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Thread: Ancient DNA from Americas

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    Ancient DNA from Americas

    Since people here mostly interested about aDNA from Eurasia, I propose to put interesting papers and discussions about ancient DNA from Americas here.

    So, yesterday a preprint was uploaded on biorxiv:

    https://www.biorxiv.org/content/early/2017/10/13/203018

    Paleo-Eskimo genetic legacy across North America

    Pavel Flegontov, Nefize Ezgi Altinisik, Piya Changmai, Nadin Rohland, Swapan Mallick, Deborah A. Bolnick, Francesca Candilio, Olga Flegontova, Choongwon Jeong, Thomas K. Harper, Denise Keating, Douglas J. Kennett, Alexander M. Kim, Thiseas C. Lamnidis, Inigo Olalde, Jennifer Raff, Robert A. Sattler, Pontus Skoglund, Edward J. Vajda, Sergey Vasilyev, Elizaveta Veselovskaya, M. Geoffrey Hayes, Dennis H. O'Rourke, Ron Pinhasi, Johannes Krause, David Reich, Stephan Schiffels

    doi: https://doi.org/10.1101/203018

    Abstract

    Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Inupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

    Samples description:

    Code:
    ID1	Date, calBP	Sex	mtDNA	Y haplogroup	Coverage
    
    Ust’-Belaya II, Chukotka, Russia
    I1526	4410 – 4100	M	C4a1a3	Q1a2a		4.523	
    
    Old Bering Sea, Uelen, Chukotka, Russia	
    I1525	1970 – 1590	F	A2a			1.031
    I1524	1180 – 830	M	A2a	Q1a2a1a1	2.618
    
    Athabaskan, Tochak McGrath, Upper Kuskokwim River, Alaska, USA
    I5319	790 – 640	M	A2a1	Q1a2a1a1	5.731
    I5320	790 – 640	M	A2+(64)	Q1a2a1a1	5.038
    I5321	790 – 640	F	A2+(64)			4.851
    
    Paleo-Aleut, Chaluka Midden, Umnak Island, Aleutian Islands, USA
    I0721	2320 – 1900	M	D2a1a	CT		0.025
    I0712	1270 – 930	F	D2a1a			0.431
    I1126	1250 – 780	M	D2a1a	Q		0.092
    I0719	770 – 390	M	D2a1a	Q1a2a		3.432
    
    Neo-Aleut, Ship Rock Island, Aleutian Islands, USA 
    I1125	760 – 490	M	D2a1a	Q1a2a1a1	1.335
    
    Neo-Aleut, Kagamil Island, Warm Cave, Aleutian Islands, USA 
    I1127	630 – 310	F	D2a1a			1.354
    I1128	610 – 290	F	D2a1a			0.433
    I1129	600 – 270	M	D2a1a	Q1a2		0.687
    I1118	530 – 230	F	D2a1a			3.551
    I1123	520 – 140	M	A2a	Q1a		0.128
    I1124	500 – 140	M	D2a1a	Q1a2a		0.156

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    Great paper. We're just scratching the surface of the complexity of American prehistory from the genetics perspective. With time and more aDNA, we may be able to significantly reconstruct the prehistory of an area where as much of 90% of the pre Columbian population perished in epidemics, taking their cultures and genetic diversity with them. With aDNA from South America, for example, we stand a chance of finding the mysterious "Population Y" that contributed Oceanian/Papuan related ancestry to some Amazonian groups.

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    An interesting article on the DNA of the lost Beothuk people of modern-day Newfoundland. Some surprises I was not anticipating!

    DNA deepens mystery of Newfoundlands lost Beothuk people
    https://beta.theglobeandmail.com/new.../?cmpid=PM1017
    Last edited by spruithean; 10-15-2017 at 11:43 PM.

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    The paper finds support for Paleo-Eskimos having been Dene-Yeniseian speakers, and, on the basis of their yDNA results, of yDNA Q1a2a.

    Other related findings: ”1) Paleo-Eskimos are closely related (but not identical) to the founding population of Neo-Eskimos and 2) Paleo-Eskimos contributed substantially to Na-Dene speakers.”

