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Thread: New DNA Papers - General Discussion Thread

  1. #2731
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    https://www.researchgate.net/publica...KnveG2CHpm7Z8j

    Triangulation fails when neither linguistic, genetic, nor archaeological data support the Transeurasian narrative

    "Robbeets et al.'s "Triangulation supports agricultural spread of the Transeurasian languages" (Nature 599, 616-621, 2021) argue that the dispersal of the so-called "Transeurasian" languages, a highly disputed language superfamily comprising the Turkic, Mongolian, Tungusic, Koreanic, and Japonic language families, was driven by Neolithic farmers in the West Liao River region of China. They adduce evidence from linguistics, archaeology, and genetics to support their claim. An admirable feature of the Robbeets et al.'s paper is that all their datasets can be accessed. However, a closer investigation of all three types of evidence reveals fundamental problems with each of them. Robbeets et al.'s analysis of the linguistic data does not conform to the minimal standards required by traditional scholarship in historical linguistics and contradicts their own stated sound correspondence principles. A reanalysis of the genetic data finds that they do not conclusively support the farming-driven dispersal of Turkic, Mongolian, and Tungusic, nor the two-wave spread of farming to Korea. Their archaeological data contain little phylogenetic signal, and we failed to reproduce the results supporting their core hypotheses about migrations. Given the severe problems we identify in all three parts of the "triangulation" process, we conclude that there is neither conclusive evidence for a Transeurasian language family nor for associating the five different language families with the spread of Neolithic farmers from the West Liao River region"

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  3. #2732
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    For this new article I can't find table S1 even though it is advertised can any of you find it? All I can find are figures.
    The genomic landscape of contemporary western Remote Oceanians
    Lara R. Arauna, Jacob Bergstedt, Jeremy Choin, Javier Mendoza-Revilla, Christine Harmant, Maguelonne Roux, Alex Mas-Sandoval, Laure Lemee, Heidi Colleran, Alexandre Francois, Frederique Valentin, Olivier Cassar, Antoine Gessain, Lluis Quintana-Murci, Etienne Patin
    bioRxiv 2022.01.10.475623; doi: https://doi.org/10.1101/2022.01.10.475623
    This article is a preprint and has not been certified by peer review [what does this mean?].
    Share This Article:
    https://www.biorxiv.org/content/10.1...01.10.475623v2
    Maternal Uncle y-line= F0R1b1-L21

  4. #2733
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    Which studies (or study) have academic samples of Manjak, Serere and Diola?
    Last edited by Tomenable; 07-10-2022 at 03:59 PM.

  5. #2734
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    Quote Originally Posted by venustas View Post
    For this new article I can't find table S1 even though it is advertised can any of you find it? All I can find are figures.
    The genomic landscape of contemporary western Remote Oceanians
    Lara R. Arauna, Jacob Bergstedt, Jeremy Choin, Javier Mendoza-Revilla, Christine Harmant, Maguelonne Roux, Alex Mas-Sandoval, Laure Lemee, Heidi Colleran, Alexandre Francois, Frederique Valentin, Olivier Cassar, Antoine Gessain, Lluis Quintana-Murci, Etienne Patin
    bioRxiv 2022.01.10.475623; doi: https://doi.org/10.1101/2022.01.10.475623
    This article is a preprint and has not been certified by peer review [what does this mean?].
    Share This Article:
    https://www.biorxiv.org/content/10.1...01.10.475623v2
    It is sooooo annoying to do your best on a paper and have it published and then to have people show you its flaws.
    If you are publishing something contentious or likely to bring lots of comments, then why not get them dealt with BEFORE publication?
    Put out a pre-print and give people a chance to comment.
    Then you can publish formally. Maybe including some corrections or some text addressing the comments.
    (There may be other reasons, but that is the one of interest here.)

    The authors maybe should have attached the supplementary stuff, so this might be a flaw in itself.
    Or maybe they are keeping those for publication itself.
    Just in case someone else took their data and published it before their formal paper.
    So you may have to wait for that.

