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Thread: Ancient DNA revealing the peopling of the Americas

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    Ancient DNA revealing the peopling of the Americas

    Montgomery Slatkin and Fernando Racimo provide an open access review of the progress of ancient DNA worldwide in "Ancient DNA and human history", PNAS, vol. 113, no. 23 (June 7, 2016), pp. 6380–6387. http://www.pnas.org/content/113/23/6380.full

    I thought we could use their coverage of the Americas to start a thread on that topic. I won't cut-and-paste it all for copyright reasons, but enough to get the idea.

    Arctic

    The first humans started expanding into the New World Arctic 4,500 years ago. Archaeologists distinguish three major cultures in this expansion: Early Paleo-Eskimos, Late Paleo-Eskimos, and Thule. Paleo-Eskimo groups had similar technologies throughout their geographic range and persisted until roughly 1,000 years ago, when they were replaced by the Thule, who are the direct ancestors of present-day Inuit. The first ancient human genome was recovered from a Paleo-Eskimo individual (6). It provided evidence for an early Paleo-Eskimo migration from Siberia that was different from the later migrations that gave rise to present-day Native Americans. More recently, Raghavan et al. (41) obtained 26 genomic sequences from ancient bones throughout the Arctic, and found genetic continuity in both time and space among all Paleo-Eskimos. They descended from immigrants from eastern Asia and dispersed quickly throughout the American Arctic.....

    North and South America.

    Native Americans in North and South America are descended from a different and earlier immigration event than the Paleo-Eskimos and the Thule (6, 41). There is widespread archeological evidence that North America was colonized by peoples associated with the Clovis technology by 13,000 years ago, and some sites in North and South America suggest earlier occupation. These observations are consistent with immigration from Eastern Siberia via Beringia, which was above sea level 22,000–17,000 years ago (41)....

    The sequence of a 24,000-year-old fossil from Mal’ta in southcentral Siberia is important for understanding the origins of Native Americans (43). The Mal’ta genome is both basal to present-day western Eurasians and closely related to Native Americans, but it has no close affinity to present-day East Asians. Raghavan et al. (43) estimated that 14–38% of present-day Native American ancestry derives from the Mal’ta population, resulting from admixture that probably took place in Asia after the ancestors of Native Americans diverged from East Asians and before the divergence of Native American groups from one another.

    The first complete genomic sequence from a Native American was presented by Rasmussen et al. (44). The individual, called Anzick-1, was associated with Clovis artifacts and is about 12,600 years old. The Anzick-1 sequence is closer to present-day Native Americans than it is to any non-American group, and hence the population to which it belongs is either directly ancestral to present-day Native American populations or very closely related to their direct ancestors. Rasmussen et al. also reported that there was a deep branch separating present-day northern Native American populations from those of southern North America and South America.

    Later, Rasmussen et al. obtained a low coverage (∼1×) sequence of the 8,340- to 9,200-year-old remains of an individual known as the “Kennewick Man” (45). These remains were found in the state of Washington. Its relationship to present-day Native American groups has engendered both historical and legal questions. The genomic sequence showed affinities with several present-day Native American groups living in the same geographic area....

    Two large-scale genomic studies published in the past year have helped further elucidate the history of Native Americans. Raghavan et al. (46) surveyed 31 present-day human and 23 ancient modern human genomes ranging in age from 200 to 6,000 years. They concluded that all Native Americans separated from their ancestors ∼20,000 years ago, with an upper limit of 23,000 years. Within North America, Raghavan et al. (46) inferred that northern Amerindians, including Athabascans, diverged from southern North Americans and Central and South Americans ∼13,000 years ago. This divergence time is close to the earliest well-established archaeological sites in the Americas, suggesting that the separation of these lineages occurred there, and not before immigration from Asia.

    Raghavan et al. (46) also concluded, however, that there was not a single wave of immigration. Instead, Native Americans received significant recent gene flow from East Asians and Australo-Melanesians, possibly via the ancestors of present-day Aleutian Islanders. Raghavan et al. (46) found no evidence that any present-day Native American groups are relicts of an earlier wave of colonization....Skoglund et al. (47) analyzed a large SNP dataset that included 63 individuals from 21 present-day Native American populations and reached a conclusion similar to that of Raghavan et al. (46), but one that differs somewhat. Skoglund et al. (47) found that some but not all Native American populations contained a strong signal of Australo-Melanesian ancestry, especially among certain South American populations. ....The problem for both the Skoglund et al. (47) and Raghavan et al. (46) scenarios is explaining why there is a stronger signal of Australo-Melanesian ancestry in native South Americans than in native North Americans.
    Last edited by Jean M; 06-11-2016 at 08:39 PM.

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    Any scenario of migration into America must account for the yDNA relationships between the Old and New Worlds.

    Just to review, here are YFull's estimates of when Native American yDNA lineages diverged from Eurasian lineages:

    Q-Z780 (Native American) diverged from Q-M930 (Native American, Siberian, and northwest European) about 16,200 years ago
    Q-M3 (Native American and Siberian) diverged from Q-L804 (northwest European) about 15,000 years ago
    C-P39 (Native American) diverged from C-F1756 (West Eurasian) about 13,200 years ago

    Other potentially significant datapoints include:
    Q-YP1500 (Saqqaq)
    Q-F746(xM120) (Greenlander), documented as Q-NWT01(xM265)--note that Q-YP1500 is also Q-F746(xM120)
    Q-M120* (Peruvian)
    Last edited by lgmayka; 06-11-2016 at 09:09 PM.

