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

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

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

In some ways the result is not too surprising. There’s a rather clear cline of declining Melanesian admixture as one moves west across the Indonesian archipelago. Intriguingly the Denisovan admixture seems restricted on the western boundary to Wallacea, though the story is made more complex by the existence of the Philippines. The latter archipelago was connected to Sundaland during the last Ice Age, not Sahul, or isolated such as the isles of Wallacea.

The more complex aspect of the paper is that Denisovan admixture is not just a function of admixture with Near Oceanians. Obviously the proportion for Polynesians is elegantly explained by this model, because there is a well known cline of admixture amongst various Polynesian groups with Melanesian populations. And as I noted earlier there is also a Melanesian cline in Indonesia. But the story is not neat for the Philippines due to geography and other genetic results.

A simple model would be that Philippine Negrito admixture with the Denisovans is also a function of admixture with Near Oceanians. An event which we have no record of or reason to suspect, but may have occurred. But they did not find evidence for this. To the left is a figure which shows some of the phylogenetic relationships which they report from their analysis of SNP data. First, you see the admixture of Neandertals with all non-Africans. Second, you see the admixture of Denisovans with the very distant common ancestors of the Philippine Negritos and Near Oceanians. Next, you see an admixture of what I term “Western Negritos” (Andaman Islanders + Malaysian Negritos) with the ancestral Near Oceanian population, but not with the Philippine Negritos. Then you see admixture of an East Asian element, probably Austronesian, with various Negrito groups. The distinction between Philippine and Malaysian Negritos from each other is not that surprising if you look at PanAsian Consortium SNP data. It is a nice result though that the Andaman Islanders seem to be related to the Malaysian Negritos. The geography of the Ice Age implies the origin of this group on western mainland Southeast Asia, in close proximity to the domains of the Negritos of southern Thailand and peninsular Malaysia.

Probably the most tantalizing element to me is that the ancestry and genesis of what we term Near Oceanians may be a more complex affair than we had previous thought. This brings me to the next paper, An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia:

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

This figure distills the model down to its essence:

The main technical issue which is straightforward when comparing the previous paper to this one is that here they sequenced a whole genome of an Australian Aboriginal man who lived 100 years ago. So while the previous paper was working with tens of thousands of markers, this paper could play with millions of SNPs (though do recall that the previous paper had a much wider set of populations covered, which isn’t trivial). The top line finding seems to be that Europeans and East Asians are closer to each other than either is to the Australian Aboriginal. I’ve seen this result before. But, a major issue which is resolved here with their methods is that Aboriginals are closer to East Asians than they are to Europeans! This is the major problem I’ve always had with the idea that there were “two waves” of migration Out of Africa. If this was so, why isn’t it that Australian Aboriginals exhibit equal distance from East Asians and Europeans? The answer here is simple: admixture between the two waves, but only amongst those going east.

In other words I was confused by excessive “tree” thinking, and neglected the possibility of admixture. The first paper also hints as a possible candidate source for the admixture event: the same source population of the Western Negritos! From what I can gather this population falls into the “eastern” branch Eurasian humanity. Not quite close to East Asians, but definitely closer to them than West Eurasians. Therefore the affinity of East Asians to Aborigines may be due to this broader global “East Eurasian” heritage, which was injected into the Aboriginal man’s genome at some point in the past. Interestingly the authors found no difference in admixture from Neandertals between the populations, in line with earlier results. This implies to me, though does not prove, that the Aboriginals are a basal outgroup to other non-Africans, who all underwent the same rough admixture dynamic with Neandertals as they pushed out of Africa. Instead of two waves Out of Africa, perhaps two pulses just outside of Africa?

Finally, the fact that the gene flow seems to pre-date the separation of Native Americans from East Eurasians serves as a “peg” on the populating of Australia. The authors conclude that at a minimum we’re talking 15-30,000 years before the present. The distinctiveness of Australian Aboriginal mtDNAs, as well the localization of Denisovan admixture amongst Near Oceanians, in addition to the archaeology, makes me credit this early founding event. The populations of Sahul may have avoided being swamped out by newcomers by and large since their arrival ~50,000 years ago. I will speculate that this may explain their relatively high quantum of “archaic” ancestry. It may be that in pre-agricultural Eurasia there were many groups with higher fractions of Neandertal ancestry on the margins of the wave of anatomically modern human advance, which were only later assimilated by the demographic swell of the farmers.

