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Human Ancestry Is Complex with Ancient DNA
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The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans:

Some present-day humans derive up to ∼5% …of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals…We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry…In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Take a look at the supplements for the functional stuff. I am not going to address that. Much of those results have been circulation or in other papers over the years. Rather, I want to highlight the variation in patterns of Denisovan admixture in non-Oceanian groups. Here is an important section:

Taken together, the evidence of Denisovan admixture in modern humans could in theory be explained by a single Denisovan introgression into modern humans, followed by dilution to different extents in Oceanians, South Asians, and East Asians by people with less Denisovan ancestry. If dilution does not explain these patterns, however, a minimum of three distinct Denisovan introgressions into the ancestors of modern humans must have occurred.

You see it on the figure above. The South Asian groups consistently jump well above the trend line for inferred Denisovan as a function of shared ancestry with Australians non-West Eurasian ancestry. Also, if you look at the admixture patterns for Denisovan ancestry in South Asia you see they follow the ANI-ASI cline. That is, it seems to come into the South Asian populations through the “Ancestral South Indians.” Interestingly, the Onge sample of Andaman Islanders has less Denisovan than low caste South Asian groups, reminding us that though the Onge and their kin are the closest modern populations to the ASI, they are not descended from the ASI. The highest fraction of inferred Denisovan is in the Sherpa people of Nepal.

sherpa The figure to the right is from Admixture facilitates genetic adaptations to high altitude in Tibet, and the authors find that the Sherpa are at one extreme in an ancestry cline in comparison to other East Asians. The figure is hard to make out, so I will tell you that many of the Sherpa are fixed for the red component, while other Tibetans are in positions in the middle, and most East Asians have low fractions of the red, with the Dai having none. The Gujarati sample form the HapMap have low fractions of both East Asian components. This is almost certainly an artifact of the shared ancestry of all eastern Eurasians (and perhaps Oceanians), of which the ASI were one descendant group. The proportion of Denisovan in low caste South Asians indicates that the fraction in ASI was about at the same level as the Sherpa. I suspect that ASI and the Tibetan groups got their Denisovan via different paths, but it doesn’t seem like we know yet.

Overall I do marvel at what ancient DNA can tell us. Without it we wouldn’t be talking about any of these admixture events; they’d be signals too weak to have left an obvious mark in the genome.

 
• Category: Science • Tags: Denisovan, Neanderthal 
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  1. Zimriel says:

    Based on that map, I would set the Denisovan-protoMelanesian mating to the northeastern coast of India. The pro-altitude Denisovan genes would not have helped the products of that union very far southwest of that; nor in the jungles south*east* of that through Burma.

    The Sherpas and Tibetans are closest to that contact-point. So any fugitives from the Assam / Bengal tribal wars (which, Hobbes teaches us, are a feature of our species) would have been able to get to the Himalayas. The luck of their genome helped their descendents to stay in the Himalayas.

    (As for the protoMelanesians themselves, they just kept running southeast.)

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  2. ohwilleke says: • Website

    “The South Asian groups consistently jump well above the trend line for inferred Denisovan as a function of shared ancestry with Australians.”

    The chart is actually based on the trend as a function of non-West Eurasian ancestry, not Australian ancestry.

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  3. “though the Onge and their kin are the closest modern populations to the ASI, they are not descended from the ASI”

    I would appreciate it if someone could explain how this works in laymans terms.

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    • Replies: @Tobus
    @Martian_Observer: I would appreciate it if someone could explain how this works in laymans terms.

    Imagine there is a very early population living in South Asia, which splits into two and one group migrates to the Andaman Islands and becomes the Onge, while the other migrates to India and becomes ASI. Over thousands of years, a series of incursions into India dilutes the ASI genome to a point that there are no unadmixed ASI in existence anymore. Onge are now the closest living population to the ASI, even though they aren't descended from ASI.

