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Thread: New DNA Papers - General Discussion Thread

  1. #2401
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    Quote Originally Posted by Tomenable View Post
    Okay, I responded to this in a private message, but I think I can post it in public.

    You know that this is simply not true. What you posted is just a made-up excuse.

    The reason why there is no German DNA study has nothing to do with the Proto-Indo-Europeans or with the Middle East.

    The reason in my opinion is that... Germans are VERY scared of finding out how ethnically mixed they are. How much of Slavic & Baltic admixture there is in East Germany, and how much Celtic and Romance in West and South Germany. As well as Jewish etc. You simply DO NOT want to know this.

    It is just my hypothesis, of course!

    This is IMO why there is no proper research. Nothing to do with prehistoric PIE times, nothing to do with the Middle East.

    Who really cares about what was 5000 years ago, seriously?

    Come on... if historical politics is influencing science, it has to be something more recent, not some prehistoric PIE stuff.

    I admit I got interested in Elbe-Oder genetics after watching Russian documentary "East Germany: Slavic Graveyard" - I wanted to find out, how true it was, how much Germans exterminated Polabian Slavs and how much assimilated. I also read Piskorski's books about Ostsiedlung and other sources.
    My image of Germany is totally different, it's just the opposite, genetics is still kind of contaminated in Germany....due to ww2 they want to keep fare away from that....

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  3. #2402
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    Quote Originally Posted by evon View Post
    This study looks very interesting, and I am curious about the proposed basque Icelandic connection that is mentioned in the study:
    Basque whalers?
    https://en.wikipedia.org/wiki/Histor...haling#Iceland
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    Quote Originally Posted by Kale View Post
    I have noted a few instances of basque people in western Norwegian sources dating back to the 1500's. So it is possible that a similar situation occurred here too. But I also suspect that the signal might be something else entirely. I need to have a good look at the article, and I hope it catches the attention of people with enough time and experience to take a look at the findings and try to duplicate them.

    See here for basque people in Norwegian sources (note the ones from the 1500's): https://www.digitalarkivet.no/search/persons?s=Basker
    Last edited by evon; 04-26-2020 at 06:17 PM.

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    Quote Originally Posted by pmokeefe View Post
    Korean Genome Project: 1094 Korean personal genomes with clinical information
    Sungwon Jeon, Youngjune Bhak, Yeonsong Choi, Yeonsu Jeon, Seunghoon Kim, Jaeyoung Jang, Jinho Jang, Asta Blazyte, Changjae Kim, Yeonkyung Kim, Jungae Shim, Nayeong Kim, VYeo Jin Kim, Seung Gu Park, Jungeun Kim, Yun Sung Cho, Yeshin Park, Hak-Min Kim, Byoung-Chul Kim, Neung-Hwa Park, Eun-Seok Shin, Byung Chul Kim, Dan Bolser, Andrea Manica, Jeremy S. Edwards, George Church, Semin Lee and Jong Bhak

    Abstract
    We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

    When mitochondrial and chromosomal Y haplogroups among the Korean individuals (figs. S12 and S13) were investigated, the common types identified were D (34.19%), B (13.89%), and M (13.80%) mitochondrial and O (73.49%), C (16.9%), and N (6.58%) chromosomal Y (26, 27). The O male haplogroup is widely distributed in East Asia and Southeast Asia, while the C haplogroup is prominently distributed in East Asia and Northeast Asia (26). We also identified other fairly common mitochondrial haplogroup types (A, G, and F) in East Asia (28).

    Genomic features of Koreans compared to other populations
    We assessed the genetic distinctiveness of our Korea1K sample using principal components analysis (PCA) with the small size variants (SNP and indel) in our dataset and 1KGP. As previously reported, principal components PC1 and PC2 with worldwide populations showed a separate East Asian group (Fig. 2A). Although Koreans, Chinese, and Japanese are genetically very close relative to all other individuals (29), we found that those three populations clustered distinctly from each other (Fig. 2B ). This pattern was replicated by ADMIXTURE analysis with K = 3 (fig. S14).
    "The majority of the genomic data (984 samples) were from volunteers with clinical information on 79 quantitative traits that were measured at Ulsan University Hospital. ... In total, 1094 complete genomes, including 916 unrelated and healthy individuals, mostly from the Ulsan metropolitan region, were compared to the human genome reference (hg38). ... Furthermore, we note that our samples are mostly from the Ulsan metropolitan area and cannot reflect the whole Korean peninsula, although Ulsan has a population size of 1 M and the residents are from all across the peninsula due to rapid industrialization. Together, the sample size of 1094 from mostly Ulsan is still far from sufficient to represent the Korean population or to map latent genomic structural variations."

