, the earliest splitting ones are all in Taiwan, and there's like eight or nine or so deep splits, and all but one of them are in Taiwan. And then there is a cascade of splits that are reconstructed that suggest a possible expansion route through the Philippines, and then in different branches, both toward western parts of Indonesia and also eastward, jumping into places like the open Pacific for the first time, like Vanuatu, Fiji, Samoa, Tonga, and then bursting even further out into Polynesia. And so there's this whole cascade of linguistic bifurcations that has been used to argue for possible spreads of people.

0:53:44.9 DR: The genetic data creates a tracer dye. If you look at Taiwanese, Aboriginal-related ancestry, that is present in essentially all groups that speak these languages, including in Madagascar who are [0:53:56.2] ____ with mostly Sub-Saharan African ancestry, but about a third Austronesian ancestry that's hardly present or not present in the rest of mainland Africa, and is consistent with being spread by these movements of people. So what we see in the Indo-European case and also in the Austronesian case are these tracer dyes, which are distinctive genetic frequency distributions that are characteristic of the ghost population that you think may have originally spread these languages, and the genetics adds to the linguistic data in allowing one to trace the possible and likely movements of it.

0:54:28.9 DR: One particular case that's very interesting about this, in the case of the Austronesian language spread, is that... First spreads that brought people out into the previously uninhabited islands of the Pacific, the last major uninhabited habitable places for humans on Earth, which were really only began to be inhabited about 3000 years ago.

0:54:52.4 SC: Okay.

0:54:54.0 DR: So humans get to the Solomon Islands and Bismarck Islands archipelagos, off the coast of New Guinea and Australia, about 40 or 50... 30, 40, 50,000 years ago, very anciently, very close, soon, after the original spread of modern humans out of Africa, and stopped. So there's other islands, not so distinct... Well, they are pretty distinct, but not so distinct from those that are empty of humans, and then after 3000 years ago, they began to be peopled by humans, and that's...

0:55:20.5 DR: They're peopled by people using ocean-faring technology that was invented by these... Almost certainly by these Austronesian speakers who use it to spread from the Philippines and ultimately from Taiwan, starting the coast of New Guinea, and then they make it to places like Vanuatu and New Caledonia and eventually... And quickly Fiji and Tonga and so on, and these people are able to go over large ocean spaces and navigate much earlier than other Chinese and European navigators were able to cross these large ocean spaces. If you look at the genetics of the first people who bring this ancestry, they look almost entirely East Asian, like Taiwanese, Aboriginals, but the people who live in Vanuatu today have almost no ancestry from this group, and what you see is there's this initial expansion 3000 years ago or so that gets to Vanuatu with almost entirely Taiwanese-related ancestry. Today it's maybe only 10%, and then maybe 500 years later, there's a massive wave from New Guinea... From people related to present day New Guinea that almost completely displaces the local population... Sporadically in different ways, in different parts of the islands, and leaves only, ultimately, maybe 10% from this initial wave, that may not even be originally, mostly from Vanuatu itself, but from other groups that were picked up along the way. It's a very sex-biased process where primarily male people from New Guinea mixed with these seagoing ocean people.

0:56:41.0 DR: You might have thought that the seagoing technologists from ultimately from Taiwan might be the... Your bias might be to think that those are the expanding males, but it's not true, it's the Papuans who are the male-biased expanding population in that case. So there's many instances like this that we're learning about from DNA and that are very surprising. This was a surprise, one what might have thought that the mixed populations of the Pacifics with both large amounts of Papuan ancestry and all of them in large amounts of Taiwanese ancestry and at least some of them, including Polynesians, where it's maybe 75%, might be evidence of a long-drawn-out process of expansion. But when you look at the data, it's a nearly unadmixed initial Taiwanese-related expansion followed by massive movements from New Guinea, a place where most people in their prejudiced picture of the world might not expect large scale movements of people, but in fact, it's the primary ancestry of many of these groups.

0:57:36.1 SC: So it's an extremely dynamic picture of human beings. It's not like a population goes, takes over a land and just dominates it for the next 10,000 years. There's ways of people coming all over the place in Europe and everywhere else.