    Some interesting findings about Neo-Eskimos:
    1) We find that the ancient Aleutian Islander is most closely related to present-day Eskimo-Aleut speakers. This confirms the continuity with present-day Aleuts as seen in PCA and other analyses.
    2) Here we show that substantial proto-Paleo-Eskimo ancestry contributed to the founder lineage of Eskimo-Aleut speakers and think this explains the observed admixture as well as the presence of mitochondrial haplogroups D2a in the North Slope Iñupiat.
    3) The first American ancestral lineage that contributed to Eskimo-Aleut speakers was likely located in southwestern Alaska since the Alaskan Peninsula and Kodiak Island have long been suggested as a source of infuences shaping the NeoEskimo material culture.

    As all yDNA in this paper is Q1a (except for one CT), and due to the fact that Koryaks and Itelmens who speak Chukotko-Kamchatkan languages are mostly C2 (M217), I would suggest that there is a connection between C2 (M217) and this language family.

    I see from Wikipedia that M. Fortescue, linguist specializing in Arctic and native North American languages, has nowadays argued for Nivkh as the closest relative of Chukotko-Kamchatkan, and suggests interpreting the similarities to Uralo-Siberian through language contact.”

    Nivkhs are majority yDNA C2 as Koryaks and Itelmens.
    Last edited by Kristiina; 10-16-2017 at 08:07 PM.

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    Quote Originally Posted by Kristiina View Post
    The paper finds support for Paleo-Eskimos having been Dene-Yeniseian speakers, and, on the basis of their yDNA results, of yDNA Q1a2a.
    The only Paleo-Eskimo Y hg I know of is Saqqaq, and he is Q1a1a-NWT01. Q1a1a is the modal haplogroup of Inuit; Koryaks have some also, Aleuts have lots of Q(xQ-M3) and Russian Yupiks of P1(xQ-M3, R1a1) which might be Q1a1a but has not been tested.

    Q1a2a1a1-M3 is clearly Amerindian(-ish), and modern Aleuts have lots of it, in fact it seems to be their most common non-European Y haplogroup (though the sample is small). Inuit also have lots (but less than Q1a1a) and Russian Yupiks also have some (but less than N).

    In this study there are CT, Q, Q1a, Q1a2, Q1a2a but all are low coverage, so they could be Q1a2a1a1-M3 or Q1a1a-NWT01 just unidentified - except for Ust'-Belaya, who is I guess really Q1a2a*, because he has decent coverage.

    In this paper the common Inuit-Aleut ancestor is modelled as 67% related to Paleo-Eskimos and 33% northern Amerindian, and the ancient Aleuts have an additional Amerindian shift from Inuit in ADMIXTURE and PCA. Also the Aleuts have way more D2a1a, which is maternal Paleo-Eskimo, than A2a, which is maternal Amerindian. So I'd say Q1a1a-NWT01 is the Paleo-Eskimo haplogroup and most (if not all) of the Q1a2 is from the Amerindian side. But I am not claiming anything for certain here, there is too much untested stuff floating around.

    I don't think it really gives us much for Dene-Yeniseian: there is no direct connection to Kets, multiple language families linked to this autosomal ancestry, C2-P39 connects to Chukotko-Kamchatkan and we haven't found it in Paleo-Eskimos (or any ancient DNA) yet (though it could plausibly be from them).

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    Quote Originally Posted by Megalophias View Post
    The only Paleo-Eskimo Y hg I know of is Saqqaq, and he is Q1a1a-NWT01. Q1a1a is the modal haplogroup of Inuit; Koryaks have some also, Aleuts have lots of Q(xQ-M3) and Russian Yupiks of P1(xQ-M3, R1a1) which might be Q1a1a but has not been tested.
    I noticed that difference, which means that things are not neat and simple. I wrote the comment because I think that the paper would be worth a discussion. As Eskimo-Aleut yDNA is mostly M3 (Amerindian) and Q1a1a-NWT01 (Paleo-Eskimo), Neo-Eskimos seem to have arisen from this admixture.

