The year of the Other human

By Razib Khan | December 22, 2010 10:58 am

Update: Please see follow up post.

Carl Zimmer, Siberian Fossils Were Neanderthals’ Eastern Cousins, DNA Reveals:

An international team of scientists has identified a previously shadowy human group known as the Denisovans as cousins to Neanderthals who lived in Asia from roughly 400,000 to 50,000 years ago and interbred with the ancestors of today’s inhabitants of New Guinea..

John Hawks, The Denisova genome FAQ:

The most significant finding in the paper is the demonstration that some living humans trace significant fraction of their ancestry to the population represented by the Denisova genome. As in the case of Neanderthals, different human populations show significantly different levels of similarity to the Denisova sequence. For Neanderthals, the similarities indicated between one and four percent Neanderthal ancestry for living people outside of Africa. In the case of the Denisova sequence, the greatest similarities are with living people in Melanesia – in this paper, represented by genome samples from Papua New Guinea and Bougainville. The similarities are consistent with approximately 4% contribution of a Denisova-like population to the ancestry of these living Melanesians.

The paper, Genetic history of an archaic hominin group from Denisova Cave in Siberia. It isn’t open access, but I assume the supplements are.

I’ll have more later after the media gets its fill.

Update: Wired. Dienekes. Nature. Gated, but another Nature piece.

Update II: This doesn’t work yet: http://genome.ucsc.edu/Denisova. But this does: http://bioinf.eva.mpg.de/download/DenisovaGenome.

CATEGORIZED UNDER: Genetics, Genomics, Human Evolution
  • T. Kosmatka

    I’d love to see if the Denisova specimen had the “tawny” gene.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    don’t see it as the ucsc browser yet
    http://genome.ucsc.edu/

  • pconroy

    A few years ago when Dr Cochran asked people where could Neanderthal DNA be found today, one of my suggestions was in Melanesians/Polynesians, as we know that some Melanesians have reddish hair and often Polynesians are very robust – like all the Somoan NFL players – two traits associated with Neanderthals.

    Who would have thought then, that there would be another ancient Hominin living at the same time as Neanderthal, on the same Eurasian landmass, that would also have left a genetic signature in Modern Huamns??!!!

    Of course, we don’t know for sure what Denisovans looked like, from a skeleto-muscular perspective, but I’d bet real cash that the Samaons are somehow involved here. I’d try and genotype Troy Polamalu. This article on American Samoa estimates that a Samoan is 40-56 times more likely to play in the NFL, than a non-Samoan American, due to their size, strength and speed.

    I know the announcement did NOT say Polynesians, rather Melanesians, but I don’t think they checked too many populations yet for DNA matches.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    paul, i don’t think they found it in cambodians. if polynesians have it prolly it is through their melanesian ancestry. they’re ~20% melanesian.

  • pconroy

    Also, maybe check the Ainu of Hokkaido, and other such isolates

  • gcochran

    _I_ would have thought that another hominid population, different from Neanderthals, existed in east Asia: it’s well-known.

  • http://www.kinshipstudies.org German Dziebel

    “if polynesians have it prolly it is through their melanesian ancestry. they’re ~20% melanesian.”

    80% in Y-DNA. I could never understand how they could absorb 80% of Papuan male-biased genes in a matter of just a few thousand years.

    “Also, maybe check the Ainu of Hokkaido, and other such isolates”

    They should do a better digging among Amerindians. The earliest Amerindian skulls are “Australo-Melanesian.” In Razib’s recent gallery of trees and charts, Amerindians and Papuans/Melanesians often cluster next to each other. Unlike the Krause study, this one at least used one Amerindian group, namely Karitiana, but then they lumped it with other “Eurasians.” Why? They need a geography major on the team. From other studies (such as dystrophin gene) we know that an “archaic introgression” is often found at higher frequencies in Amerindians than elsewhere.

    They should also consider the possibility of mutation rate heterogeneity. Higher mutation rate in Africa can explain why San and Yoruba are so divergent but obviously not as old as Neanderthals or the Denisova hominin. Why should mutation rate be independent of population size dynamics?