0:57:51.0 DR: Yeah, and I think we forget that in our cultural memory. I come from a Jewish background from Europe, that's where my second degree and third degree ancestors are from, and the history of Jews in Europe, in Northern Europe, is one where people get comfortable, become integrated in the community and are valuable, valued members of their community, or at least tolerated members of their community for a couple of generations, and then there's a pogrom and the community's wiped out, and it's a disaster, everybody's worried. And then they come back, the next generation, they get comfortable, they think they forget that there was a problem, and then a few generations later, there's another pogrom. So I think on a deeper, longer time scale, I think human history is often like this, people often have a picture in their mind that they descend from people who have been there forever, and that there hasn't been migration and mixture between groups that are quite different and maybe even alien is not an important part of their past, but in fact, looking at genetic data makes it absolutely clear that there are very few of maybe no groups in the world that don't have major mixture as part of their history. So I think that's a bigger pattern that becomes very clear when one studies this type of data, which is that migration and mixture are very central and integral to us when we think at the temporal scale of many thousands or tens of thousands of years.

0:59:14.7 SC: Yeah, it's longer than a human lifetime, so we just think that anything longer than hundred years is permanent as far as those people are concerned.

0:59:19.8 DR: That's right.

0:59:22.3 SC: But there are two examples... You have many, many wonderful examples in the book, and I encourage people to read it, but there are two that I don't want to let pass by without talking about them, India and the Americas. We already mentioned India a little bit, but what was remarkable is the idea that these population flows can be relevant to the caste system in India today, and there's different populations that have a rough correspondence to how Indians live today. Is that a fair thing to say?

0:59:50.7 DR: I think that there is correlation to the caste hierarchies and variation. The caste system in India is, I think very hard to understand for everybody, including for me, and certainly hard to understand for people outside of the system, but has multiple aspects to it, including a kind of organization into strata of people who are in hierarchy and maybe five or four strata of priests and warriors or rulers or merchants and commoners, and people who are outside the caste system, and people who are even lower on the scale. So that's one stratification, but there's also stratification into groups that have different local economic and tribal identities, and there's at least 5000 of those groups, and many of them are endogamous, they really don't mix with other groups, even though they live amongst... And the genetic data that we've studied, this has been probably the single biggest focus of my laboratory over the last 12 years. The genetic data shows that many of these groups really have not mixed with very much with other groups, they've lived amongst for thousands of years, and you can see the signatures of that in the genetic data where groups that may today have population of a couple of million people, in fact have lived [1:01:07.5] ____ next to other groups, and in fact have, through social norms, made it almost impossible for members of their groups to mix with neighbors.

1:01:16.4 DR: So what you have in India is, to some extent, a frozen picture of the structure that existed thousands or a couple of thousand years ago after the system locked in, at least in the ancestry of some of these groups. So maybe it makes it possible to use present day groups to go back a little bit deeper in time and to record a little bit about what the population structure might have been like a couple of thousand years ago, where there's more mixture and there's less barriers amongst groups, although there were still barriers amongst groups in some groups in Europe. So, what you see in India is that there are gradients. The people in India today have a very complicated mix of ancestry, but many groups in India today can be relatively well-approximated statistically as a mixture, as a mathematical mixture of two ancestral populations, one could be called the ancestral North Indians, which are a group that are relatively more closely related to Central Asians and Middle Easterners and Europeans ultimately, and another is called the ancestral South Indians who bear much less relationship to those groups. And we've known that since 2009, and we now know through analysis...

1:02:24.9 SC: That's sort of crazy recent though. Sorry.

1:02:28.8 DR: We now know this through analysis of ancient DNA, and these groups are quite different from each other, as different from each other as Europeans and East Asians, and people range all across the spectrum of proportions from these groups although everybody is mixed. There are exceptions to this, but most people fall in this category, and they follow the two major language groups in India, Dravidian and Indo-European. But those two groups, we now know from co-analysis with ancient DNA are themselves mixed more anciently, a three-more ancient groups. One is an Iranian-related group, one is a steppe pastoralist-related group, and a third is a ancient Southeast Asian-related group related to indigenous Southeast Asians, New Guineans, Andamanese islanders, and more tribal groups from Southeast Asia.

