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Razib Khan's "Unsupervised Learning". Hey everybody. This is Razib Khan with the unsupervised learning podcast. And I am here today with Max Larena. Max, could you introduce yourself?
Hi, Hi everyone. I'm I'm Maximilian Larena, and you can call Max for short and I'm affiliated with the human evolution program of Uppsala University. I'm originally from the Philippines. So I grew up, I was born and grew up in the Philippines and studied
in university studies and did my medical degree in Philippines and then went to Australia for a PhD then transferred to Sweden, for an academic research career. Yep.
Yeah, that's - it's great. So I, I assumed you were from the Philippines, partly by the topics of the papers that we're going to be discussing. And just for the listeners, I will just call them out right now, "Multiple migrations to the Philippines during the last 50,000 years" in PNAS, that one came out a little while ago, there was actually another paper related to the Philippines that I also think came out by another group at a similar time. And then more recently, the reason I reached out to you, "Philippine Ayta possess the highest level of Denisovan ancestry in the world". So the second, you know, is a result I'm not entirely surprised by. But, - you really did some deep digging and kind of analyzed it in the greatest detail that I've seen so far. But let me - let me first start with the initial paper. So this paper came out. I think it came out in the spring, like March 2021. And so, multiple migrations for the Philippines. I think a lot of listeners, they will have read various pieces of various articles in the last say like five years about the Austronesian migration. There used to be the idea of a slow boat, and, you know, express train out to the Pacific with the Polynesians. And where did it all begin? And the hypothesis that is currently, I would say its dominant right now is that the Amis the Atayal, the Aboriginal people of Taiwan who speak Austronesian languages, and in fact, are still present in Taiwan in the mountainous east of the island. The current Taiwanese president is a fourth, what a fourth, Aboriginal? So these are Austronesian people. And the hypothesis is on the order of say, 3,000 to 4000 years ago, they began to spread out of Taiwan go southward first go into the Philippines. And then from the Philippines, there's two different major streams. One stream goes West into Island Southeast Asia maritime Southeast Asia, leading to the Javanese, the Malays, all these other Austronesian speaking groups, and then another stream goes eastward into the Pacific, skirting northern New Guinea, and outward becoming the Polynesians. So your paper kind of complicates that. I mean, ultimately, like you say it in the title, but really, it seems to kind of refute, I guess that simple model is is more complicated, right, can you can you talk about that?
Yeah, sure. You presented it too well. So there's - most scholars who would agree that the first modern human inhabitants in the region like Southeast Asia, are the Australasian related groups like the Phillipine Negritos, the ancestors of Philippine Negritos, it's more controversial or disputed when it comes to the next wave of migrants. So there's two competing theories; One, it's either the next wave of migrants came from the north in the "out of Taiwan", or Austronesian expansion, which was espoused by Peter Bellwood, way back before in the late 80s and early 90s. And it's, as you said, is the predominant view currently, and it's mainly based on linguistic analysis and some archaeological data. On the other side of the coin is the "out of Sunda" hypothesis that some groups migrated from south to the north into the Philippines from Sunda, which was a large continent way back before this was espoused by Wilhelm Solheim, and in was modified later by Stephen Oppenheimer, which is He wrote a book about it "Out of Eden" , like, because of the geological changes during the end of last Glacial Maximum in Sundaland, the subsequent inundation of Sundaland led to the migration of different groups in two different directions. So what we did I mean, there are like earlier, genetic studies, but these are limited and only it only covered like a few ethnic groups in the Philippines and Indonesia. And some of it are only looking at look at uniparental markers. So, what we did is to do a larger study
hey Max, can you can you can you tell the listener what a uniparental marker is.
So you need a parental marker for either, the mitochondrial DNA or the Y chromosomal DNA, so it's something that's inherited from your mother or from the maternal side or paternal side. So these are only looking at one locus. But when you say autosomal DNA, you're looking at the entire genome. And yes, so that's in all chromosomes. It can either be full genome sequences, like everything, or some sites in the genome called single nucleotide polymorphism, which are known to be different between different individuals or different populations. And what we look at are the, the autosomal DNA, which is around 2.3 million snips, what we call snips. Is that ... ?
Yep. Yeah, that's good.