    The participants in the Korean Genome Project are mostly from Ulsan, a city located between Gyeongju and Busan in the southeastern corner of the Korean Peninsula.

    The most notable difference between the mtDNA of this large sample, mostly from Ulsan, and the mtDNA of the samples from every region of South Korea analyzed by Hong et al. 2014 is that the Korean Genome Project sample is 2.01% R(xB, F), whereas the data set of Hong et al. 2014 included only 2/708 = 0.28% N(xN9, Y, A, F, B4, B5). Furthermore, the two potential R(xB, F) individuals in the data set of Hong et al. 2014 were not from Gyeongsang, the region in which Ulsan is located, but rather from Chungcheong and Jeolla. Otherwise, there is not much difference; the regionally diverse pool of samples from Hong et al. 2014 has slightly greater proportions of the two most frequent haplogroups (251/708 = 35.45% D vs. 374/1094 = 34.19% D, 105/708 = 14.83% B vs. 152/1094 = 13.89% B ), whereas the Ulsan- (hence, Gyeongsang-)biased sample in the present study contains slightly greater than average proportions of G and F (90/1094 = 8.23% G vs. 43/708 = 6.07% G, 86/1094 = 7.86% F vs. 50/708 = 7.06% F). A higher than average proportion of haplogroup G was also found in samples from the east coast of South Korea (11/114 = 9.6% G in Gangwon and 10/112 = 8.9% G in Gyeongsang vs. 43/708 = 6.07% G South Korean total) in Hong et al. 2014. However, Gangwon showed the highest proportion (11/114 = 9.6% F) and Gyeongsang showed the lowest proportion (6/112 = 5.4% F) of haplogroup F in Hong et al. 2014. Haplogroup Y is also less frequent in this study's samples compared to the pooled set of samples in Hong et al. 2014, but that is due to the very high proportion of samples from Jeju (19/113 = 16.8% Y) and, to a lesser extent, Seoul-Gyeonggi (5/134 = 3.7% Y) who belonged to that haplogroup in the earlier study; the proportion of haplogroup Y in their sample from Gyeongsang (2/112 = 1.8% Y) is not significantly different from the proportion of the present study's samples who belong to this haplogroup (19/1094 = 1.74% Y).

    On the Y-DNA side, the Korean Genome Project's sample, mostly from Ulsan, has slightly higher than average C (16.9%) and N (6.58%) and slightly lower than average Q (1.6%) and D (1.42%).
    Last edited by Ebizur; 05-28-2020 at 04:41 AM.

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    I'm guessing the Japanese would cluster with the Koreans were it not for their minor Jomon ancestry.
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    Quote Originally Posted by Michalis Moriopoulos View Post
    I'm guessing the Japanese would cluster with the Koreans were it not for their minor Jomon ancestry.
    This study agrees with previous studies in positioning Koreans along a cline between northern Chinese on one side and Japanese on the other. However, they do not appear to be equally similar to Chinese and Japanese; rather, the Koreans are somewhat more similar to northern Chinese than they are to Japanese, resembling a homogenized admixture of approximately 2/3 Chinese + 1/3 Japanese. Another detail is that the Chinese-like contribution to the Koreans seems to be more northern than present-day Han Chinese in Beijing. I wonder how much this has to do with the recently published Shandong Neolithic samples; Neolithic specimens from northern China seem to be mostly Y-DNA N, whereas present-day Koreans and Han Chinese are mostly Y-DNA O2, so I suppose it might be that Koreans share (at least patrilineal) ancestry with Han Chinese deriving from some population that has lived south(west?) of the Neolithic N-heavy populations and which has admixed (with a Japanese-like population) to form the base of the present Korean gene pool prior to homogenization within the Chinese population that has brought ancestry of southern origin northward to Beijing.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    I'm guessing the Japanese would cluster with the Koreans were it not for their minor Jomon ancestry.
    That would make sense since their Yayoi ancestors came from what is now Korea originally.

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    Quote Originally Posted by Ebizur View Post
    This study agrees with previous studies in positioning Koreans along a cline between northern Chinese on one side and Japanese on the other. However, they do not appear to be equally similar to Chinese and Japanese; rather, the Koreans are somewhat more similar to northern Chinese than they are to Japanese, resembling a homogenized admixture of approximately 2/3 Chinese + 1/3 Japanese. Another detail is that the Chinese-like contribution to the Koreans seems to be more northern than present-day Han Chinese in Beijing. I wonder how much this has to do with the recently published Shandong Neolithic samples; Neolithic specimens from northern China seem to be mostly Y-DNA N, whereas present-day Koreans and Han Chinese are mostly Y-DNA O2, so I suppose it might be that Koreans share (at least patrilineal) ancestry with Han Chinese deriving from some population that has lived south(west?) of the Neolithic N-heavy populations and which has admixed (with a Japanese-like population) to form the base of the present Korean gene pool prior to homogenization within the Chinese population that has brought ancestry of southern origin northward to Beijing.
    The "southern" shift of modern Han relative to ancients from North China is expected IMO.

