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Thread: Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY)

  1. #841
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    "atypical" haplogroup C5c1 from chamber graves placed in medieval cemetery in Pień

    >>The obtained results for the nuclear allele and mtDNA do not corroborate the Scandinavian origin of the analyzed population.<<

    In the populations of Central and Eastern Europe, frequency of haplogroup C is very low [34]. Nevertheless, some subclusters of haplogroup C, like C5c1 clade was reported to occur almost exclusively in Europe [34]. C5c1 haplogroup was previously observed in three Poles [34], four Europeans [46], one Russian [47], one Caucasian and one person of unknown origin [34], [46], [47]. In this study we present an additional haplotype belonging to C5c1 clade, which was found in the Ukrainian mtDNA pool (Figure 4). As the components of the C5c1 haplogroup are virtually absent in Asia and were reported only in the populations of Central Europe, the previous hypothesis by Derenko et al. [34] that the C5c1 clade might be a marker of Siberian ancestry in Central European populations could be further supported by the results of this study. Thus, the presence of C5c1 clade among recent Europeans may reflect their ancient contacts with Asian populations, that could be traced back to the Neolithic period, as the evolutionary age of C5c1 clade was calculated to around 4–9 kya (Table S4).

    The History of Slavs Inferred from Complete Mitochondrial Genome Sequences
    Marta Mielnik-Sikorska, Patrycja Daca, Boris Malyarchuk, Miroslava Derenko, Katarzyna Skonieczna, Maria Perkova, Tadeusz Dobosz, and Tomasz Grzybowski, Luísa Maria Sousa Mesquita Pereira
    PLoS One. 2013; 8(1). Published online 2013 Jan 14.
    http://journals.plos.org/plosone/art...l.pone.0054360

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  3. #842
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    What I want to know is where the R1b-P312 in Bell Beaker came from. I am waiting for something definitive on that front, which I suspect is going to come from the Pontic steppe and/or the Carpathian Basin or maybe Single Grave/Protruding Foot Beaker Corded Ware on the Lower Rhine.

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  5. #843
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    1: Dong Hoon Shin will study more aDNA from India: http://shinpaleopathology.blogspot.c...n-college.html

    BRIEF SUMMARY OF RESEARCH: ... Main concentrations of these megalithic graves and habitation sites have been found in Kerala, Tamilnadu, Karnataka, Andhra Pradesh and Maharashtra (especially Vidarbha) regions of Central & Peninsular India. ... PROJECT 2: Next, based on the above-obtained information, the scholars of both countries will visit and investigate the megalith sites of the Vidarbha area, re-confirming the fundamental archaeological information of megalith trends in the region. Anthropological, paleoparasitological, ancient DNA, and stable isotope analyses would also be performed on the human and animal samples we obtained during the investigation when available. PROJECT 3: We would do the study on DNA analysis using the human samples obtained from the Vidarbha area (ancient and modern). ...
    2: Eske Willerslev gave a talk in Brazil. Usually he talks about the same stuff, so I expected another rehash of his old talks, but since I was bored, I decided to watch: https://www.youtube.com/watch?v=09DO9-VfF6c

    Well, it was mostly a rehash, though couple of things were somewhat new, at least for me. Around 47:50(https://www.youtube.com/watch?v=09DO...tu.be&t=47m38s) he says that soon they have a study with many more samples than Allentoft 2015 with 101 sample. I wonder how many is that? 500? 1000?

    Then around 1:24:29(https://www.youtube.com/watch?v=09DO....be&t=1h24m29s) he says that they are working on spread of Indoeuropean languages into South Asia.

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  7. #844
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    ESHE 2017 abstracts are available: http://www.eshe.eu/static/eshe/files...2017_FINAL.pdf . There are very few aDNA abstracts, so I'll post here some of them:

    Population history of late Neandertals

    Mateja Hajdinjak1, Qiaomei Fu2, Udo Stenzel1, Alexander Hübner1, Martin Petr1, Fabrizio Mafessoni1, Steffi Grote1, Hélčne Rougier3, Isabelle Crevecoeur4, Patrick Semal5, Marie Soressi6, Sahra Talamo7, Jean-Jacques Hublin7, Ivan Gušić8, Željko Kućan,8 Pavao Rudan8, Liubov V. Golovanova9, Vladimir B. Doronichev9, Cosimo Posth10,11, Johannes Krause10,11, Petra Korlević1, Sarah Nagel1, Birgit Nickel1, Kay Prüfer1, Janet Kelso1, Matthias Meyer1, Svante Pääbo1