Yep. And yes, so yeah, we, and this time, we covered as much as a lot of ethnic groups all all throughout the Philippines. And, yeah, this was made possible with partnership with the official heritage body of the Philippines, the National Commission for Culture and the Arts, as well as a lot of local institutional partners and some in the indigenous partners as well. So in the initial study, there were around 150. And even to the to the second studies, it reached 218 ethnic groups. And anyways, so what we found out is that there's actually complex waves of migration. And what we see that is that there's there's first two waves of Australasian related Negritos, the Phillipine Negritos, we divide them into Northern Negritos and Southern Negritos, they're very different from each other. So the Northern Negritos would include like the Ayta, the Maniq, their different names, and the Southern Negritos predominately the Mamanwa, which is more related to Australians and Papuans. So there's two corridors entering the Philippines like going through Palau and Mindoru into the north and the other ones to the Sulu archipelago, it's a longer peninsula to the major island in the south called Mindanao. So that's where likely the Southern Negritos entered. And these Negritos are, we think - it's still currently under analysis - They're also genetically related to other Negritos in mainland Southeast Asia, such as the Malay Negritos and the Pilay Negritos or Thai Negritos, called the Maniq ethnic group of Southern Thailand, as well as the Andaman Island....
Okay, I want to ask you about, I want to ask you about that because there's a paper, I think it's not quite 10 years old yet, maybe it's like from 2012 out of David Reich's lab. Yep. And that paper claimed that the Negritos of interior Malaya and the Andamanese. And so you know, just when you say Negritos, I guess like the listeners, they should know, these are dark skinned people, very dark skinned people with curly hair. And they tend to live on these islands or isolated areas of Southeast Asia. And they descend from probably the indigenous substrate of Southeast Asia before the arrival of... this is the theory and I think you kind of problematize this, in terms of perhaps overturning it of rice farmers from Southeast Asia, they were overwhelmed eventually. And so in the Reich paper, from what I recall, there are two deep branches of Negritos, Western and Eastern the Filipinos are with the Eastern and the Phillipine Negritos are in a clade, with AusraloPapuans, as you would say in your papers, whereas the Negritos of the Andamanese, the Malayians and the ones in southern Thailand, they're in a separate clade. I mean, do you find something different in your analyses? I mean, this is a fascinating topic. So I really want to know that
That's okay. Yeah, we haven't gone that far with regards to the relationship with Andaman Islands Negritos but I assume that that's what you explain is the expected one - that the Philippines is related to AustraloPapuans one so there's there's this basal Sunda population in Sundaland, that split later on going into the Philippines and into Austrialia and Papua.
Okay, okay, so go out I'm sorry, I'm interrupted you.
Yeah, so this is those, those are the first two waves of migration. And just to let the listeners know that the Philippines videos, they're actually very diverse groups of ethnic groups ethically. And it's around 30 to 36 Negrito populations within the Philippines and each of them has their own distinct language. And these are very distinct language because they are like primary branches of - some of the primary branches of Malayo-Polynesian branch of Austronesian language family, which is the... the main language of most of Southeast Asia. And when you... when you say that - it's something like the distance between a Russian and an English speaking person. So it's very different between different regions. And aside from that, after some time, what we find is that there's also the subsequent waves of migration, which we refer to as the Manobo related population going into the southern Philippines, into Mindanao . And the next wave is the Sama related populations, which are which has an ancestry that is found predominantly among the Sama sea nomads of southwestern Philippines. And and distinctively this particular genetic ancestry is affiliated with some Austroasiatic speaking ethnic groups in mainland Southeast Asia, such as the Htin and Mlabri ethnic groups. And when we look at split times between Aboriginal Taiwanese and northern Filipinos - Northern non-Negritos - called Cordilleran, it's around 12 to 15,000 years ago, which is around the time there were changes in the region, which we associate with - perhaps it's the geological changes during that time, and the inundation of Sundaland, which precipitated migration of these ethnic groups into multiple directions. And because the islands become isolated, they become differentiated into different ancestral populations. That's the thing. And the last major wave of migration, the fifth major wave of migration, are what we termed as Cordilleran related groups, which is an ancestry that that we find mostly among Austronesian speaking populations, all throughout the Asia Pacific region. And interestingly, the divergence time as well, when we estimate it, not only us but also a paper, by Jeremy Schwan, from the Institut Pasteur et al. , which we are also part of, it's around at least seven to 8000 or older between Aboriginal Taiwanese, and the Cordillerans. And so this would indicate that this is this would precede the concept of agriculture - people moving together with agriculture and language, because the evidence for agriculture is much more recent, like 4000 to 5000 years