1:03:13.0 SC: Would all of these qualify as ghost populations? Or some of them?

1:03:15.9 DR: So these would all be ghost populations that no longer existed on mixed form, but we have them all sampled in DNA, and in fact, the Andamanese we have directly sampled with relatively little mixture, and we're not arguing these people come from the Andaman islanders, but rather that the Andamanese descent from a group that had little mixture compared to the group that's actually the true source population. So this is a model for South Asians today, and if you look at the proportion of ancestry from steppe pastoralists, it's not very high in India today, it's never more than about 20%, and it goes down to almost 0% in some groups. But we can tell that that steppe ancestry pulsed into India between 4000 and 3500 years ago by comparison to diverse genetic data we have from Central Asians and people from the northern parts of South Asia. We know exactly when it comes in, it's relatively much higher in frequency in people who have traditionally such higher social status in the Indian caste system, and it's especially high frequency adjusting for other factors in people who are from the traditionally custodians of the Indo-European texts, like the Brahmins and Bhumihars in the Indo-European text.

1:04:26.0 DR: And so this suggests that this steppe ancestry is associated with Indo-European associated culture in South Asia, adding another line of evidence to this pulse of ancestry from the steppe about 4000 to 3500 years ago with earlier ancestry from the Yamnaya we talked about before being responsible for spreading these languages into India and militating against other explanations for the spread of these languages. There's very strong evidence now from genetic data that cross-Iranian plateau spread is very unlikely.

1:05:00.0 SC: And I was gonna say that the time scale is about that of the Rig Veda, the classic Indian text that is still very important to modern India.

1:05:08.5 DR: Yeah, critical as well as many other texts, but people reconstruct the writing of the Rig Veda to maybe 3000 to 4000 years ago, and that would be consistent with a rising something around this time of this spread.

1:05:21.2 SC: We could probably do a whole podcast just on that, but I know that you have to go, so let me just ask a little bit about the Americas because I was fascinated to learn there is one of the populations that settled in the Americas is called the first Americans, but it turns out they were not the first Americans.

1:05:36.9 DR: Yeah, it's a kind of tautological kind of name, first Americans, and in some ways, maybe it's not an ideal name because it's a statement about priority or about history in the name itself, and maybe we should try to avoid such names in the future, but almost all the ancestry of Native Americans prior to today that doesn't come from European and African migrants in the last 500 years comes from a single ancestral group that we call First Americans, that likely spread into the Americas maybe around 15,000 years ago, or before almost certainly across the Bering land bridge from Eurasia. We know a lot about that group, we have many early skeletons from that group, although not from the earliest times, and we actually know about their earlier formation from different strands of ancestry present in Eurasia and represented by different ghost populations represented from DNA data. So that's very interesting.

1:06:34.0 DR: However, there are hints in the genetic data, and maybe strong hints that actually, the earliest spreads in the Americas were not homogeneous, and in fact, there might have been a substructured spread of modern humans into the Americas after 15,000 years ago. The Americas was uninhabited by humans before that time, or much before that time, although there's now increasing hints in the data and the archeological data of maybe people argue there might have been earlier presence, but large-scale occupation really begins only after 15 or even after somewhat after that time.

1:07:06.3 SC: Okay.

1:07:06.4 DR: And in Brazil, in particular, there are some groups that bear relatively more close relatedness to people in Southeast Asia and Australia, New Guinea than do the early spreads, than the major population. So that suggests the possibility that the early spread is substructured and a later expansion maybe 12,000 or 13,000 years ago of people that are the primary first American population created small pockets of remaining groups that exist in mixed form in some parts of the Americas today like Amazonia and bear greater relationship attesting to this earlier population spread. It would be really exciting to get ancient DNA that has a large proportion of ancestry from this group. I am not 100% sure this group even really existed. These are four Sigma effects, I don't know. I don't think they rise to expose on level of significance, and so maybe we should treat them as not yet compelling.