    1 - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany · 2 - Key
    Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, China · 3 -
    Department of Anthropology, California State University Northridge, Northridge, California, USA · 4 - Université de Bordeaux, CNRS, UMR 5199-PACEA, France · 5 - Royal Belgian Institute of Natural Sciences, Brussels, Belgium · 6 - Faculty of Archaeology, Leiden University, The Netherlands · 7 - Department of Human Evolution, MPI-EVA, Leipzig, Germany · 8 - Croatian Academy of Sciences and Arts, Zagreb, Croatia · 9 - ANO Laboratory of Prehistory, St. Petersburg, Russia · 10 - Max Planck Institute for the Science of Human History, Jena, Germany · 11 - Institute for Archaeological Sciences, University of Tübingen, Germany

    The Middle to Upper Palaeolithic transition in Europe is characterized by major cultural and biological changes and coincides with the arrival of anatomically modern humans and the disappearance of Neandertals [1]. In order to investigate the population history of late Neandertals and their possible genetic interactions with early modern humans, we studied the genomes of Neandertals from the time when they, or their immediate ancestors, could have met modern humans. We screened 78 hominin bones and teeth, as well as morphologically undiagnostic bone fragments, from 21 late Neandertal sites across Eurasia for ancient DNA preservation.

    We identified five Neandertal specimens from the sites of the Troisičme caverne of Goyet (Belgium), Spy (Belgium), Les Cottés (France), Vindija Cave (Croatia), and Mezmaiskaya Cave (Russia) (individual ‘Mezmaiskaya 2’) with sufficient amounts of endogenous DNA to enable the sequencing of their nuclear genomes to an average coverage of between 1- and 2.7-fold. The specimens were radiocarbon dated either directly or by dating of associated finds to between ~ 39,000 and ~ 47,000 years calBP. We analyzed the genomes of these five Neandertals together with previously determined genome sequences from three Neandertal individuals: one from Croatia (Vindija 33.19), directly dated to >45,000 years calBP, one from Denisova Cave in the Altai Mountains (Russia)[2], which was discovered in a layer dated by thermoluminescence to ~ 90,000 years BP, and one from the Mezmaiskaya Cave (Russia), dated to ~ 60-70,000 years BP (individual ‘Mezmaiskaya 1’). We find that all late Neandertals were genetically more similar to each other than to the Altai Neandertal, regardless of their geographical origin. Moreover, the genetic diversity of the nearly contemporaneous late Neandertals was substantially lower than that of humans today. The reconstruction of multiple late Neandertal genomes from individuals who lived across a wide geographic range allowed us to investigate whether geographical proximity may be a predictor of genetic relatedness, as was previously shown for present-day human populations [3]. The Neandertals from Vindija Cave were more similar to each other than to any other Neandertal; as was the case for the three Neandertals from Belgium and France, supporting the presence of geographical substructure in Neandertal populations. All these individuals in turn were more closely related to each other than to the younger Neandertal individual from Mezmaiskaya Cave (Mezmaiskaya 2). Nonetheless, the latter individual is more closely related to the other late Neandertals than to the older Neandertal individual from the same site (Mezmaiskaya 1). This may point to a genetic population turnover towards the end of Neandertal history. We compared the Neandertal genomes from this and previous studies to the genomes of present-day humans to investigate which Neandertal individual was closest to the Neandertal population that contributed Neandertal genetic material to present-day humans. We find that all the late Neandertals and the older Mezmaiskaya 1 Neandertal are genetically more similar to the introgressing Neandertal than the Altai Neandertal. Thus, the majority of the gene flow into ancestors of present-day non-Africans originated from a Neandertal population that was equidistant or ancestral to the late Neandertals and Mezmaiskaya 1 but had diverged from the Altai population. The generation of additional Neandertal genomes in the future will allow the reconstruction of Neandertal population history at a finer resolution and across more of their temporal and geographical range.