ago. And it's we don't see a single pulse event as well as we don't see a north to south unidirectional movement, or monolith or a monolithic block, but instead multiple pulses, because the admixture dates that we have the oldest latest found all throughout the archipelago, not from north to south, but quite scattered. So it's very difficult to make sense out of it. So it seems to be a complex process of migration going to the Philippines. And we have to take note that there, there's also geological changes happening between 12 to 7000 years ago, in the landmass that connects Taiwan and southern China. And again, we - because of these changes maybe perhaps this precipitated populations to move in different directions and hence, we have multiple diverse ethnic groups found in the Philippines. Yes, and there are minor migrations later on, which are the Papuan related ancestry, which, like Papuan groups, also migrating westward into eastern Indonesia and into South Eastern Philippines. We think that this also happened at the same time when Papuan related groups migrated eastward into Vanuatu or into Oceania. And there's there's also South Asian gene flow into some
some ethnic groups in southwestern Philippines which happened around 1000 years ago, and then Some limited Spanish colonial legacy In less than 1% of the population. Yes,
Let me - Yeah, I mean, that was great Max. Let me um, let me set the... let me summarize and set the stage a little bit for the listener. So a lot of listeners are going to be American. They obviously know where the Philippines are. They probably know Filipinos personally. One thing that I think surprises A lot of us Americans, though is there is no real ethnic group, I guess maybe that's Filipino. There's a lot of different ethnic groups in the Philippines from the different islands from Luzon to the north. So you're talking about the Cordillerians they are in the northern interior. And then there's obviously Mindanao where there is the Moro Muslim minority. It was a lot of political things. But then there's there's other islands like Palawan, or where there's a variety of islands where people are from these different islands. When I you know, lived in California, you know, people will say, yeah, I'm from the Philippines, and my family's from this island. So there's a lot of distinctiveness in these localities that I think a lot of us forget. And also the Philippines... I think one way, a stylized fact, that maybe you know outsiders. I mean, I'm thinking particularly Americans Westerners can think of is, you know, when when the Spaniards arrived on Manila Bay, in, you know, in the 16th century, the Philippines was already on the edge of the Austronesian Malayan world. There were already Muslims in Luzon. And there were already sanskritized, sanskritic loanwords in the various languages of the Philippines. So it's part of this whole maritime Southeast Asian landscape united by austronesian languages. And obviously, the Philippines took a different cultural trajectory. It is a predominantly Roman Catholic country, because of centuries of Spanish colonialism. You know, if we had an alternative history, the Spaniards never arrived, I think the Philippines would probably... the same thing thathappened to the Philippines that happened to Malaysia and Aceh at first and then later to Java, and eventually was happening to the... Austronesian speaking Chams in Southeast Asia in Cambodia, I think they probably would have become part of Islamic maritime Southeast Asia. But obviously, that didn't happen. And so we think of the Philippines is very distinct, and it is religiously, but I think the broader cultural matrix is this Austronesian maritime Southeast Asian, you know, world. Now, your paper complicates a simple narrative of southward expansion on the order of 2500 years ago, triggered by rice, you're introducing all sorts of other possibilities because of these diversions that you're talking about. I want to, I want to repeat, this will be in the show notes for the listener, but I think I want to just repeat like these populations you're talking about. So we have one clade of, say, northeast, northeast Asians. And you start out in your graph on the left with the Cordillerans, who are this northern Filipino group in Luzon. And then next to them. In the clade, do you have Amis who are Taiwanese indigenous populations, you say separated on the order of 8000 years ago. And then next to them, you have the Dai, which are a South Chinese group in the highlands of southern China, then, of course, the Han of northern China. This looks like the separations on the order of 10,000 years ago, there are some lateral gene flows for various other groups. Further out, you have the various Austronesian groups. And then finally, the northern East Asian groups and indigenous Americans. So, you know, that I think that fits our intuition. So you are saying here, if I get you correctly, in this paper, that the expansion of populations that are more similar to North East Asians, like, you know, kind of like lineages descended from maybe what we would say, listeners on this podcast will know, the sample from Tianyuan 40,000 years ago, right? This happened , considerably before the spread of agriculture into Southeast Asia. So are you asserting here that perhaps the interaction between the indigenous - you know - I don't want to say Australo-Melanesian, although that's the term I think Bellwood uses, but basically the -you know- the earlier populations that are ancestral to Negritos and what we think of as the rice farmers actually predates the rice farmers being rice farmers like is that the implication here that the Austroasiatic people were pushing into Southeast Asia before they were agriculturalists.