  • Ray

    Melanesia, you say? How likely do you think it is that H. Floresiensis might be involved somehow in this story?

    I know Floresiensis supposedly diverged much earlier based on morphology, but then, iirc the Denisova hominin has mitochondria that are an outgroup as compared to Humans and Neanderthals. So maybe the Denisova hominin is a hybrid itself. Any way this shakes out, the human lineage is getting more interesting by the day.

  • T. Kosmatka

    2010 is the year that everything changed.

  • Pingback: Tweets that mention The year of the Other human | Gene Expression | Discover Magazine -- Topsy.com()

  • pconroy

    Greg,
    Well I meant in addition to Asian Erectines, which are known, and possibly contributed to East Asians and/or South East Asians?!

  • http://ted.kosmatka@yahoo.com T. Kosmatka

    Now I’m curious if the Denisova specimen had microcephalin haplogroup D.

  • Matt

    Wow.

    I would think an implication of this would be that

    A) Presumably, the hybridisation events occured relatively proximate to Denisova and not within the West Eurasian Neanderthal range.
    B) Yet genetic affinities are not present in contemporary East Asians or other Asian populations, who are, nonetheless, relatively more closely related to Melanesians (than other world populations). Closeness to Denisovans is instead flat in Eurasians.

    Therefore:

    C) This would suggest to me that hybridization occured between part of a wave of advance by Out of Africa “humans”, which were themselves replaced in Eurasia by a later wave and was only preserved through interbreeding in Melanesia.

    I find this conclusion quite odd – why should this admixture between Denisova admixed humans and other later(?) modern humans occur only in Melanesia? why would replacement occur elsewhere? it also doesn’t seem to square with the Southern route and Northern route idea that closely… – but I am not quite sure how to avoid it. I’d guess my first premise would be the one to change if either of them was to.

  • pconroy

    Unless of course you are suggesting that Denisovans=Asian Erectines??

  • http://www.kinshipstudies.org German Dziebel

    “I find this conclusion quite odd – why should this admixture between Denisova admixed humans and other later(?) modern humans occur only in Melanesia? why would replacement occur elsewhere? it also doesn’t seem to square with the Southern route and Northern route idea that closely”

    I agree nothing of this makes sense. I think the elephant in the room is the growing possibility of non-African humans being in fact older than African humans (San and Yoruba in this study) and that African was colonized from Eurasia and not the other way around. In this case, the greater degree of survival of the original “Asian hominin” component, which founded our species, in the coastal Melanesian refugium and its progressive loss as human colonized inner Asia, Europe and Africa is a very likely and natural scenario. The extreme divergence of San and Yoruba becomes then the function of a higher mutation rate, as was suggested in the very first paper on mtDNA genetics (Johnson et al. 1983).

  • gcochran

    “Unless of course you are suggesting that Denisovans=Asian Erectines??”

    Of course I am. The dates in this paper are functions of the assumed mutation rate. We have two different estimates for that, one much-used standard rate based on essentially nothing, and a recent, much lower one one based on parent-offspring rates and known mutation rates for Mendelian diseases. In the paper, they used the standard rate. Switch to the lower rate and you get population split times that fit the fossil record better in both Europe and Asia.

    Yet it’s a great paper for all that.

  • http://washparkprophet.blogspot.com ohwilleke

    One of the really striking observations of John Hawks is that there is a gap in the record of hominin remains from about 200,000 years ago, when the last of the Homo Erectus specimens are dated to the appearance of the earliest arguably modern human specimens, certainly 50,000 years ago, but perhaps even 75,000 to 100,000 years ago at low frequencies. A gap is troubling. It is hard to explain how a species that had roamed Asia for 1.6 million years would suddenly disappear leaving virgin territory of modern humans to fill without being promptly replaced by some other occupant of the same ecological niche. The working hypothesis until the Denisovia find had been that Homo Erectus were present until and co-existed with early modern humans in Asia much as Neanderthals did in Europe.