    So it's just branching of the family tree - in the same way that my brother might be the closest living human to me genetically but he is not descended from me, Onge and ASI can be considered "brother" clades from a common ancestor, neither descended from the other, but still sharing ancestry not shared by any other population.
  4. Shaikorth says:

    Interestingly the Dravidian-speaking Brahuis of Pakistan have extremely low Denisovan, lower than nearby Indo-Europeans such as Balochi and especially Sindhi and Pathans. In fact they’re more comparable to Iraqi Jews in that regard. But South Indian Dravidian groups like Irula have extremely high Denisovan as pointed out.

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    • Replies: @ohwilleke
    This corroborates the hypothesis that the Brahuis are a population that underwent language shift ca. 1000 CE, presumably guided by a small Dravidian superstrate population. Iranians also have low Denisovan ancestry is a fairly dramatic shift from its South Asian and Central Asian neighbors and presumably the substrate population was Iranian.
  5. Vijay says:

    I want to point to the work of clarkson petraglia at jwalapuram identifying hominids 74kya either wiped out by mt.toba ash or survived. A conjecture would involve survival of hominids and being subsumed by snsequent migrations out of Africa. Here, I believe Denisovan DNA represents any and all non-homo erectus DNA.

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  6. ohwilleke says: • Website
    @Shaikorth
    Interestingly the Dravidian-speaking Brahuis of Pakistan have extremely low Denisovan, lower than nearby Indo-Europeans such as Balochi and especially Sindhi and Pathans. In fact they're more comparable to Iraqi Jews in that regard. But South Indian Dravidian groups like Irula have extremely high Denisovan as pointed out.

    This corroborates the hypothesis that the Brahuis are a population that underwent language shift ca. 1000 CE, presumably guided by a small Dravidian superstrate population. Iranians also have low Denisovan ancestry is a fairly dramatic shift from its South Asian and Central Asian neighbors and presumably the substrate population was Iranian.

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  7. I suspect that ASI and the Tibetan groups got their Denisovan via different paths, but it doesn’t seem like we know yet.

    We should be able to test this to some extent with existing data though, no? For example, we know that in most of Oceania, Denisovan ancestry correlates with Papuan ancestry – suggesting a common source.

    On the other hand, if we compare Oceanian and Denisovan ancestry in Native American groups, the populations with the greatest Oceanian ancestry have the least Denisovan ancestry. That seems to suggest a separate source for Denisovan ancestry in the Americas I think?

    http://www.eva.mpg.de/documents/Oxford/Qin_Denisovan_MolBiolEvo_2015_2246887.pdf

    http://www.nature.com/nature/journal/v525/n7567/full/nature14895.html

    Could something similar be done by comparing f4 statistics with Sherpas and Denisovans to see if the two correlate?

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  8. Tobus says:
    @Martian_Observer
    "though the Onge and their kin are the closest modern populations to the ASI, they are not descended from the ASI"

    I would appreciate it if someone could explain how this works in laymans terms.

    : I would appreciate it if someone could explain how this works in laymans terms.

    Imagine there is a very early population living in South Asia, which splits into two and one group migrates to the Andaman Islands and becomes the Onge, while the other migrates to India and becomes ASI. Over thousands of years, a series of incursions into India dilutes the ASI genome to a point that there are no unadmixed ASI in existence anymore. Onge are now the closest living population to the ASI, even though they aren’t descended from ASI.

    So it’s just branching of the family tree – in the same way that my brother might be the closest living human to me genetically but he is not descended from me, Onge and ASI can be considered “brother” clades from a common ancestor, neither descended from the other, but still sharing ancestry not shared by any other population.

    Read More
    • Replies: @Karl Zimmerman
    One should keep in mind that it's pretty unlikely the Andaman Islands were settled from India. They were probably connected to Burma during the Ice Ages, meaning the ancestors of the modern Andamanese could have just walked there. Therefore they are probably more closely related to the (now extinct) original population of Burma than Ancient South Indians. I wouldn't even be surprised if they're closer to the Semang in Malaysia than they are to Ancient South Indians, but to the best of my knowledge no one has looked at this.
  9. terryt says:

    “We document more Denisovan ancestry in South Asia than is expected based on existing models of history”

    Quite possibly the ‘ existing models of history’ are wrong.