  6. #2735
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    Genetic characterization of two North Italian villages: A story of isolation, ancient admixture, and genetic drift

    Interesting results of this two Asiago plateau isolated populations. The High presence of J2-L26 is an interesting fact, it would be interesting to know more details regarding the specific subclades. I do think, some J2-L70 should be part of them, at least most of J2-L25.

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  8. #2736
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    Quote Originally Posted by J.delajara View Post
    The High presence of J2-L26 is an interesting fact, it would be interesting to know more details regarding the specific subclades. I do think, some J2-L70 should be part of them, at least most of J2-L25.
    L25 is included as Terminal SNP in the study: 6 from Rozo are under J2a-L25 but 66 (Stoccaredo) + 11 (Rozo) = 77 under J2a-L26(xL25).
    I have the suspicion those J2a-L26(xL25) are mostly in J2a-[email protected],[email protected]>[email protected],[email protected] ("brother of M319").
    Another big question is if R1b-U106 is not present in those two villages or hidden under R1b-P311,L52. I1 and R1b-U106 IMO are low for a paternal origin supposedly predominantly in Medieval Bavaria (SW of Munich). Else the following two alternatives come to my mind: the earlier Y-lineages in the Asiago area (or from elsewhere not in South Germany) where also "founding fathers" or later patrilineal influences have reached modern dominance over original Cimbrian Y-Lines.

    I certainly would like to analyze the raw data. I'm now looking into
    The genetic data belonging to Rotzo and Stoccareddo cohorts have been submitted to the European Variation Archive (EVA) information on allele frequencies in each cohort are accessible in Variant Call Format (VCF) at the following link: https://www.ebi.ac.uk/ena/browser/view/PRJEB53507
    Currently I can't understand the logic of the published files: Study Accession is PRJEB53507, Analysis Accession ERZ11420542 and the Sample Accession is SAMEA110103620 etc. (848 Samples?). The Submitted files FTP seem to be the same 8 (4 at/X? and 4 Y) for all samples: if you click on one the same file gets also selected for all other samples. So for Y
    RTZ_Y_20220609.vcf.csi
    RTZ_Y_20220609.vcf.gz
    STC_Y_20220609.vcf.csi
    STC_Y_20220609.vcf.gz
    CSI are index files and gz contain VCF files. They may be the aggregate of all Y-variation separatedly for Rozo/RTZ and Stoccaredo/STC. Parts of the STC_Y_20220609.vcf with my emphasis
    ##fileformat=VCFv4.2
    ##source=PLINKv1.90
    ##bcftools_pluginCommand=plugin fill-tags -- /netapp08/EVA_BAU_20220428/20220512/STC/24/STC_MALES_splitted_20220512_VCF.vcf.gz -t all; Date=Fri May 20 17:05:04 2022
    ##bcftools_annotateCommand=annotate -a /netapp/nfs/resources/dbSNP/human_9606_b154_GRCh37p13/VCF/GCF_000001405.25.chrY.vcf.gz -c ID -O z -o /netapp08/EVA_BAU_20220428/20220601/STC/MERGED/ALL_FIX/Y/STC_Y_20220512_DBSNPann.vcf.gz /netapp08/EVA_BAU_20220428/20220601/STC/MERGED/ALL_FIX/Y/STC_Y_20220512_PREANNOT.vcf.gz; Date=Fri Jun 3 14:35:22 2022
    #CHROM POS ID REF ALT QUAL FILTER INFO
    Y 2657176 rs2534636 C T . . PR;NS=277;AN=277;AF=0.00722022;MAF=0.00722022;AC=2 ;AC_Het=0;AC_Hom=0;AC_Hemi=2;HWE=1;ExcHet=1
    I would like to ask if this MALES_splitted/merged format is known/documented so to allow discovery of terminal Y-clades and number of samples in those clades?