    South China was only annexed by the Qin Dynasty after various expeditions against Yue and related (likely Austronesian, Austro-Asiatic, and Hmong-Mienic) peoples circa 200 BC. After this date we would expect substantial Southeast Asian admixture into core China, similar to how Rome became more "Near Eastern" during its Imperial period.

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    Chao Ning, Tianjiao Li, Ke Wang, et al. (2020), "Ancient genomes from northern China suggest links between subsistence changes and human migration." Nature Communications (2020) 11:2700. https://doi.org/10.1038/s41467-020-16557-2.

    They tested a Middle Neolithic specimen (HMMH_MN HMF32) from the Hamin Mangha site, which is located approximately 15 km southeast of Xibet (Shebotu) Town in Horqin Left Middle Banner, Tongliao, Inner Mongolia, on the eastern part of the plain of the West Liao (Xiliao) River, between the West Liao and its left tributary, the Xinkai River. The Hamin Mangha site is famous for a claim that it may be the most ancient known "ghost town," a Neolithic human settlement that is suspected of having been abandoned after some sort of communicable disease decimated the population to an extent that whoever survived decided it would be best to burn a house filled with corpses to the ground and never return. When projected onto a PCA plot of extant Eurasian variation, the Hamin Mangha specimen appears close to several present-day speakers of Tungusic languages (the genetically "southernmost" of the tested Ulchi, the two southernmost of the tested (presumably Russian) Nanai, the second most "northern" of the tested Hezhen (PRC Nanai), and three Oroqen) as well as the ancient specimens from Devil's Gate Cave in southern Primorye. HMF32 is a female specimen whose mtDNA has been assigned to haplogroup D4j.

    This is yet another paper in which the authors repeatedly claim that there is remarkable population continuity among populations of the Amur River basin, from the "Early Neolithic" pottery-using hunter-gatherers of the Amur River basin to the present-day Tungusic peoples and Nivkhs. They tested two "Early Neolithic" specimens from the Zhalainuo'er area north of Lake Hulun in Hulun-Buir, Inner Mongolia, which is essentially located in the opposite corner of the Amur basin from Devil's Gate Cave. Both these specimens are female, with one (WQM4) belonging to mtDNA haplogroup C4a1a and the other (ZLNR-2) belonging to mtDNA haplogroup C5. On the PCA plot, they appear somewhat "northeast" of the specimen from the Hamin Mangha site, overlapping a cluster composed of the majority of the tested present-day Ulchi, Nivkh, and Negidal individuals. (Note that this does not agree with geography; Zhalainuo'er is geographically far northwest of Devil's Gate Cave, and the specimens from Zhalainuo'er are from approximately the same era as the specimens from that cave, yet the specimens from Zhalainuo'er appear to be genetically "north(east)ern" rather than "northwestern" vis--vis the specimens from Devil's Gate Cave. The Zhalainuo'er specimens belong to mtDNA haplogroups C4a and C5, which are the most common mtDNA haplogroups among members of several present-day populations of arctic Siberia, e.g. Nganasan, Siberian Evenk, Even, Yakut, Yukaghir, whereas the Devil's Gate Cave specimens belong to mtDNA haplogroup D4, which is the most common mtDNA haplogroup among present-day people in a triangle defined by Altai, Tibet, and Japan.)

    However, yet again, the authors have not found any specimen that belongs to mtDNA haplogroup Y1a or mtDNA haplogroup G1b, which together account for an absolute majority of mtDNA among the present-day Tungusic peoples and Nivkhs who supposedly exhibit such remarkable autosomal continuity from the "Early Neolithic" inhabitants of the Amur basin.
    Last edited by Ebizur; 06-01-2020 at 03:46 PM.

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    Quote Originally Posted by pmokeefe View Post
    Ancient admixture into Africa from the ancestors of non-Africans
    Christopher Bernard Cole, Sha Joe Zhu, Iain Mathieson, Kay Prfer, Gerton Lunter

    Abstract
    Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species' history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species' demographic history around the out-of-Africa event is more complex than previously appreciated.
    I skimmed through this paper, but it is not clear to me how they distinguished early Eurasian ancestry from (African) proto-Eurasian ancestry? Especially considering the inferred "Eurasian" ancestry predates the divergence of East/West Eurasians, and shows no association with excess Neanderthal ancestry (which traces to an admixture event roughly 50-60 kya in Eurasians, based on Ust'-Ishim).

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