    Quote Originally Posted by Megalophias View Post
    I don't think it really gives us much for Dene-Yeniseian: there is no direct connection to Kets, multiple language families linked to this autosomal ancestry,
    According to the paper: Ust'Belaya individual [Q1a2a*] is closely related to both Saqqaq and Kets. Moreover, this individual has a high level of Mal'ta ancestry according to F4-statistics.

    From the paper: "Taken together, our results from several analyses show remarkable consistency: PCA, haplotype and rare allele sharing, GLOBETROTTER, and qp/Wave/qpAm suggest that present-day NA-Dene speakers lacking post-Columbian admixture have roughly 10% to 25% Paleo-Eskimo ancestry."

    "Although the Dene-Yeniseian macrofamily is not universally accepted among historical linguists, and correlations between linguistic and genetic histories are far from perfect, evidence of a genetic connection between Siberian and Na-Dene populations mediated By Paleo-Eskimos suggests that future research should further explore the genealogical relationships between these language families."

    Please correct me if I am wrong, but my understanding is that Kets are under Q1a2a as Ust Belaya while NWT01 is at the root of Q1a1, and Q1a1a1-M120 is very much a southeast Asian haplogroup. The point is that Paleo-Eskimos (or Paleo-Eskimo language) came from Asia and both Q1a2a and NWT01 are found in Asia.
    Last edited by Kristiina; 10-17-2017 at 06:24 AM.

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    However, it has also been argued that Dene-Yeniseian languages backmigrated from Beringia to Siberia.

    Back-migration of Yeniseian into Asia from Beringia.PNG

    In this hypothesis, Paleo-Eskimo Saqqaq (NWT01) could have spoken a language which is ancestral to modern Eskimo-Aleut, and Na-Dene languages would have arrived earlier in America. In this case, there would have been Paleo-Eskimo gene flow into Na-Dene but they retained their original Beringian language while received a technical advantage that helped them to spread southwards.
    Last edited by Kristiina; 10-17-2017 at 07:52 AM.

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    I copy here the relevant data from the recent paper "Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia" (https://link.springer.com/article/10...438-017-1363-8)

    Q1a1a1-M120 TMRCA/expansion time 9.8/5.8

    Q1a1a1-M120 DYS391 allele 9 (Han Chinese) TMRCA/expansion time 6.5/5.2

    Q1a1b-M25 (Turkic) TMRCA/expansion time 3.1/2.0

    Q1a2a1-L54 (Yenisei basin) TMRCA/expansion time 0.3/0.4

    Q1a2a1a2-L804 (Northwestern Europe, Scandinavia) TMRCA/expansion time 5.3/5.

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    Quote Originally Posted by Kristiina View Post
    I copy here the relevant data from the recent paper "Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia" (https://link.springer.com/article/10...438-017-1363-8)

    ...

    Q1a2a1-L54 (Yenisei basin) TMRCA/expansion time 0.3/0.4
    The typical Yeniseian Q appears to belong to Q1b1a-L54 > Q1b1a3-L330 > Q1b1a3b-B287. Karmin et al. (2015) have found Q-B287 in two Kets and one Selkup, with a TMRCA estimate of 2,764 [2,037 <-> 3,502] ybp between the Selkup and one of the Kets, and a TMRCA estimate of 5,068 [4,328 <-> 5,793] ybp between that pair and the other Ket. YFull id:YF02788 (Astana, Kazakhstan) also belongs to this clade. YFull has given Q-B287 an intraclade TMRCA estimate of 4,700 [95% CI 3,200 <-> 6,600] ybp, but I cannot guarantee that any sample of Ket Y-DNA has been taken into account when calculating the YFull TMRCA estimate.

