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Thread: DISCUSSION THREAD FOR "Genetic Genealogy and Ancient DNA in the News"

  1. #2591
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    Quote Originally Posted by Kopfjäger View Post
    Would the Southern China influence stem from early rice farmers, or is this a different time period?
    The only point at which the author has mentioned anything like a "Southern China influence," as far as I recall, is when he has written about early AMHs moving northward along the coast from Southeast Asia.

    He has written about testing specimens from two different strata from Ie Island of Okinawa Prefecture, but he has not indicated where they are located on the PCA plot nor whether they appear anywhere on that plot in the first place. The question of whether samples from the Jomon Period in western Japan or from the contemporaneous shellmidden period of Okinawa have been taken into consideration or not when constructing that PCA plot is left unclear.

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  3. #2592
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    Quote Originally Posted by Ebizur View Post
    The only point at which the author has mentioned anything like a "Southern China influence," as far as I recall, is when he has written about early AMHs moving northward along the coast from Southeast Asia.

    He has written about testing specimens from two different strata from Ie Island of Okinawa Prefecture, but he has not indicated where they are located on the PCA plot nor whether they appear anywhere on that plot in the first place. The question of whether samples from the Jomon Period in western Japan or from the contemporaneous shellmidden period of Okinawa have been taken into consideration or not when constructing that PCA plot is left unclear.
    Early AMH predates the first rice farmers, much earlier. Thanks for elaborating.
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  5. #2593
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    Quote Originally Posted by Kopfjäger View Post
    Early AMH predates the first rice farmers, much earlier. Thanks for elaborating.
    Quoting the author:

    「縄文人の中にもかなりの変異があること
    が分かるが、彼らは現代のアジア集団からか
    け離れた遺伝子構成をしている。これは縄文
    人の祖先集団が他の集団と非常に古い時代、
    恐らく東アジアにホモ・サピエンスが進出し
    て間もない時期に別れたためであるという
    解釈ができる。恐らく、東アジアの海岸線に
    沿って北上したグループが大陸の南から北、
    台湾付近からカムチャッカ半島に至るまで
    の広い地域に定着し、その中から個別に日本
    列島に進出する集団が現れたのだろう。ミト
    コンドリア DNA のハプログループの成立年代
    からは、縄文人につながる人たちの日本列島
    への進出は2〜3万年前から始まったと推
    定される。また、縄文人の内部の変異が大き
    いのは、南北に広がる沿岸の各地から日本列
    島に人々が流入したためなのだと解釈でき
    る。」

    ("One may see that there is also a considerable degree of variation among the Jomon people, but they have a genetic structure that is divergent from modern Asian populations. One may interpret this as being due to Jomon people's ancestral population's having separated from other populations in an extraordinarily ancient era, perhaps in a period not long after Homo sapiens' advance into East Asia. Perhaps a group that moved northward along the coastline of East Asia became established over a wide area from the south to the north of the continent, extending from the vicinity of Taiwan to the Kamchatka Peninsula, and from among them appeared some group[s] that advanced into the Japanese Archipelago individually/separately [個別に]. From the age of establishment [成立年代] of mitochondrial DNA haplogroups, it may be inferred that the advance into the Japanese Archipelago of people leading/connecting [つながる] to the Jomon people has begun 20,000 to 30,000 years ago. Furthermore, the fact that the internal variation of the Jomon people is large may be interpreted to be a result of an influx of people into the Japanese Archipelago from various places along the coast that stretches north and south.")
    Last edited by Ebizur; 07-06-2019 at 11:21 AM.

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  7. #2594
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    https://www.biorxiv.org/content/10.1101/687384v1

    Genetic evidence suggests relationship between contemporary Bulgarian population and Iron Age steppe dwellers from Pontic-Caspian steppe.



    LOL from this paper. Anybody reads it?

    They use PAST only, and didn't even tell what data they used for it (I can guess that values taken from Eigenstrat or PLINK PCA but it is not said in the text).
    No format stats, no ADMIXTURE.
    For PCA with ancient and moderns they have probaly huge projection bias.
    Such PAST PCA and trees could be posted on this forum, but not on biorxiv

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  9. #2595
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    Quote Originally Posted by gene.test View Post
    https://www.biorxiv.org/content/10.1101/687384v1

    Genetic evidence suggests relationship between contemporary Bulgarian population and Iron Age steppe dwellers from Pontic-Caspian steppe.



    LOL from this paper. Anybody reads it?

    They use PAST only, and didn't even tell what data they used for it (I can guess that values taken from Eigenstrat or PLINK PCA but it is not said in the text).
    No format stats, no ADMIXTURE.
    For PCA with ancient and moderns they have probaly huge projection bias.
    Such PAST PCA and trees could be posted on this forum, but not on biorxiv
    This paper's garbage.