    Finding hominin bones from the Palaeolithic using collagen peptide mass sequencing (ZooMS)


    Tom Higham1, Samantha Brown1, Katerina Douka1, Cara Kubiak1, Viviane Slon2, Petra Korlevic2, Mateja Hajdinjak2,Thibaut Devičse1, Daniel Comesky1, Noemi Procopio3, Ivor Karavanic4, Sinsia Radovic5, Michael Shunkov6, Anatoly Drevianko6, Matthias Meyer2, Svante Pääbo2, Michael Buckley3

    1 - University of Oxford · 2 - MPI-EVA, Leipzig · 3 - Faculty of Life Sciences, University of Manchester · 4 - Department of Archaeology, University of Zagreb · 5 - Croatian Academy of Sciences and Arts, Zagreb · 6 - Institute of Archeology and Ethnography, Novosibirsk

    Ancient DNA sequencing has shed significant light upon our knowledge of archaic and modern humans during the Middle and Upper Palaeolithic. Many Palaeolithic sites contain large numbers of bones, but due to the combination of post-depositional influences and carnivore processing of bone remains, many of them lack the diagnostic features required for identification of bone to specific taxon. Human remains dating to this period are, therefore, very rare. We have been applying a method of collagen finger-printing to screen Palaeolithic bone fragments to identify the species/taxon of the bone, and importantly, to identify bone which has characteristic unique human peptides. The method utilizes mass spectrometry (MALDI-ToF-ToF) to produce a spectrum of peptide masses. Different species disclose small differences in the sequence of these peptides that enable them to be identified. Thus far we have found four new human fossil bone fragments from >4,000 undiagnostic bone remains, ranging down to as small as 23 mm in length. We have screened bones from the Palaeolithic archaeological sites of Denisova Cave (Russia) and Vindija Cave (Croatia). We then carried out DNA sequencing of the human bone fragments to identify into which human group they fall. At Denisova Cave, we previously identified a tiny bone as a hominin and showed, using DNA methods, that its mitochondrial DNA was of the Neanderthal type (Denisova 11) [1]. We have identified 2 additional bones which have been genetically analysed. At Vindija Cave we identified a new bone fragment from the G1 level and found that it had the same mtDNA sequence as another Neanderthal from the same site but a deeper level. We also found evidence for human processing on this bone in the form of cutmarks. We directly dated the bones using single amino acid dating of hydroxyproline. We will describe the significance of the new fossil finds in terms of the archaeological sequences at both sites. Collagen fingerprinting has immense potential for identifying hominin remains in highly fragmentary archaeological assemblages. Coupled with DNA analysis and direct dating, this method should be widely applied to previously excavated archaeological materials.

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  9. #845
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    I was pleased to see a new Iberian aDNA paper whose lead author is Anna Szecsenyi-Nagy. She knows a thing or two about Beaker DNA outside Iberia, because she's seen Beaker DNA outside Iberia. [Allusion to a current series of TV advertisements for an insurance company in the USA.] Anyway, here's a post that links one of her "old" papers (from 2015). http://www.anthrogenica.com/showthre...ll=1#post77927

    Isidro posted about the new paper today, here: http://www.anthrogenica.com/showthre...l=1#post279755

    It's about mtDNA, disappointing but not unusual. Actually I had read some of her earlier work because my own mtDNA is T2f3, and she is one of the very few people who have published anything useful about that.
    Last edited by razyn; 08-28-2017 at 02:42 PM.

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  11. #846
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    Quote Originally Posted by razyn View Post
    I was pleased to see a new Iberian aDNA paper whose lead author is Anna Szecsenyi-Nagy. She knows a thing or two about Beaker DNA outside Iberia, because she's seen Beaker DNA outside Iberia. [Allusion to a current series of TV advertisements for an insurance company in the USA.] Anyway, here's a post that links one of her "old" papers (from 2015). http://www.anthrogenica.com/showthre...ll=1#post77927

    Isidro posted about the new paper today, here: http://www.anthrogenica.com/showthre...l=1#post279755

    It's about mtDNA, disappointing but not unusual. Actually I had read some of her earlier work because my own mtDNA is T2f3, and she is one of the very few people who have published anything useful about that.
    To me, what is disappointing is that the mtDNA is only HVS-I. As usual.
    If they tested full mtDNA we might really start working out something interesting.