    As for the deeper relations of the Yeniseian Q lineage,

    TMRCA 26,000 [95% CI 24,100 <-> 27,900] ybp Q1-F903/L472 > Q1a-F1096 vs. Q1b-M346
    ----------
    TMRCA 20,000 [95% CI 18,300 <-> 21,800] ybp Q1b-M346 > Q1b1-L53/S326 vs. Q1b2-Y2659 [sparsely distributed from Europe and the United Arab Emirates in the west to Kerala, Sri Lanka, and Nepal in the east]
    TMRCA 18,200 [95% CI 16,600 <-> 20,000] ybp Q1b1-L53/S326 > Q1b1a-L54 vs. Q1b1b-YP4004 [Poland; Russia]
    TMRCA 16,200 [95% CI 15,100 <-> 17,400] ybp Q1b1a-L54 > Q1b1a1-CTS11969/M930 [indigenous Americans; Germanic Europeans] vs. Q1b1a2-CTS1780/M981 [Anzick-1, deceased approximately 12,556 to 12,707 ybp in Montana, USA; modern Mexicans; one individual from modern Germany] vs. Q1b1a3-L330
    -----------
    TMRCA 8,100 [95% CI 6,900 <-> 9,400] ybp Q1b1a3-L330 > Q1b1a3a-Y20260 [Nógrád, Hungary; Uzbek] vs. Q1b1a3b-SK1944/YP1102/Z35941 (or B287) [Astana, Kazakhstan; Ket x 2; Selkup x1]

    So the most recent genealogical connection between Ket Y-DNA and indigenous American Y-DNA seems to be the Q1b1a-L54 MRCA of Q1b1a1-CTS11969/M930, Q1b1a2-CTS1780/M981, and Q1b1a3-L330 ca. 16,200 [95% CI 15,100 <-> 17,400] ybp. The ancestral population seems to have fractured around that time into one part that created the Clovis culture and spread throughout the American continent, one part that eventually ended up merging into the pre- or proto-Germanics, and another part (perhaps the earliest to split off or at least the ones who remained most isolated from the others; according to the YFull YTree v5.06, Q1b1a1-CTS11969/M930 and Q1b1a2-CTS1780/M981 actually share one SNP in common, CTS3814/M1107, that they do not share with Q1b1a3-L330) that developed into the Yeniseians. In any case, it seems likely that the most common type of Yeniseian Q is more closely related to generic indigenous American (and Germanic) Q than it is related to any of the subclades of Q1a-F1096 found in Paleo-Eskimos, Chukotko-Kamchatkans, Chinese, Turkmens, etc.

    Has anyone seen any data that could be interpreted to suggest that some other present-day Kets might belong to a subclade of Q1a-F1096?

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    Ebizur, you refer to the most recent structure used in Yfull and ISOGG 2017, but I presume that the samples description of this new paper use the older yDNA Q tree in which, for example, M3 is Q1a2a1a1 while it is Q1b1a1a in ISOGG 2017.

    By the way one Q1a2 (presumably Q1b1a-L54 in ISOGG 2017?) has been found in a Mesolithic context in Latvia: I4630 / ZVEJ30, burial 52, 6000-5100 BCE.

    It would be interesting to know how the Mesolithic Latvian Q is related to the Scandinavian Q-L804, if it is L54 and not M25.

    SNPs are the following:
    Q1a2:CTS2656:14407664C->T; Q1a2:F2122:16305155T->Chet; Q1a2:L56:8148869G->A; Q1a2:M346:2887156C->G; Q1a:CTS1845:14092227G->C; Q1a:CTS2006:14151622C->T; Q1a:CTS4793:15825218C->G; Q1a:CTS5301:16195023G->A; Q1a:CTS5804:16487674G->A; Q1a:CTS7611:17560616A->T; Q1a:F903:7014317G->C; Q1a:F1304:8554432G->T; Q1a:F1426:8840134C->T; Q1a:F2840:18775212T->A; Q1a:FGC8413:13195038A->Thet; Q1a:FGC8415:13470735G->Thet; Q1a:M1155:21254696G->A; Q1a:M1168:22155597G->A; Q1:L232:17516095G->A; Q:F826:6778043G->A; Q:F1237.1:8479245A->G; Q:F1829:14746296T->C; Q:F3067:19431928C->A; Q:FGC1751:13683938A->G; Q:FGC1754:9777430G->A; Q:FGC1755:13227885C->T; Q:M1166:22001258G->A

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