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  11. #2596
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    Quote Originally Posted by Generalissimo View Post
    This paper's garbage.
    Yes, the guys, who are not professional geneticists have a political agenda, to prove the Bulgarians are mainly descendants from the old Bulgars, who were not a Central Asian, but North Caucasian tribes. To prove that they cherry pick samples from different publications(not any new tests). For example, for Bronze age Bulgarians they pick only the Yamnaya outlier and have circled it on the plot as where Bulgarians have been then. It gives the wrong impression we were where Croats are now and the huge shift towards Caucasus was only after the Middle ages. I don't think they don't know that the majority of the Bronze age Balkan sample lie over the modern Tuscans and the old Minoans. The only Iron age Bulgarian is even further South over the Sicilians. The migrations during the Early Middle ages only shifted the Bulgarians North due to Slavic and possibly some more North European admixture(Goths, Celts, etc)

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  13. #2597
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    Not ancient DNA, but may be interesting:

    https://www.eurekalert.org/pub_relea...-amp070819.php

    Ancient molar points to interbreeding between archaic humans and Homo sapiens in Asia

    Analysis gives new continental bite to evolution


    https://www.pnas.org/content/early/2.../02/1907557116

    Rare dental trait provides morphological evidence of archaic introgression in Asian fossil record

    Shara E. Bailey, Jean-Jacques Hublin, and Susan C. Antón

    PNAS first published July 8, 2019 https://doi.org/10.1073/pnas.1907557116

    Edited by James F. O’Connell, University of Utah, Salt Lake City, UT, and approved June 12, 2019 (received for review May 3, 2019)

    Abstract

    The recently described Denisovan hemimandible from Xiahe, China [F. Chen et al., (2019) Nature 569, 409–412], possesses an unusual dental feature: a 3-rooted lower second molar. A survey of the clinical and bioarchaeological literature demonstrates that the 3-rooted lower molar is rare (less than 3.5% occurrence) in non-Asian Homo sapiens. In contrast, its presence in Asian-derived populations can exceed 40% in China and the New World. It has long been thought that the prevalence of 3-rooted lower molars in Asia is a relatively late acquisition occurring well after the origin and dispersal of H. sapiens. However, the presence of a 3-rooted lower second molar in this 160,000-y-old fossil hominin suggests greater antiquity for the trait. Importantly, it also provides morphological evidence of a strong link between archaic and recent Asian H. sapiens populations. This link provides compelling evidence that modern Asian lineages acquired the 3-rooted lower molar via introgression from Denisovans.

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  15. #2598
    https://www.biorxiv.org/content/10.1101/694299v1

    West Asian sources of the Eurasian component in Ethiopians: a reassessment

    Abstract
    Previous genome-scale studies of populations living today in Ethiopia have found evidence of recent gene flow from an Eurasian source, dating to the last 3,000 years. Haplotype and genotype data based analyses of modern and ancient data (aDNA) have considered Sardinia-like proxy, broadly Levantine or Neolithic Levantine populations as a range of possible sources for this gene flow. Given the ancient nature of this gene flow and the extent of population movements and replacements that affected West Asia in the last 3000 years, aDNA evidence would seem as the best proxy for determining the putative population source. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ~50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called NAF for Non African) and ancient and modern proxies area after having extracted NAF from Ethiopians through ancestry deconvolution, and unveil a genomic signature compatible with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization.
    It's as if they haven't seen on any paper from NE Africa since 2014. I have no idea what to make of this.

    Definitely Minoan-like people showing up in Ethiopia 3,000 years ago to contribute 50% of the ancestry of Amharas. Let's ignore those 15,000 Ibermaurusians who carried the same ydna and mtdna and Eurasian admixture levels of Amharas, those 4,000- 2,000 year old nomads from Southeast Africa, and basically act as if none of that happened and we are in 1960. Even Carletoon Coon and other earlier racialists who long predated our genomic age had a better idea than this literal waste of paper.

    Why in the world do they conflate Amhara to mean Ethiopian?

    The IoG should probably stick to Europe. This paper serves its purpose only as evidence of willful negligence on their part.

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  17. #2599
    http://smbe2019.org/programme/interactive-programme/

    The genetic landscape of Ethiopia: diversity, intermixing and the association with culture - Garrett Hellenthal

    The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure. Here we report results from analyses of new genome-wide autosomal DNA from >1100 Ethiopians representing 69 different ethnic groups. Using novel statistical approaches, we report the extent to which genetic similarity among Ethiopians correlates with birthplace, ethnic identity, shared language and the sharing of 31 cultural practices. We demonstrate significant associations between genetic similarity and each of geographic and elevation distance, both among present-day Ethiopians as expected and, more surprisingly, between present-day Ethiopians and a 4,500-year-old Ethiopian. We also show how ethnic groups that reported engaging in particular cultural practices are more genetically similar than expectations based on language and spatial distance. Furthermore, we give examples of how social behaviours have directly -- and strongly -- increased genetic differences among groups, though also providing evidence of recent intermixing among peoples from different language groups and religious affiliations.

