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Thread: Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)

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    Quote Originally Posted by Krefter View Post
    That link sends us to our Drive homepage. Did you get a share link for your Drive file?

    Sorry, try this.

    https://docs.google.com/document/d/1...hKJg4v5YNIhRrc

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    result: Samara_HG Yamnaya Lezgin Chimp -0.0007 -0.137 9648 9661 206623
    result: Samara_HG Yamnaya Lezgin Ust_Ishim -0.0154 -3.011 8942 9222 206173
    result: Samara_HG Yamnaya Lezgin Bougainville -0.0155 -4.001 8885 9164 206623
    result: Samara_HG Yamnaya Armenian Chimp -0.0072 -1.449 9542 9680 206623
    result: Samara_HG Yamnaya Armenian Ust_Ishim -0.0224 -4.377 8825 9229 206173
    result: Samara_HG Yamnaya Armenian Bougainville -0.0225 -5.948 8790 9194 206623
    result: Samara_HG Yamnaya Kalash Chimp 0.0031 0.617 9642 9583 206623
    result: Samara_HG Yamnaya Kalash Ust_Ishim -0.0116 -2.183 8890 9099 206173
    result: Samara_HG Yamnaya Kalash Bougainville -0.0117 -3.048 8773 8980 206623
    result: Samara_HG Yamnaya Dai Chimp 0.0150 2.754 9569 9286 206623
    result: Samara_HG Yamnaya Dai Ust_Ishim 0.0009 0.160 8620 8604 206173
    result: Samara_HG Yamnaya Dai Bougainville 0.0010 0.261 8141 8125 206623
    result: Samara_HG Yamnaya Burusho Chimp 0.0045 0.940 9614 9527 206623
    result: Samara_HG Yamnaya Burusho Ust_Ishim -0.0102 -2.042 8809 8992 206173
    result: Samara_HG Yamnaya Burusho Bougainville -0.0103 -2.895 8688 8868 206623
    result: Samara_HG Yamnaya Georgian Chimp -0.0082 -1.659 9554 9712 206623
    result: Samara_HG Yamnaya Georgian Ust_Ishim -0.0235 -4.593 8832 9258 206173
    result: Samara_HG Yamnaya Georgian Bougainville -0.0235 -6.156 8807 9232 206623
    result: Samara_HG Yamnaya Tajik_Pomiri Chimp 0.0068 1.370 9686 9555 206623
    result: Samara_HG Yamnaya Tajik_Pomiri Ust_Ishim -0.0076 -1.451 8953 9090 206173
    result: Samara_HG Yamnaya Tajik_Pomiri Bougainville -0.0076 -1.975 8852 8987 206623
    result: Samara_HG Yamnaya GujaratiA Chimp 0.0020 0.386 9596 9558 206623
    result: Samara_HG Yamnaya GujaratiA Ust_Ishim -0.0129 -2.449 8807 9038 206173
    result: Samara_HG Yamnaya GujaratiA Bougainville -0.0130 -3.337 8692 8920 206623
    result: Samara_HG Yamnaya Karitiana Chimp 0.0371 6.411 9926 9216 206623
    result: Samara_HG Yamnaya Karitiana Ust_Ishim 0.0250 4.079 9028 8588 206173
    result: Samara_HG Yamnaya Karitiana Bougainville 0.0261 5.317 8728 8284 206623

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  5. #653
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    Quote Originally Posted by Chad Rohlfsen View Post
    Wow, all the ancient pops look a lot more diverse than I expected.

    If you had the same test pop and ref1 but gave every pop a turn as ref2 you'll probably see a trend of relatedness. Ex: Irish, Sardinian, and Lithuanian as test, and Baalberg_MN as ref1, would show everyone but Sardinians get very negative scores with ANE-rich pops as ref2, revealing a trend of Ameridian/MA1/EHG/etc. related ancestry absent in Sardinians. If you used a similar method maybe other forms of ancestry will reveal themselves.

    I got the idea from this section of Haak 2015(described here), hopefully by reading that you'll get a better idea of what I'm saying. Can you do F3 and F4 statistics?

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    Moderators - Would it be possible to return this thread to "ancient DNA in the news". Every day I see new posts and click on the thread hoping for new papers or articles in the media on ancient DNA. Could the posts on analysis perhaps be moved to a thread entitled "Analysis of components in Ancient DNA"?
    Last edited by Jean M; 03-17-2015 at 01:23 PM.

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    R. O. Trapezov et al., 2015, Russian Journal of Genetics: Mitochondrial DNA diversity in the gene pool of the Neolithic and Early Bronze Age Cisbaikalian human population
    Abstract:
    This paper presents the results of a study of a mitochondrial DNA sample (N = 15) from the remains of representatives of the Neolithic and Early Bronze Age (VI–III millennia BC) Cisbaikalian human population. It was found that the mitochondrial gene pool of the ancient population under study contains lineages of East Eurasian haplogroups D, G2a C, Z, and F1b. The results of the comparative analysis of the group under study with ancient and modern Eurasian populations suggest that the development of autochtonous East Eurasian genetic components was the main mechanism of the formation of the population of the Baikal region. Genetic contacts with populations of neighboring regions of Central Asia also contributed to the formation of the gene pool of the Cisbaikalian population.

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    I have been conceiving this idea for a while, and I wonder if some of the more logical, open-minded people here would help all of us walk through the concept.

    We often hear the hypothesis that "there was no R1b in pre-Neolithic Europe." I wonder if perhaps the following may be a key to this theory.

    I was reading a book on prehistoric Italy, and it talked about the convergence of three cultures in the epoch immediately before the Roman Republic. Those three cultures were Etruscan, Latin, and Oscan.