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    Quote Originally Posted by lgmayka View Post
    Any scenario of migration into America must account for the yDNA relationships between the Old and New Worlds.

    Just to review, here are YFull's estimates of when Native American yDNA lineages diverged from Eurasian lineages:

    Q-Z780 (Native American) diverged from Q-M930 (Native American, Siberian, and northwest European) about 16,200 years ago
    Q-M3 (Native American and Siberian) diverged from Q-L804 (northwest European) about 15,000 years ago
    C-P39 (Native American) diverged from C-F1756 (West Eurasian) about 13,200 years ago

    Other potentially significant datapoints include:
    Q-YP1500 (Saqqaq)
    Q-M120* (Peruvian)
    Can this be explained by the flow of people in both directions across the Bering strait after initial settlement of America?

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    Here is the map from Raghavan M, et al. (2015) Population genetics. Genomic evidence for the Pleistocene and recent population history of Native Americans, Science 349(6250): aab3884. http://science.sciencemag.org/content/349/6250/aab3884


    Raghavan2015.jpg

    The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than ~23 ka, separate from the Inuit (green), and diversified into “northern” and “southern” Native American branches ~13 ka. There is evidence of post-divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo-Melanesians (yellow).
    Last edited by Jean M; 06-13-2016 at 09:42 AM.

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    Guido Valverde et al., Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon, PLoS ONE, 11(6) (June 1, 2016): e0155508. doi:10.1371/journal.pone.0155508

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.
    http://journals.plos.org/plosone/art...l.pone.0155508

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    Thus far we have only two decent ancient full genomes from Americas - Anzick-1 and Kennewick man. Almost a year ago Alan Cooper gave a presentation: https://www.youtube.com/watch?v=e8B7cq-UaVE , it seems they getting more of them(he mostly talked about animal DNA, but mentioned human DNA too), but AFAIK the results are not yet published.

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    Quote Originally Posted by rozenfeld View Post
    Thus far we have only two decent ancient full genomes from Americas - Anzick-1 and Kennewick man. Almost a year ago Alan Cooper gave a presentation: https://www.youtube.com/watch?v=e8B7cq-UaVE , it seems they getting more of them(he mostly talked about animal DNA, but mentioned human DNA too), but AFAIK the results are not yet published.
    Ancient pre-Columbians from South America will be coming soon, and this abstracts gives a good idea what to expect.

    http://smbe-2016.p.asnevents.com.au/...abstract/35375

    According to genetic evidence, the ancestors of Native Americans entered the Americas through the Beringian land bridge circa 16,000 years ago(1). However, the exact arrival time and dispersal routes across the double continent and South America in particular remain unclear. Due to their unusual cranial morphology, Fuegians from the south of South America have been suggested to belong to a relic Paleoamerican population(2). Here we address this question using ancient DNA from five human samples from Tierra del Fuego dated between 200 and 4,600 years ago. We generated the full nuclear genomes of these samples, with average depth ranging between 2x and 10x, and analysed them jointly with modern sequences from public data sets. F3 and D statistics revealed no ancestral component in the Fuegians other than typical Native American, consistent with previous genetic studies(3), unlike the Karitiana population from Brazil that shows an Australasian component(4). We used Rarecoal(5) to construct a population model of 1000 Genome populations including post-colonial admixture events and discerned that the Fuegians are more closely related to Colombians than to Peruvians, and more closely related to those than to Mexicans. We estimate that Fuegians diverged from the Colombian branch ~10,500 years ago, shortly after the Colombian/Peruvian divergence (~11,700 years ago). Our results demonstrate that rare variant analyses have the resolution required to make population history inferences between highly similar populations, like those of South America.

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    Quote Originally Posted by rozenfeld View Post
    Thus far we have only two decent ancient full genomes from Americas - Anzick-1 and Kennewick man. Almost a year ago Alan Cooper gave a presentation: https://www.youtube.com/watch?v=e8B7cq-UaVE , it seems they getting more of them(he mostly talked about animal DNA, but mentioned human DNA too), but AFAIK the results are not yet published.
    Fuego-Patagonian (Selknam) specimen MA577 had 1.7x coverage and they could have sequenced to 3x and Fuego-Patagonian (Yaghan) specimen 895 had 1.3x coverage. Both are from Raghavan 2015 and there is plenty of data on them in the supplementary PDF.

    The Saqqaq Palaeo-Eskimo had 20x coverage

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    Quote Originally Posted by ArmandoR1b View Post
    Fuego-Patagonian (Selknam) specimen MA577 had 1.7x coverage and they could have sequenced to 3x and Fuego-Patagonian (Yaghan) specimen 895 had 1.3x coverage. Both are from Raghavan 2015 and there is plenty of data on them in the supplementary PDF.

    The Saqqaq Palaeo-Eskimo had 20x coverage
    Well, Fuego-Patagonean samples are not that old - at most 200 years old.

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    Quote Originally Posted by rozenfeld View Post
    Well, Fuego-Patagonean samples are not that old - at most 200 years old.
    Right, but there was "No evidence of European admixture in Pericúes or ancient Fuego-Patagonians" per page 51 of the supplement so the specimens are very useful. I just remembered, there are also the PRH ancients Prince Rupert Harbour (PRH) region of British Columbia, Canada that are in Linda et al. (2016) pre-print and were sequenced to 7.97x and only two seem to show a possible minute amount of European introgression in the admixture results at k=5. The other don't seem to have any European introgression.
    Last edited by ArmandoR1b; 06-13-2016 at 01:55 PM.

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