    The Denisovian DNA divergence date could simply be too young, with it being contemporaneous with Homo Erectus, rather than more later, due to poor population models, or it could coincide neatly with the gap time period.

    Of course, there are good preservation of remains related reasons why you might not find remains of a species who primary range was in tropical and subtropical Asia, but did find remains of that species in Southern Siberia at what might have been the fringe of its range in space and time, because the preservation conditions were better.

    The fact that the genetic affinities with Denisovians seem largely limited to Melanesians is suggestive of the idea that Denisovians could have been wiped out everywhere else but existing in relict island populations that Melanesians admixed with upon arrival. H. Florensis provides precedent for this kind of scenario, and perhaps H. Florensis was even a member of the Denisovian clade. But, this creates the same problem that spontaneous Homo Erectus extinction leaving virgin terrority – what killed off the Denisovians in most of their range?

    A scenario in which (1) Homo Erectus is rendered extinct by Denisovians (who are a distant part of the same clade as the Neanderthal), (2) the Denisovians are in turn rendered exinct as a consequence of a very early wave of early modern humans (perhaps 100,000 years ago) that admix at elevated rates with Denisovians, and (3) first wave early modern humans are then routed from every place but Melanesia by a subsequent wave of early modern human expansion (perhaps 50,000 years ago) with the settlement of Australia and New Guinea perhaps constituting flight and exile from the mainland in the face of this new wave of invaders, is one possible story.

    In another scenario (1) Denisovians replace Homo Erectus, (2) first wave early modern humans wipe out Denisovians outside select refugia with little or no admixture, (3) early modern humans of the first or a subsequent wave of expansion colonize Melanesia in low numbers, (4) early Melanesians admix with relict Denisovians who cease to exist in non-admixed form, (5) Papuan isolation prevents admixed individuals from admixing with later continental Asians until the Austronesians admix with Melanesians.

    At any rate, this is certainly the greatest vindication that the multiregionalists have seen in my lifetime.

  • diana

    Neandertals, Denisovans….any other extinct human ancestors out there? (that we haven’t found?)

  • http://www.kinshipstudies.org German Dziebel

    “At any rate, this is certainly the greatest vindication that the multiregionalists have seen in my lifetime.”

    How can it be a vindication for Multiregionalism? Multiregionalists claimed that Neanderthals have a special connection to modern Europeans. Ancient DNA study refutes it time and again. Multiregionalists couldn’t dream of Denisovians. Ancient DNA identified them as a new hominid population. There’s no evidence so far of any introgression of Homo erectus genes into modern humans. The fact that ancient DNA refutes out-of-Africa, too, doesn’t mean it supports the other camp. Both camps are wrong.

  • http://ted.kosmatka@yahoo.com T. Kosmatka

    Considering the shared background of Papuans and Australian Aborigines, it seems reasonable that Aborigines might share this Denisovan admixture. Does anyone know if this has been ruled out? If not…I think it’s time to take another look at Mungo Man’s aberrant mitochondial sequence in light of this new information. Perhaps it is not so aberrant after all.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    can’t see why aborigines wouldn’t have the 5% denisovan. the recent paper from last summer showed quite clearly common ancestry with papuans > $40,000 years

  • Rafe

    When I was an anthropology undergrad I was fascinated by the implications of the then recent findings on hybridization in canids and what it implied for the human population history.

    It seemed to me that canids as cursorial social carnivores provided an interesting analogy for population history in humans. If the eastern wolf Canis Lycaon could act as conduit for genes from the coyote Canis latrans into the gray wolf Canis Lupus it seemed to me that the model of a perfect cladistic tree splitting but never coming back together would likely not work in human lineage either. Its very exciting to see similar results coming out now in humans. At that time wolves were considered one holarctic species expect the controversial canis lycoan, now we see evidence for distinct populations in the Himalayans and india that have been seperate for hundreds of thousands of years. This kind of cryptic population structure seems like it to might be a good model for Pleistocene population dynamics in humans with much of the structure from that period wiped out by later demic expansion leaving just tantalizing hints like this.