1:08:01.0 SC: Well, this is a perfect segue into the final question, which is, Where are we going? This whole field is so young. I have this slight resistance to the existence of any field that came into existence after I got my PhD, but still okay, new sciences come along all the time. What are the next steps? Where are we going in the decades to come? What should people be looking out for in the front page of The New York Times?

1:08:23.6 DR: Well, I think it's been a bit of a Wild West field, it's been really exciting. Every new sample from a previously unexcavated archeological context has been incredibly exciting. We're a little bit in the kind of prospecting phase where there's been an emphasis on getting even one or a few samples from previously unknown archeological context, and the field is also in the hands of the technicians, the people who know how to generate this data reliably and convincingly, and also people who are custodians of the set of tools, both laboratory tools and technical tools to convincingly analyze the data. Now, this creates a bit of a problem because the actual people who know the most about the topics that are being interrogated are not the people who are doing the primary research, and so someone like myself can have the great privilege of analyzing data on the one hand from Vanuatu, data on the other hand from Europe and learning about all these places. But I'm not really deeply trained to know the context, we have to collaborate with archaeologists, and we try to do that and we aim to do that.

1:09:37.1 DR: But really the future is one where the people who really know about these topics will be able to learn enough about these fields, to use the technology to address the questions that they know are most interesting, and I think that transition is now happening in the last couple of years, and for example, we have a paper coming out in two weeks, which is a really good example of that. It's a case of paper where we were writing a paper on the history of Britain in the last few thousand years, and we were reporting data from 793 individuals in one paper. That paper is gonna be published in December 22nd and dumped in the back of the paper was a family tree we had reconstructed from a single tomb in Britain from about a hundred years after farmers got there almost 6000 years ago. So in this figure, we had found a big family that we've now reconstructed 27 people all buried in the same tomb, all we know exactly how they're related to each other.

1:10:29.6 DR: And this co-author of our paper, which had 223 authors, almost all of them archeologists who had contributed samples to this large paper, he had contributed some samples not relevant to that story, but something else. But he noticed this data and he said, That's my expertise. I spent almost all my time looking at Cotswold-Severn long cairn in Southern England dating from this time, and there's all these archeological questions about their meaning and what they meant to their communities, and I'd like to look harder at that. So he talked to one of our geneticists co-authors, and they looked really hard at this family, and what we can tell is that the tomb was one where it was entirely patrilineal, everybody buried in the tomb, it descends from the same patriarch who reproduced with four women, and we can see that, and it wasn't a normal patrilocality though, and because kinship and fatherhood was defined not just biologically, but we actually see multiple cases of adoption. So, this man and his descendants adopted other sons that their wives previously had with other men and incorporated them into the pedigree.

1:11:36.9 DR: So what we're seeing is a community where there were different rules of kinship, and you can learn about that, it answers questions for these people and these archeologists about what these tombs meant to the people who used them, and it's the kind of thing that I think archeologists are particularly excited about, is the kind of study that archaeologists can lead. And so, that's I think sort of the future, one of the futures of this field, which is really taking this technology and midwifing it and handing it and translating it and transferring it to the people who really can pose the questions the best. I've seen genomics field after genomics field doing this. I remember genome-wide association analysis, which I've done a lot of work in, especially in the 2000s, trying to see associations to diseases like diabetes or prostate cancer. And remember, those studies originally were carried out in studies of hundreds or thousands of individuals by geneticists who are technicians, who really knew how to carry out these studies.

1:12:31.3 DR: But quickly, these were transferred to the hands of the epidemiologists, the people who really knew the questions best, and were able to assemble cohorts of hundreds of thousands of people, and that's where that field is now, and that's where genetics and ancient DNA are coming.

1:12:44.0 SC: I foresee specialization in the future but it sure is exciting to be there on the ground floor when you can do the Americas in Africa, in Europe and Asia, all at the same time. And so, David Reich, thanks very much for giving us this introduction to a really exciting time.

1:12:57.2 DR: Good. Thank you.

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