    In addition, we describe the ancestral history of different Ethiopian groups, revealing a southwest-northeast cline across Ethiopia defined by ancestry related to Central and West African groups versus Egyptian groups. We date distinct admixture events that show correlations with major language classifications and geography, including events dated to ~1600-2800 years ago involving sources carrying DNA similar to present-day Egyptians versus events starting ~1,450 years ago involving sources carrying DNA related to western Sub-Saharan Africans. Overall these results showcase the ability of genetics to help shed light on the ancestral histories of different ethnic groups, for example corroborating oral traditions. They also illustrate the necessity of accounting for ethnicity, geography, and sometimes even occupation, when designing sampling strategies (e.g. for genome-wide association studies, GWAS) to study Ethiopians.
    A never ending clown carnival.

    Now why in the world would they bring up West/Central African? they are the worst proxy for any ancestry in NE Africa outside the smaller portion of Nilo-Saharan ancestry. They are extremely hybridized population that is made of up mixing the most divergent populations of humans known, who carry ancestry from archaics we haven't even identified yet. Just seeing difference between the Luo and the West Africans in the archaic paper, with only 40% already West/Central African-admixed Dinka ancestry in the Luo depressing the archaic signal in the Luo heavily compared to West Africans and more Bantu populations.

    Horn African's Eurasian ancestry is Egyptian-like? did they try saying that with a straight face?. Does anyone wonder were all the Iran Chl ancestry went? Might as well say the non Semitic ancestry in Egyptians is Horner-like.

    And why is it Horn Africans are the only ones that papers try to model with modern populations? Is there some sort of anti-Horner bias in population genomics and amongst geneticists? this stupidity can't possibly be this endemic in this field. 2 papers, all released the same week. One talks about Sea peoples, the other about West Africans and Egyptians. And the admixture dates never change. Why in the world do they care so much about Egyptians or West Africans when there are dozens of genomes from 15,000 to 1,500 years ago from the Maghreb to Tanzania? And this paper literally states 2,800? 1,450? This is pseudo-science at this point. Shriner looks sane now damnit.

    The whole presenting that ancestral East African - the ancestry that makes up 60 - 50% of the ancestry of these samples Horn African populations - as West/Central African related than say, more related to Somalis is an beyond joking. aEA is closer to Eurasian ancestry than the basal Human ancestry West/Central Africans carry, not to mention the unknown and significant archaic ancestry from at least 2 distinct sources. It makes more sense that Cushitic groups model West/Central African ancestry than anything else.

    Yet again - let us obsess with Mota, not with those literally Cushitic speaking thousands of years old samples we have from Kenya and Tanzania. Even if they want to use a paleolithic/mesolithic Horn African HG surrogate, they could have used the Chabu who seemingly have no Eurasian ancestry unlike Mota, who was likely already admixed with some Afroasiatic group, whether Omotic or Cushitic.

    Out of these 4 things, its the fact they are using modern populations to model other modern populations, and always singling out Horn Africans to consistently perform these moderns modelling moderns studies and pseudo-genomics that is most infuriating. What is it about Horn Africans that makes all argumentation revolve around Eurasia vs "sub-Saharan"? there is no sub-Saharan clade, and the overwhelming majority of Africans have some degree of significant Eurasian ancestry, as the Yoruba were shown, the Khoi-San, and all Southeast African HG. Only the Chabu and possibly the Nilotic groups and eastern Pygmies can be said to lack Eurasian ancestry. But the case isn't stong for no Eurasian ancestry in these groups, especially knowing they carry West/Central African ancestry.

    Seriously - what is it recently with all this modelling Horn Africans with the most retarded and impossible of models? Now it's Egyptians and West/Central Africans? Funny, because reality is that it was Horn African-like groups that contributed to both these populations - however minimal - not the other way around.

    This problem needs to get stamped sooner than later. Pseudo-genomics - with it's ideological bases and racialist bias - needs to be rooted and driven out, and die out in the cold.

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  19. #2600
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    Quote Originally Posted by rozenfeld View Post
    https://www.pnas.org/content/early/2.../09/1903984116

    A genetic analysis of the Gibraltar Neanderthals

    Lukas Bokelmann, Mateja Hajdinjak, Stéphane Peyrégne, Selina Brace, Elena Essel, Cesare de Filippo, Isabelle Glocke, Steffi Grote, Fabrizio Mafessoni, Sarah Nagel, Janet Kelso, Kay Prüfer, Benjamin Vernot, Ian Barnes, Svante Pääbo, Matthias Meyer, and Chris Stringer

    PNAS first published July 15, 2019 https://doi.org/10.1073/pnas.1903984116
    This is under a paywall. Is this article aviable for free?

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