There’s a lot more one could say, but I’ll leave it to readers….

(Republished from Discover/GNXP by permission of author or representative)
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  1. Both are very interesting results, thanks for posting.

    It should be noted that they reach contradictory conclusions. From the first paper:

    ” This study has shown that Southeast Asia was settled by
    modern humans in multiple waves: One wave contributed
    the ancestors of present-day Onge, Jehai, Mamanwa, New
    Guineans, and Australians (some of whom admixed with
    Denisovans), and a second wave contributed much of
    the ancestry of present-day East Asians and Indonesians

    In particular, our data provide no evidence for multiple
    dispersals of modern humans out of Africa, as all non-
    Africans have statistically indistinguishable amounts of
    Neandertal genetic material.12,18 Instead, our data are
    consistent with a single dispersal out of Africa (as proposed
    in some versions of the early southern route hypothesis1)
    from which there were multiple dispersals to South and
    East Asia”.

    That is one Ooa, but two arrivals to SEA of the same Ooa peoples in sequence. In second they claim two paralel arrivals to SEA of two different Ooa.

    I´ve not acces to the second paper, that claims two dispersals. Tomorrow I will study the suplementary material. If they conclude the “two dispersals model” only as a way of explaining first that “Europeans and East Asians are closer to each other than either is to the Australian Aboriginal” and second that “the fact that the gene flow seems to pre-date the separation of Native Americans from East Eurasians serves as a “peg” on the populating of Australia”, their “two dispersal” conclusion is very posibly wrong: as I explained in previous comments these two facts (and uniparental NR DNA known past and present distribution) can be explained better with only one Ooa, early separation of a branch to Europe (as in the map, these will turn out to be E NRYC) but later one dispersal to EA through a northern route. Some remained there (C NRYC), some continued to SEA. In SEA separation in two branches: admixed denisovans and not admixed as explained in first paper. This model is more parsimonious.

    Ainu seems to be always neglected in EA, SEA and Oceania studies and might be highly informative.

  2. haven’t had time to read supplements. tell me what you find….

  3. btw, since no one has mentioned it, i think the ancestral ASI-west negrito clade is the connection between australian aboriginals and south asians. if there is one.

  4. since no one has mentioned it, i think the ancestral ASI-west negrito clade is the connection between australian aboriginals and south asians. if there is one.

    That was my thought as well.

  5. I have a feeling Denisova remains may be found west of papua soon. The mixing in the asian landmass would have surely left a genetic imprint.

  6. how would you identify remains as ‘denisovan’?

  7. I guess the chances of finding a Denisovan fossil, let alone retrieving Denisovan DNA, in the tropical climate of Southeast Asia is very low due to the very low preservation capabilities of organic materials in such climates. So it is much more likely for us to find in the future Denisovan fossils (as we currently know almost nothing about their anatomy, for now we will be able to identify them as Denisovan only through genetic tests of course) in the more northerly parts of Asia, especially the cold zones such as Siberia, which is among the best places in the world for fossil and DNA preservation.

  8. BTW, the lack of Denisovan admixture in Western Negritos (including Andaman Islanders) explains the lack of Denisovan admixture in ASI and, consequently, in South Asians.

  9. After first quick reading of suplementary material and without having read the paper, I´ve seen nothing that contradicts my model yet. However split datations (which are result of demo parameter estimations) and this “Native American result” forces a much more accurate analysis. Without datations (that is just ordering populations split and admixture events) this fact could be accomodated without problem; but I´m not sure the model would stand including datations of all parameters.

    P.s. Summary: mtDNA (O1a), NYRC (MNOPS*, likely xM), archaic admixture (neanderthal confirmed), demo parameters estimations (see table S17 in page 91 and figure S32 page 167). Also many data of GWSNP and ABBA-BABA. Relevant for your today´s post might be mtDNA analysis part (13.1.1).

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