    “if you look at the admixture patterns for Denisovan ancestry in South Asia you see they follow the ANI-ASI cline. That is, it seems to come into the South Asian populations through the ‘Ancestral South Indians’.”

    What if the ASI entered South Asia from the east, missing the Andaman Islands as they passed westward?

    “I suspect that ASI and the Tibetan groups got their Denisovan via different paths, but it doesn’t seem like we know yet”.

    If the Denisovan element in South Asia does in fact come from the east, dilution does indeed explain these patterns.

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  10. @Tobus
    @Martian_Observer: I would appreciate it if someone could explain how this works in laymans terms.

    Imagine there is a very early population living in South Asia, which splits into two and one group migrates to the Andaman Islands and becomes the Onge, while the other migrates to India and becomes ASI. Over thousands of years, a series of incursions into India dilutes the ASI genome to a point that there are no unadmixed ASI in existence anymore. Onge are now the closest living population to the ASI, even though they aren't descended from ASI.

    So it's just branching of the family tree - in the same way that my brother might be the closest living human to me genetically but he is not descended from me, Onge and ASI can be considered "brother" clades from a common ancestor, neither descended from the other, but still sharing ancestry not shared by any other population.

    One should keep in mind that it’s pretty unlikely the Andaman Islands were settled from India. They were probably connected to Burma during the Ice Ages, meaning the ancestors of the modern Andamanese could have just walked there. Therefore they are probably more closely related to the (now extinct) original population of Burma than Ancient South Indians. I wouldn’t even be surprised if they’re closer to the Semang in Malaysia than they are to Ancient South Indians, but to the best of my knowledge no one has looked at this.

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    • Replies: @Razib Khan
    http://www.sciencedirect.com/science/article/pii/S0002929711003958
  11. @Karl Zimmerman
    One should keep in mind that it's pretty unlikely the Andaman Islands were settled from India. They were probably connected to Burma during the Ice Ages, meaning the ancestors of the modern Andamanese could have just walked there. Therefore they are probably more closely related to the (now extinct) original population of Burma than Ancient South Indians. I wouldn't even be surprised if they're closer to the Semang in Malaysia than they are to Ancient South Indians, but to the best of my knowledge no one has looked at this.
    Read More
    • Replies: @Karl Zimmerman
    Razib,

    Thanks for the link. I remember seeing that study when it came out. I suppose I didn't recall it in this particular case because they refer to the Semang tribe that they included by their language name, rather than the more well known umbrella term. While I wonder if the particular Semang group they chose to study was more admixed than average, it does appear the Peninsular Malay Negrito population is relatively close to Onge. Whether it's closer to them than Ancient South Indian certainly was not answered in this study however.
  12. the point that the ASI may have come from the east is pretty intriguing, and seems likely.

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    • Replies: @terryt
    Have you seen this yet?

    http://biorxiv.org/content/biorxiv/early/2016/04/06/047456.full.pdf

    It claims ASI definitely came from the east.
  13. @Razib Khan
    http://www.sciencedirect.com/science/article/pii/S0002929711003958

    Razib,

    Thanks for the link. I remember seeing that study when it came out. I suppose I didn’t recall it in this particular case because they refer to the Semang tribe that they included by their language name, rather than the more well known umbrella term. While I wonder if the particular Semang group they chose to study was more admixed than average, it does appear the Peninsular Malay Negrito population is relatively close to Onge. Whether it’s closer to them than Ancient South Indian certainly was not answered in this study however.

    Read More
  14. terryt says:
    @Razib Khan
    the point that the ASI may have come from the east is pretty intriguing, and seems likely.

    Have you seen this yet?

    http://biorxiv.org/content/biorxiv/early/2016/04/06/047456.full.pdf

    It claims ASI definitely came from the east.

    Read More

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