Yes, that's what we think. And even not only the Austroasiatic people into Southeast Asia, but also the Austronesian speakers, or maybe there's a pre austronesian language arriving in the Philippines. So we also think that first earliest Cordilleran in the Philippines were hunter gatherers. And yeah, there are multiple evidence can support this, I think I enumerated in this paper, but there are recent publications that are nice as well. So one is the archaeological analysis that was done by Chao Chuan around, which dates around 7,000 to 5000 years ago in the area around southern China in coastal Vietnam, her analysis that most of these populations are actually hunter gatherers. The second thing is that an analysis on rice, rice genetics, the demographic spread of rice, which is the main component of the Bellwood, or out of Taiwan hypothesis, which was published last year, and this year by last year was by Rafael Guttaker, and this year by Ornab Alam. Both of these are from [Michael Pura Gannon], who is a rice expert. So what they found is that the indigenous rices' origin in the Philippines is actually coming from Indonesia. And that split more than 3500 years ago, and indigenous rice in Taiwan, it's a combination of rice from mainland Asia, or China, like the temperate rice and rice coming from Northern Philippines. So it's the opposite direction. So yeah, it's complex as well, in terms of the spread the farming, it's more recent, in terms of the spread of rice, paddy field, paddy field agriculture. And it's way after the boom when the people...
Yeah, I'm still, you know, I, honestly, this is like, this is kind of, to me, it's like, finding out the Clovis first was wrong, like I can accept it. But it's hard to integrate it in my mind about what's going on, because I associated mentally with the Bellwood hypothesis so closely, and I thought, I thought it had been, you know, pretty much validated. I what has been the reaction when the peer reviewer saw this, and just in the academic community among archaeologists and whatnot,
I didn't have any problems with Philippine archaeologists as well as a Taiwanese archaeologist. I mean, I visited various museums in Taiwan. And even in the museum, they would pose there, they would explain the art of Taiwan. But there's a note that this is not what we see, given the local evidence. Yes. And ... most archaeologists that I spoke to would, wouldn't dispute this. And maybe it is a different story when talking to linguists. But I think I'm not sure on how would they view this one? And yeah, I think there will be an increasing number of evidence in the future. The thing is, there's a lack of archaeological data to really have a more meaningful analysis. And, yeah, it's a sampling bias. And I think in the future, there will be more and, and which would either likely support or dispute this one and or add more complexity to this one.
I want to talk about the Cordillerans who... So I think that they're unique. And you know, they're important in a way because of this to the next paper as well. They have almost no Negrito ancestry. Yep. And so they probably arrived in the Philippine Islands about 8000 years ago, 6000 BC, they show up and somehow they are totally they remain totally separated from the Negrito people.
Yes. So yeah, that's something strange for us. And they're they're in a very in more or less an isolated area in the mountains in the Cordillera mountains of northern Philippines. And strangely, we don't, I don't know what's the reason How come for a long time they remained less admixed or unmixed with Philippine Negritos. And yes, there's only some of the groups that's outside of Cordillera mountains, which are also Cordilleran related populations have signs of admixture with Negritos. But not the not the ones that are really in the mountains. Like there's six groups that I enumerated Tuwali, Ayangan, and yeah, Ibaloi, Kankanay. Yep. And I think this was also I mean, presented way back before by Pontus Skoglund in the Lapita paper, they find that they only have one Cordilleran layer and they are the Kankanay Cordilleran and they also find it like they didn't find any Papuan related ancestry. Yeah, because the Lapita, the first Lapita individuales, these are 2900 to 3000 years old and hardly have any Papuan related ancestry. So yeah, I think way back, like more than 3000 years ago, - there's a lot of populations that are either admixed, or less admixed. And it's a bit random when populations admix, we, we sometimes assume once one population arrives in an area, they are expected to admix right away, or in a few 100 years. But in some cases, like in the case of Cordillerans, it's been more than 5000, or atmost 8000 years ago. They still didn't admix.