    Supp. 8 Table 1 edited/extended by me:
    Italy Northeast Asiago-Cimbri Rozo Stoccaredo Y-Hg-n136 - Massimo Mezzavilla et al 2022 Freq ajp.png

    EDIT: seems like there is no additional detail in this data at least for J2a-L26. I found positive/present in the VCF:
    SNP rs# hg19 (GRCh37p13)
    L26 rs34459399 22942897
    L24 rs35248080 14286528
    L25 rs34534058 19136822
    Not found in the VCF:
    PF5088 8107430
    PF5125 9089648
    M67 21878809
    FGC17667/Z17199/Y5014 22521698
    PF5160 8265737
    Z393 7608911
    Z6064 21260216
    So unfortunately it seems just the very basic haplogroup stats can be used, autosomally probably no individual or further use. Unfortunate.
    Last edited by ChrisR; 09-30-2022 at 03:55 PM.
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372; mtDNA J1b1b, J1c1d2-A11884G, U5a2b2-G10685A, U5b1b1-b-T16192C! Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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  10. #2737
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    Quote Originally Posted by ChrisR View Post
    L25 is included as Terminal SNP in the study: 6 from Rozo are under J2a-L25 but 66 (Stoccaredo) + 11 (Rozo) = 77 under J2a-L26(xL25).
    I have the suspicion those J2a-L26(xL25) are mostly in J2a-[email protected],[email protected]>[email protected],[email protected] ("brother of M319").
    Another big question is if R1b-U106 is not present in those two villages or hidden under R1b-P311,L52. I1 and R1b-U106 IMO are low for a paternal origin supposedly predominantly in Medieval Bavaria (SW of Munich). Else the following two alternatives come to my mind: the earlier Y-lineages in the Asiago area (or from elsewhere not in South Germany) where also "founding fathers" or later patrilineal influences have reached modern dominance over original Cimbrian Y-Lines.

    I certainly would like to analyze the raw data. I'm now looking into

    Currently I can't understand the logic of the published files: Study Accession is PRJEB53507, Analysis Accession ERZ11420542 and the Sample Accession is SAMEA110103620 etc. (848 Samples?). The Submitted files FTP seem to be the same 8 (4 at/X? and 4 Y) for all samples: if you click on one the same file gets also selected for all other samples. So for Y

    CSI are index files and gz contain VCF files. They may be the aggregate of all Y-variation separatedly for Rozo/RTZ and Stoccaredo/STC. Parts of the STC_Y_20220609.vcf with my emphasis

    I would like to ask if this MALES_splitted/merged format is known/documented so to allow discovery of terminal Y-clades and number of samples in those clades?

    Supp. 8 Table 1 edited/extended by me:
    Italy Northeast Asiago-Cimbri Rozo Stoccaredo Y-Hg-n136 - Massimo Mezzavilla et al 2022 Freq ajp.png

    EDIT: seems like there is no additional detail in this data at least for J2a-L26. I found positive/present in the VCF:

    Not found in the VCF:

    So unfortunately it seems just the very basic haplogroup stats can be used, autosomally probably no individual or further use. Unfortunate.
    Thanks Chris. So if I understood well, from the last part of your comment, all of the J2-L26 are positive to J2-L25?. Thanks in avance

  11. #2738
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    Quote Originally Posted by Curious one View Post
    https://www.researchgate.net/publica...KnveG2CHpm7Z8j

    Triangulation fails when neither linguistic, genetic, nor archaeological data support the Transeurasian narrative

    "Robbeets et al.'s "Triangulation supports agricultural spread of the Transeurasian languages" (Nature 599, 616-621, 2021) argue that the dispersal of the so-called "Transeurasian" languages, a highly disputed language superfamily comprising the Turkic, Mongolian, Tungusic, Koreanic, and Japonic language families, was driven by Neolithic farmers in the West Liao River region of China. They adduce evidence from linguistics, archaeology, and genetics to support their claim. An admirable feature of the Robbeets et al.'s paper is that all their datasets can be accessed. However, a closer investigation of all three types of evidence reveals fundamental problems with each of them. Robbeets et al.'s analysis of the linguistic data does not conform to the minimal standards required by traditional scholarship in historical linguistics and contradicts their own stated sound correspondence principles. A reanalysis of the genetic data finds that they do not conclusively support the farming-driven dispersal of Turkic, Mongolian, and Tungusic, nor the two-wave spread of farming to Korea. Their archaeological data contain little phylogenetic signal, and we failed to reproduce the results supporting their core hypotheses about migrations. Given the severe problems we identify in all three parts of the "triangulation" process, we conclude that there is neither conclusive evidence for a Transeurasian language family nor for associating the five different language families with the spread of Neolithic farmers from the West Liao River region"
    Wow, I remember thinking what a groundbreaking and well argued paper that was regarding Transeurasian language family but it's actually not accurate at all, based on this new research. This is the power of science, always correcting and refuting previous scientific claims.
    Modern Ancestry
    1. East Alpine 52%
    2. Pannonian 25.2%
    3. Northeast German 15.8%
    4. Volga-Uralic (Bashkir) 7%
    Ancient Ancestry
    1. Yamnaya 47.2%
    2. Anatolia 39.0%
    3. WHG 11.6%
    4. Han 2.2%