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    Africans who carry Neanderthal DNA show gene flow from Eurasians

    The idea that Africans fail to carry Neanderthal DNA has recently been proven as wrong. Marc Haber, a British geneticist from the Wellcome Trust Sanger Institute in Hinxton, has found that the Touboo in Chad and the Amhara in Ethiopia carry Neanderthal genes. Whereas Eurasians carry ~2% Neanderthal ancestry, Ethiopians carry ~1% Neanderthal ancestry and Central Africans carried ~0.5% Neanderthal ancestry.
    Haber maintains that Africans who carry Neanderthal DNA show gene flow from Eurasians. The detectable Neanderthal DNA in Africans is found among Africans that carry the R1b haplogroup.
    Haber believes that the R1b haplogroup penetrated Central Africa via two migrations. The first migration he believes took place 6000 years ago (6kya), and the second migration around 3kya. The major problem with this theory is that there is no archaeological evidence of a back migration from Eurasia to Africa.
    The discovery of Eurasian "admixture" among Africans is not a recent discovery. Pickrell et al. estimated Eurasian ancestry among Africans from East and South Africa ranged from 2.2-50% and that the Mande people carry 2% Eurasian admixture. This supports the original claim of the authors of the Mota article – i.e. the claim that as much as 6–7% of the ancestry of West and Central African groups was "Eurasian" was not an error.

    The Widespread Appearance of Neanderthal DNA: Africans Have It Too
    http://www.ancient-origins.net/human...-it-too-008690

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    What was the Marc Haber paper called?

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    Quote Originally Posted by Genarh View Post
    The idea that Africans fail to carry Neanderthal DNA has recently been proven as wrong. Marc Haber, a British geneticist from the Wellcome Trust Sanger Institute in Hinxton, has found that the Touboo in Chad and the Amhara in Ethiopia carry Neanderthal genes. Whereas Eurasians carry ~2% Neanderthal ancestry, Ethiopians carry ~1% Neanderthal ancestry and Central Africans carried ~0.5% Neanderthal ancestry.
    Haber maintains that Africans who carry Neanderthal DNA show gene flow from Eurasians. The detectable Neanderthal DNA in Africans is found among Africans that carry the R1b haplogroup.
    Haber believes that the R1b haplogroup penetrated Central Africa via two migrations. The first migration he believes took place 6000 years ago (6kya), and the second migration around 3kya. The major problem with this theory is that there is no archaeological evidence of a back migration from Eurasia to Africa.
    The discovery of Eurasian "admixture" among Africans is not a recent discovery. Pickrell et al. estimated Eurasian ancestry among Africans from East and South Africa ranged from 2.2-50% and that the Mande people carry 2% Eurasian admixture. This supports the original claim of the authors of the Mota article – i.e. the claim that as much as 6–7% of the ancestry of West and Central African groups was "Eurasian" was not an error.

    The Widespread Appearance of Neanderthal DNA: Africans Have It Too
    http://www.ancient-origins.net/human...-it-too-008690
    Are you just paraphrasing here?
    There are at least three Y lineages that seem to have back migrated to Africa - R1b, T, and J1. I believe the latest information has R1b in an older wave, J1 in a younger wave. I'm not convinced where T fits in it all since it pops up in the African tribes rich in J1 but also R1b. The former two are typically isolated in central (R1b) and eastern (J1) Africa.
    YDNA: R1b-BY50830 Stepney, London, UK George Wood b. 1782 English <-> Bavarian cluster 1100 BC
    m gf YDNA: ?? Gurr, James ~1740, Smarden, Kent, England.
    m gm YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    m ggf YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    p ggf YDNA: R1b-Z17901. Gould, John Somerset England 1800s.
    p ggf YDNA: R1b-L48. Scott, William Hamilton Ireland(?) 1800s

    other:
    Turner: R-U152
    Welch: early 1800s E-M84 Kent, England.

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    I guess many of us have porterhouse stake taste, unfortunately there is still pork chop budgets. They were very clear in their introduction.

    Quote Originally Posted by Saetro View Post
    To me, what is disappointing is that the mtDNA is only HVS-I. As usual.
    If they tested full mtDNA we might really start working out something interesting.
    Last edited by Isidro; 09-05-2017 at 01:55 PM.

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