Yeah, it's it's fascinating. I'm... it's kind of a mystery. You before I move on to the next paper, you know, so two things. So the Cordillerans, they do not have any gene flow from Northeast Asia or northern North East Asians, right. So there's this model now presented by the ancient DNA, where Qiaomei Fu and her group and other groups that there's kind of a good deep structure between northern and southern North East Asians. And there was a massive gene flow that occurred in kind of modern Han Chinese are kind of like the products of the middle, right. But, uh, I guess what I'm saying there is the Cordillerans they don't have any northern North East Asians. So they're purely Southern, Southern, East Asian, and they are they the only ? Are they the most? I wouldn't say pure, those lineages in your in your data set?
Here. You can say that. Yeah, I think a lot of people also tried to, I mean, borrow our data and analyze it, it seems like and we are still analyzing our data together with the ancient DNA database, Qiaomei Fu , which is a very good paper. And so it's more affiliated with Southern East Asians, what they call a southern East Asians those example the Liangdao individuals, which are around 7,000 to 8000 years old, we also have those samples. Yes. And even in those individuals, when they analyze the Liangdao individuals, they have some amount of Northern East Asian ancestry, but we hardly - we don't find it in Cordillerans.
Hmm. Okay. I mean, that's, again, that's a Well, I mean, I guess it kind of makes sense. If they arrive, you know, 8000 years ago, it's before the Great exchange and the gene flow, and agriculture, and so on, before we move on to the Denisovan paper, which is why I reached out to you, but then I reread the Philippine paper, and I was like, I got to talk about this. Because, you know, I mean, I think, honestly, like, I did read that paper, but part of me was just like, Wait a second, but wait out of Taiwan was so simple. Oh, my god, you're adding way too much complication into the into my my mental models right now? Yeah. Yeah, so, um, you know, are you so are you? Are you thinking that the Cordillerans, then were essential in the Austronesian expansion? Or, I mean, how do we think of that right now?
For population geneticists? I think they are very good surrogate of the least admixed signal for Austronesian expansion, because they hardly - I mean, we don't find Negrito ancestry or Northeast Asian ancestry. So yeah, they're quite significant in terms of analyzing, comparative data.
Yeah, okay. Okay, let's move to let's move, let's move to the second pay point. So, so "the Ayta people have the highest level of Denisovan ancestry". This was kind of suspected and evident or not as robustly, like, about 10 years ago. And so, before we talk about the Denisovans, which, you know, have been an obsession of mine over the last, you know, three, four years, partly because I think they're way more interesting in a lot of ways from a population genetic perspective than Neanderthals. But I'll get to that later. I tell us about the Ayta A-Y-T-A. Like, who are these people and, you know, where are they situated?
So, so, the Phillipine Negritos have different names. There's what you call Ayta, Agta, Ati the so, yeah. And the Ayta are mostly situated in central Lazon which is in south western part of Luzon Island. And there there are also different Ayta groups like Ayta Ambala, Ayta Magbukon... And these two groups are happen to have one of the highest Denisovan ancestries and phenotypically, they are. shorter and curly hair and dark skin. And that's why they are termed as Negritos way back before. And just also to emphasize because sometimes when I present, some people would ask me if it's politically correct to call them Negritos when I visit these communities, I mean, when they ask them, Is it fine to call you Negritos? They own the term, they are proud to be Negritos they find nothing wrong with having a dark skin or being called Negritos. And, yep.
I have a question. Because I did read a little bit about the Ayta, before I talked to you. And you know, I'd known about them before, but um, it says some of them have light hair. Is that correct?
What do you mean? Like the hair? Like,
like a non black hair color? Like? Like, you know, there? Are you never, you never saw any of those people with light hair.
Okay, nope. Nope. It may be referring to the sea nomads? the Sama sea nomads? some have to be the light or almost bland here. Okay, yeah. Okay. All right. All right. Anyway, go on. Yep. Yes, and the Ayta of Magbukon is located in Bataan And there's only a few 1000s of Ayta Magbukon. And what we.. what is known, like, way back before, like 10-11 years ago, the initial papers from David Reich - They have a Phillipine Negrito, the group included in the analysis, and that's Mamenwa, which is much more lower Denisovan ancestry. So the focus of where Denisovan ancestry is found is in Papua, among Papuans, and Australian Aborigines. But this one, yeah, we included a lot more populations. And these are populations who are more into the remote areas of - of the Philippines. And yeah, and we just so happened to find that some of them actually has very high Denisovan ancestry. And the thing that the advantage, I think that we can do in our study is that we have different Negrito of groups. And we can actually correlate or plot that Denisovan ancestry relative to Negrito ancestry, and we can extrapolate how would a fewer or less admixed Negrito would look like how much Denisovan ancestry they would have. And we did that and it can be as high as up to 46% or 50% Denisovan ancestry relative to the Papuans or Australian Aborigines. And that's pretty high.