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  13. #2739
    Quote Originally Posted by Mythbuster General View Post
    Wow, I remember thinking what a groundbreaking and well argued paper that was regarding Transeurasian language family but it's actually not accurate at all, based on this new research. This is the power of science, always correcting and refuting previous scientific claims.
    It wasn't groundbreaking (basically just macro-altaic with a fancy new name) or well-argued at all. Amongst specialists in either archaeology or linguistics it had little support. The MPI just likes to a heavy dose of PR and media strategies to propagate their theories, making it look like there is a far stronger consensus behind them than there actually is. For example in 2018 they made a whole documentary series about how they "discovered" the Proto-Anatolian homeland in Armenia. With the transeurasian "pop science" articles (not the actually research article) there was little talk of the actual content and a lot of talk about how this "deconstructs nationalistic driven ethnogenesis theories" the so-called Transeurasian speaking countries - always a red flag. This just seems the latest episode of the "farmer dispersal theory" fascination many academic institutes in the west have.
    Last edited by CopperAxe; 10-01-2022 at 11:11 AM.
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  15. #2740
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    Quote Originally Posted by J.delajara View Post
    Thanks Chris. So if I understood well, from the last part of your comment, all of the J2-L26 are positive to J2-L25?. Thanks in avance
    No: 6 from Rotzo are under J2a-L25 the other 77 under J2a-L26(xL25). The "x" means they are negative for L25, at least as such I interpret the logic of the table. From the VCF I was not able to find a number/sum of samples positive for the relevant SNPs:
    Code:
    L26
    RTZ
    Y	22942897	rs34459399	T	C	.	.	PR;NS=123;AN=123;AF=0.260163;MAF=0.260163;AC=32;AC_Het=0;AC_Hom=0;AC_Hemi=32;HWE=1;ExcHet=1
    STC
    Y	22942897	rs34459399	T	C	.	.	PR;NS=277;AN=277;AF=0.862816;MAF=0.137184;AC=239;AC_Het=0;AC_Hom=0;AC_Hemi=239;HWE=1;ExcHet=1
    
    L24
    RTZ
    Y	14286528	rs35248080	G	A	.	.	PR;NS=277;AN=277;AF=0;MAF=0;AC=0;AC_Het=0;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=1
    STC
    Y	14286528	rs35248080	G	A	.	.	PR;NS=277;AN=277;AF=0;MAF=0;AC=0;AC_Het=0;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=1
    
    L25
    RTZ
    Y	19136822	rs34534058	T	C	.	.	PR;NS=124;AN=124;AF=0.153226;MAF=0.153226;AC=19;AC_Het=0;AC_Hom=0;AC_Hemi=19;HWE=1;ExcHet=1
    STC
    Y	19136822	rs34534058	T	C	.	.	PR;NS=278;AN=278;AF=0.00359712;MAF=0.00359712;AC=1;AC_Het=0;AC_Hom=0;AC_Hemi=1;HWE=1;ExcHet=1
    Last edited by ChrisR; 10-01-2022 at 11:59 PM.
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372; mtDNA J1b1b, J1c1d2-A11884G, U5a2b2-G10685A, U5b1b1-b-T16192C! Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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