    I do think given the controversy over mutation rates the most parsimonious explanation is still that Denisova is simpy an asian erectus, and the reason we do not see its genetic signature in other asian population is that it was pushed into south east asia during the last glacial maximum and encountered modern humans there. Still I would not be surprised at all to find out once again things are more complicated.

  • http://www.kinshipstudies.org German Dziebel

    “If not…I think it’s time to take another look at Mungo Man’s aberrant mitochondial sequence in light of this new information.”

    Absolutely agree. And at the “nuclear insert” (Zischler et al. 2005), too, that proved to be the closest to the Mungo man sequence. The insert and the Mungo man sequence are re-visited here. http://rokus01.wordpress.com/2010/03/27/denisova-cave-and-the-mystery-of-the-mtdna-phylogenetic-tree/#comment-349

    Also, notably the frequencies of the insert parallel the frequencies of “archaic admixture” in humans: high outside of Africa, low in Africa.

  • bioIgnoramus

    It’s reasonable to have asked “How did Eurasians etc manage to evolve away from Africans so quickly?” One answer now seems to be that it wasn’t only evolution – they also picked up new genes by crossing with hominids who had had many tens of thousands of years longer to evolve to suit their nonAfrican circumstances. How long will it be before the Forces of Progress put a stop to research of this kind – it’s out of control, I tell you!

  • http://www.kinshipstudies.org German Dziebel

    “It’s reasonable to have asked “How did Eurasians etc manage to evolve away from Africans so quickly?” One answer now seems to be that it wasn’t only evolution – they also picked up new genes by crossing with hominids who had had many tens of thousands of years longer to evolve to suit their nonAfrican circumstances.”

    Good point. Now not only do we have serial bottlenecks on the way out of Africa (at least two major ones: for all non-Africans and for Amerindians), which kept reducing the original levels of diversity, but also serial archaic admixture effects (for all non-Africans and for Melanesians), which keep increasing the depleted levels of diversity. Now we just need a couple of Toba-like events to throw into the mix and we’re good to go into 2011.

  • Sandgroper

    Paul, take a look at Fijian rugby players – big, strong and very fast. Scary people.

    http://en.wikipedia.org/wiki/File:Napolioni_Nalaga.jpg

  • http://www.tedkosmatka.com/ T. Kosmatka

    Thanks for the link, German. In which a good point was brought up. Now we have proof of admixture, but where is the missing archaic MtDNA evidence in modern populations? Again and again it seems to have been lost in favor of the Out of African’s MtDNA. There seems to be some selective advantage that begins at the base of L and was retained on up through all the various divisions of M and N, so that no pre-L mitochondria now exists.

  • pconroy

    Sandgroper,

    Napolioni Nalaga reminds me a little of the greatest Rugby player ever IMO, the outstanding Jonah Lomu, who at 6′ 5″ and 260 Lbs, was also super fast – this clips shows him swatting other rugby players like flies as he sprint home with the ball.

  • Sandgroper

    Paul, yes, Jonah was awesome. He reminded me a bit of a war elephant.

    No way would I play rugby against Samoans, Fijians or Maori. Physically they are in a different league.

    But Papuans are built much smaller.

  • http://dienekes.blogspot.com Dienekes

    Now we have proof of admixture, but where is the missing archaic MtDNA evidence in modern populations? Again and again it seems to have been lost in favor of the Out of African’s MtDNA.

    Strictly speaking the mtDNA evidence is incompatible with recent Out of Africa and is compatible with the multiple archaic scenario

    ” For mtDNA, a TMRCA of 170,000 years is within the range of values predicted by the `Multiple Archaic Populations’ scenario (P(TMRCA less than 170,000) = 0.21), but the mitochondrial TMRCA estimate is diffi cult to reconcile with the remaining three scenarios (P less than 4×10-2). “

  • prasad

    On multiregionalism, what happened to the idea that more genetic variation is found inside than outside Africa? Or is that irrelevant?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    still true. this isn’t multiregionalism. out of africa with a twist.