Yeah, yeah. So this Dennis of denisovan ancestry. So let's, you know, I'm I want to remind some listeners of what's going on with these Denisovans. I mean, everyone knows, I mean, if you're listening to my podcast, you know, I hope you know about Denisovans. If you don't, you're very ignorant person. No, I'm just joking. So let me just refresh. These are East Eurasian hominins, East Eurasian humans that are related to Neanderthals that split off from Neanderthals after an early out of Africa migration, perhaps renewed 600,000 to 750,000 years ago. Now, you know, after this, they separated from Neanderthals. And Neanderthals show a phenomenon in the ancient DNA, where they tend to be closely related, they go through these population bottlenecks. And then they seem to re expand. And so there are multiple different Neanderthal populations in the temporal transect. But at any given time, it looks like there's generally one Neanderthal population from the Altai to Spain. Denisovans are different. It looks like there's deep structure that continues over time, in different regions. There's deeply different Denisovan clades, like some of them might be as old as like split 400,000 years ago from each other, which is deeper actually, than the deepest split in modern human like, by probably about two fold than the deepest split in modern humans. And so you have like denisovans that were definitely in the Altai, obviously. And these denisovans look like to have contributed most of the low level of Deniso- ... a very low level - like point 1% area Denisovan ancestry in northeast Asians, mainland northeast Asians, there's a different group denisovans that seem to have contributed to the ancestry in the Papuans who are about like on the order of 5% denisovan. And, I mean, I think the South Asian Denisovan ancestry the Indian subcontinent is more like the Papuans, but that could be different. Now, the Philippine ones. The one the admixture into the Ayta, you are definitely claiming is distinct from the Papuan ones because you do have Papuan and Austrao-Papuan and gene flow into the southern part of the islands. It's not correlated with that. Can you talk a little bit about it? Can you talk about Browning's method and the S-method and how they used... You know, how you guys use cutting edge genomics to figure out all these differences with track lengths and the matches to the ancient genome samples?
Yep. Yes. So what we find among Phillipine Negritos is that the evidence that we enumerated in the paper, how come? We - we think that it's an independent event. One is that when you make a correlation between Denisovan versus Australasian ancestry, so either Papuan or Negrito ancestry, it falls outside the slope of Papuan related groups, like the Papua... ethnic group that has Papuan related ancestry, such as Eastern Indonesians and Oceanians, and that's one indicating it's likely a different one. And they have, as we mentioned, they have higher Denisovan ancestry. And this is not accounted for... It can be explained because Papuans might have mixed with other populations that diluted their ancestry, but we don't know of any evidence that the Highlander Papuans, admixed recently with other populations with low levels of Denisovan ancestry, it's a it's the contrary, it's the Philipine Negritos who have admixed with East Asian migrants or Cordilleran and early related populations, who have almost undetectable levels of Denisovan ancestry. And then we also tried to do an explicit population topology called an admixture graph. And when we try to model it, if it's a shared, or a single event in the ancestor of Austalopapuans, and Phillipine Negritos, it's the model is rejected. What is not rejected is a model wherein there's a distinct or independent sort of introgression event into the Phillipine Negritos. And lastly, we also did simulations. And we tried to model and see if the pattern of data that we observe among Phillipine Negritos is supported by a single shared event, or an independent event. What we cannot rule out or what is supported is that either the ancestors of Phillopine Negritos, and Australopapuans, received a shared event way back before and then the Philippine Negritos receive another Denisovan introgression event, perhaps the Papuans and the ancestors Papuans, as well, based on Jacobs et al. publication two years ago in Cell. And the thing is maybe that ancestral Phillipine Negritos have received much more impact in terms of the admixture. And then - or there's only a completely different Denisovan admixture in different islands. There's no shared admixture event way back in the past. So these are the two models, and how we measure the Denisovan ancestry... There are a couple of ways and one is what we call f4 ratio statistics, or D statistics as well. So what you look at is two, it's more, more or less counting the allele that are affiliated to the Denisovans. And it's also accounting for Neanderthal ancestry. So how much it's more or less? How much Denisovan ancestry accounting for Neanderthal ancestor? Because Yeah, the presence of Neanderthal ancestry can confound the presence of Denisovan ancestry because as you, as you mentioned earlier, they are more related to each other than to modern humans. So you have to correct for that. And that's what we do. And the other method is by Browning, but Sharon Browning in the S-prime method, which looks so you scan in the genome and look something that's very different from modern humans. So it's really deeply diverging. And these are assumed to be archaic segments, and then you try to compare these archaic segments to a reference genome like Denisovan or Neanderthal, are they more more Neanderthal? Are they more Denisovan? And then you can actually make a percentage similarity, like, Is it 100% Denisovan? 80 percent? And when you say Denisovan we're referring to the Altai Denisovan, because it's the only genome, high coverage genome, that we have available as of the moment and what we see is that the as you mentioned, mainland East Asians are a bit of the 80% similarity to the Altai Denisovan. But when it comes to Papuans, And Phillipine Negritos there's more of the Denisovan that's only 50% similar or 50 to 60%, similar to Altai, Denisovan meaning they are more deeply diverging to relative to the
Altian Denisovan. And so what it was estimated around between 200 to 400,000 years ago divergence Yes, I think.