    Of the three cultures, I believe two originally practiced exclusively cremation for human corpses, and one practiced inhumation (burial). This cultural trait was so pronounced and so consistent, that there is a dearth of ethnic Roman (or Latin) bodies in our records, because they cremated their dead, right into historical times.

    I wonder if this could explain why there has been no discovered R1b in pre-Neolithic western Europe (yet). If most of these initial R1b high-majority tribes were culturally of the X culture (whether that was Indo-European, doesn't matter), and people of the X culture always cremated their dead, might this explain the absence of samples? It would certainly reduce the odds.

    Remember, we have less than 100 ancient pre-Neolithic western European Y-Chromosome a-DNA samples. If one culture cremated their dead and the other buried it, it would be as if the cremated never existed.

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    Quote Originally Posted by Christina View Post
    I have been conceiving this idea for a while, and I wonder if some of the more logical, open-minded people here would help all of us walk through the concept.

    We often hear the hypothesis that "there was no R1b in pre-Neolithic Europe." I wonder if perhaps the following may be a key to this theory.

    I was reading a book on prehistoric Italy, and it talked about the convergence of three cultures in the epoch immediately before the Roman Republic. Those three cultures were Etruscan, Latin, and Oscan.

    Of the three cultures, I believe two originally practiced exclusively cremation for human corpses, and one practiced inhumation (burial). This cultural trait was so pronounced and so consistent, that there is a dearth of ethnic Roman (or Latin) bodies in our records, because they cremated their dead, right into historical times.

    I wonder if this could explain why there has been no discovered R1b in pre-Neolithic western Europe (yet). If most of these initial R1b high-majority tribes were culturally of the X culture (whether that was Indo-European, doesn't matter), and people of the X culture always cremated their dead, might this explain the absence of samples? It would certainly reduce the odds.

    Remember, we have less than 100 ancient pre-Neolithic western European Y-Chromosome a-DNA samples. If one culture cremated their dead and the other buried it, it would be as if the cremated never existed.
    That might be a good subject for its own separate thread, since this thread is for ancient dna in the news.

    I have some comments to make, but I will reserve them for that new thread, should you start it somewhere.

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    Stefania Vai et al., 2015, Plos One: Genealogical Relationships between Early Medieval and Modern Inhabitants of Piedmont
    Abstract:
    In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.

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    Per an article by the University of New Mexico about the leading Archeologist of the site from 2013 Paboo's team already extracted and successfully analyzed the mt-DNA genome of a 19000 years old lady from the Cave of el Miron which is in Cantabria but very close to the border with Vizcaya. This is of extreme interest to me personally.

    Svante Paabo’s team at the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany is currently attempting to extract nuclear DNA from phalanges of the “Red Lady of El Mirón,” having successfully obtained and analyzed the mitochondrial DNA.

    [...]

    Straus began his lifelong love of archeological fieldwork at the age of 14—50 years ago—and has been actively conducting research in western Atlantic Europe for over 40 years. The latest El Mirón Cave publication has just come out in Molecular Ecology; it is a study of red deer (elk) DNA , demonstrating (as with an earlier article on salmon DNA in the same journal) that Cantabrian Spain was a refugium for this species during the height of the Last Ice Age. The DNA study of the Red Lady will help test the hypothesis that the repopulation of northwestern Europe after the Last Glacial Maximum by humans also stemmed from an Iberian refugium.
    Source: Straus Has Good Field Season at El Mirón Cave in Spain

    http://news.unm.edu/news/straus-has-...-cave-in-spain

    Now these two articles are from August and September of 2013 more than 1 year ago. So why are they sitting in the results of her mt-DNA haplogroups and they haven't been released to the public? Does anybody have any info?
    Last edited by jeanL; 03-28-2015 at 04:24 PM.

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    Sandra Wilde thesis, 2014: Populationsgenetik kupfer- und bronzezeitlicher Bevölkerungen der osteuropäischen Steppe
    Abstract:
    This dissertation presents the first genetic study of prehistoric populations in the Pontic-Caspian steppe from the Upper Thracian Plain to the Volga. Hypervariable region I (HVR I) and 30 short sections of the coding region containing 32 clade- determining polymorphisms on the mitochondrial DNA, as well as 20 putatively naturally selected autosomal SNPs and a sex-determining locus were analysed using a combination of multiplex PCR and 454 sequencing. Data analysis was performed on the HVR I of 65 of the 180 Eneolithic and Bronze Age samples. (Partial) genotypes were generated from 61 individuals. Published ancient DNA data from Central and Eastern Europe and Central Asia, as well as modern DNA sequences were consulted for comparison.

    The genetic data support the inference that early Neolithic farmers from Southeast Europe were involved in establishing pastoralism in the steppes by demic diffusion. The consistently low values of the FST-statistic (the range includes zero) between the Yamnaya Culture of the steppe and a succession of Neolithic cultures in Central Europe indicate continuous or recurrent contacts between the two regions. Between the Yamnaya Culture and its successor, the Catacomb Culture, the incidence of haplogroup U4, which is at high frequency in hunter-gatherer populations of Neolithic Scandinavia and Mesolithic Northwest Russia, rises from approximately 5 % to above 30 %. It is possible that immigrants from Eastern Baltic hunter-gatherer refugia were involved in the genesis of the Catacomb Culture.

    The low FST values between the prehistoric steppe populations and the modern populations of Central and Eastern Europe indicate genetic continuity. This is supported by the nuclear genotype frequencies. According to current knowledge the modern European gene pool can be explained by three roots: indigenous Mesolithic hunter-gatherers, early farmers from the Near East, and an ancient North Eurasian component with an Upper Palaeolithic origin. Maybe the third ancestry component was introduced into the late Neolithic European genome by the North Pontic population.

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