  • wijjy

    prasad, more genetic variation is still found inside than outside Africa, but no-one (AFAIK) has been looking for novel DNA variants in Melanesians, and if they have locally common variants that are not found in other populations but are shared with Denisovans then we are looking at diversity over a longer time scale than for Africans.

    We have only really started looking at diversity, and there will be some more surprises on the way.

  • bioIgnoramus

    “this isn’t multiregionalism. out of africa with a twist.” Aye, but it’s a multiregional twist.

    “We have only really started looking at diversity”: fantastic! We’re studying DIVERSITY and so we can’t be criticised politically.

  • http://www.kinshipstudies.org German Dziebel

    @T. Kosmatka:

    “There seems to be some selective advantage that begins at the base of L and was retained on up through all the various divisions of M and N, so that no pre-L mitochondria now exists.”

    Also note that no pre-M or pre-N exist in Africa. Neither there are any L lineages found at small receding frequencies outside of Africa. All M and N lineages found in Africa (M1, U6, etc.) are derived from outside of Africa. There are several mutation steps separating M and N from L3 that haven’t spawned separate lineages. Biogeographically, too, there’s no continuity between Africa and Europe or Asia in terms of phylogenetically deeper M and N nodes being closer to Africa than phylogenetically more recent ones. This is explained sometimes as the result of a fast migration along the coast with subsequent diversification in South and Southeast Asia, but this scenario, again, doesn’t explain why there are no African lineages outside of Africa and why there was no stepwise differentiation in Africa prior to the migration of M and N out. The whole out of Africa scenario is a very mechanistic model that relies on several unproven assumptions.

  • http://washparkprophet.blogspot.com ohwilleke

    “How can it be a vindication for Multiregionalism? Multiregionalists claimed that Neanderthals have a special connection to modern Europeans. Ancient DNA study refutes it time and again. Multiregionalists couldn’t dream of Denisovians. Ancient DNA identified them as a new hominid population. There’s no evidence so far of any introgression of Homo erectus genes into modern humans.”

    It is a vindication in that modern humans are an admixture of AMH and archiac species, and that the admixture level (at least in the case of Denisovians) is not uniform for all contemporary humans. Certainly, specific multiregional predictions are wrong. But, the concept of introgression of archaic humans into modern humans was apparently right, and it is entirely possible that the Denisovians were Homo erectus or a direct successor to Homo erectus.

  • Colugo

    Brace and Wolpoff were right about sapiens (so-called amhs, ‘heidelbergensis,’ ‘neandertalensis’ etc.) being a single chronospecies. ‘Denisovans’ are simply an archaic population. ‘Moderns’ are just a regional African sapiens variant that expanded.

    Weirdo racists on some other websites claim that archaic admixture mean that Eurasians are more evolutionarily advanced relative to Africans yet at the same time archaic admixture means that Melanesians are more evolutionarily primitive than Eurasians! Which one is it? It can’t be both.

  • http://www.kinshipstudies.org German Dziebel

    “It is a vindication in that modern humans are an admixture of AMH and archiac species, and that the admixture level (at least in the case of Denisovians) is not uniform for all contemporary humans. Certainly, specific multiregional predictions are wrong. But, the concept of introgression of archaic humans into modern humans was apparently right, and it is entirely possible that the Denisovians were Homo erectus or a direct successor to Homo erectus.”

    The concept of an archaic introgression is a late compromise between classical Multiregionalism and Out-of-Africa. Classical Multiregionalism postulated independent modernization in Europe, Africa and Asia with regionally specific technological and biological continuity traits (e.g., shovel-shaped incisors and facial flatness in Asians and in Homo erectus, Mousterian-to-Aurignacian lithic continuities in Europe), with subsequent gene flow and cultural diffusion across the three continents that resulted in the sharing of biological and cultural features that we call “common humanity.” But you’re right that it’s possible that Denisovians are Homo erectus.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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