Yeah, so that was... you know, the papers open access so you guys can read the paper. I know that this sounds like a mouthful. It's partly because, you know, we are revolutioning... are revolutionising our understanding our conception of the human past of the, of the phylogenetic tree of, you know, archaic humans, you know, like, there are cousin lineages, along with the modern human origin itself. And so, you know, there's a lot of conceptual gaps to fill in. There's a lot of novelty here. And obviously, people are still discovering things along the way. So, you know, I guess at this point, Denisovans... Denisovans we don't know. We don't have a species label for them. Because, well, you know, there's no fossil attached to that. But you do you do present something, a hypothesis, which just I immediately assumed when just like reading the title, and knowing about this Homo luzonensis, you suggest could be a possibility. Let's talk about that, like, give me I mean, I'm assuming you know, a little bit more about Homo luzonensis, and the typical person listening, tell us about Homo luzonensis. And why you bring Homo luzonensis up?
Yeah, I mean, it's just, I mean, having the data presented that there's a lot of Denisovan ancestry among Phillipine Negritos, especially in northern Philippines, like the Ayta, and Agda , where the Homo luzonensis fosil was was discovered. So, the fosil was discovered in northeast Luzon, and it's in Callao Cave. And previously, it was the first one was needed to around 67,000 years ago, and the current the most recent paper, some are 67, and some are 50,000 years ago, this is uranium series dating. And what they find is that the the fossil has a combination of archaic and derived morphological characteristics, which is a combination of archaic and modern human. So they made based on that they made a classification of a new species termed Homo luzonensis. So what we mean, the thing is, as you mentioned, we don't know how Denisovans really look like so we don't know if they are Densiovans, Denisovan related, or a completely different species. So what we suggest in the paper, there might be multiple archaic species or they might be actually be related to Homo luzonensis. Yep.
So I mean, Homo luzonensis obviously, it's found on Luzon. And like, you know, in terms of ancient DNA on the Philippine Islands... so you guys got ancient DNA in your paper, I think your earlier paper or you got into DNA from like coastal South China, like Fujian. Correct? Like across from Taiwan. Yep. What are the prospects for ancient more ancient DNA in the Philippines? Because it seems like a lot of your questions would be answered if you had more into DNA from Southeast Asia itself.
Yeah, that's true. I think I mean, there's still I mean, it's a challenging environment, tropical environment, it's difficult to have successful extraction of ancient DNA. But yeah, there's a publication with Huge McColl. And they have one data from Northern Philippines from Nagsabaran, which is close to actually where the Homo luzonensis were. But this is only dated to 1900 years ago. And they tried to get the Homo luzonensis fossil, but they were unsuccessful to extract ancient DNA. I hope they would they would try to do ancient proteome. And that's one of the basis where the the Tibetan fossil, it was classified as a Denisovan. And so yeah, that I don't know if they're doing it, as of the moment, but I think it's still possible to extract ancient DNA. If we have more fossils to analyze, and the other things as well as we can add, we also have to take into consideration doing analysis on on sediments and it's becoming more optimized recently, that you can actually Yeah, yeah, extract DNA from soil. So that's one possibility that can be done in the future and future excavations.
Well So, um, you know, Homo luzonensis, Homo floresiensis, the Flores hobbit, all of these are part of like a panoply of Southeast Asia and human lineages that are deeply diverged. Seems to Southeast Asia was really speciose. So are you presuming I'm sure it was in the paper, and I may probably missed it. Are you presuming that the admixture occurred in Luzon? Or do you think maybe Homo luzonensis? And you know, I mean, Sundaland was big. So the whole so just for the listener, the whole that the watery, you know, the oceanic area south of Thailand and Cambodia today. The presumption is much of it was, you know, woodland Savanna. During the Pleistocene, when the sea level was lower, like put a lot of the genetic events that you are inferring have happened elsewhere, those populations migrated into the Philippines.
Yeah, you have a good, you're reaching a good point. Maybe some of the archaeological sites that are very important is already submerged because of the inundation of Sundaland. And so that will be an issue. But the thing is, I mean, the fossils that were discovered more recently, it's actually more inland. So there's still there's a lot of cave networks, like where the Homo luzonensis was found, like, it's only in one case network, there's, I think, more than 100, or a lot more cave networks that are not yet be investigated. So they're still still about possibility.
Okay, all right. I mean, it's I mean, it looks like, it looks like there's still a lot of a lot of work to be done. So I mean, that's good for you, right?
Yeah, I think I would, I hope that it's Florent Detroit from Musee de l'homme as well as Armand Mijares]. We're doing a very good job. On this one. Yeah, they are the experts or the archaeologists. I hope that they will do more in the future. I'm sure there should be something more here.
What so I guess the last question I want to ask you about actually is to loop back to this, Australopapuan migration. So I mean, Philippines is pretty far these people. I mean, - have you talked to archaeologists about what's going on with that, this expansion out of, you know, Melanesia, to the west of the East. Because, I mean, you've already kind of implied that the simple model out of Taiwan, rice agriculture is wrong. So these hunter gatherers, the Southeast Asian hunter gatherers, who were originally located in what we call southern China today, spread out after, after the Pleistocene. And then rice agricultural came later. So I'm imagining a situation where they're interacting with the Hoabinhian indigenous people on the mainland, and then somehow they selectively picked up the rice agricultural, where the Hoabinhian did not. And so the Negritos are these isolated relics. But we also have the situation with people moving out of... New Guinea, I mean, like, Has anyone told you anything about like, What's going on here? They like whatever, you know,
I think I didn't think earlier papers describe this phenomenon. Most, various papers, I their interpretation of the Papuan related ancestry in eastern Indonesia, is that Papuan related populations were there. And then later on austronesian expansion is the opposite. But what we find is actually the opposite. I mean, the Papuan related ancestry happened more recently, more after the divergence of between Australians and Papuans. So yeah. And if you talked to Sue O'Connor, who is an archaeologist in Australian National University, she would also argue for like a complex demographic movement of people in eastern Indonesia. Is that as simple as it seems, hmm. So there's a lot more to be discovered, I think.
Yeah, also, I mean, Max, thank you for time. I mean, you know, should I I don't know if I should call you the destroyer of Southeast Asian orthodoxies or what cuz? Yeah, I don't know what to think right now. That's fine. If what I thought in the past was false, but man that was easier than than what you're trying to like present here. Anyway, so what are you working on in the future? Like, let me ask you that before you before I let you go,
yeah. This paper we sequence only few Philippine Negrito genomes. I think it will be nice to have to sequence more so that it's possible to reconstruct what is an Islander Denisovan so you will have more their DNA tracks and then you can actually covered as much as possible the genome of the Denisovan within the Philippines. That's what we're hoping to do. And then yes, also, in the future, doing some ancient DNA work in the area.
Awesome. Awesome. Well, thank you, thank you for your time. The papers again, for the listener are in PNAS "Multiple migrations to the Philippines during the last 50,000 years." It was came out in March, it is open access. And then we also have "the Philippines Ayta possess the highest level of Denisovan ancestry in the world", very descriptive. And then that just came out on the 12th. And that's in Current Biology, and that is also open access. So, you know, I described the the figures a little bit to you guys, and, you know, this was a complicated, this is a complicated publication, I have to say. So I'm sure that I said a lot of things we said a lot of things that were confusing to you, but read the papers. They're there. They're open access, and I really appreciate Max, just jumping on and short notice and, you know, giving up his time. Thanks.
