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Thread: Genetic Genealogy and Ancient DNA in the News

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    Neolithic spread to Europe
    IMG_1770.PNG

    Mesolithic and Early Neolithic sites in the Danube Gorges.
    IMG_1772.PNG

    Y DNA results from Vlasac samples
    IMG_1773.PNG

    https://publications.ub.uni-mainz.de.../100001355.pdf
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    Neolithic spread to Europe
    IMG_1770.PNG

    Mesolithic and Early Neolithic sites in the Danube Gorges.
    IMG_1772.PNG

    Y DNA results from Vlasac samples
    IMG_1773.PNG

    https://publications.ub.uni-mainz.de.../100001355.pdf


    Late Mesolithic lifeways and deathways at Vlasac (Serbia)

    IMG_1775.PNG

    https://www.academia.edu/5945829/Lat...Vlasac_Serbia_
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    Quote Originally Posted by Hando View Post
    Sorry but what does the fact that 7 iron gates samples are xR1b1a1a2 imply? That V88 has modern descendants? I don't know what the x in front of R1b1a1a2 means? He absence?
    The x in "xR1b1a1a2" can be read as "not". In other words, all of those samples were negative (ancestral) for M269.

    So, none of them was M269+, although M269 is supposed to be old enough that they could have been. The fact that two of them were R1b-V88 may say something about the rest, since we know none of them was M269+.
     


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    Saw this article mentioned on a tweet added to Razib Khan's Twitter feed from the SMBE conference in progress in Austin. Sorry if it repeats someone else's mention of it elsewhere.
    https://www.nytimes.com/2017/07/04/s...evolution.html

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    thank you is very interesting,here the link :

    https://www.nature.com/articles/ncomms16046

    Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

    "Abstract

    Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods."

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    http://journals.plos.org/plosone/art...l.pone.0180277

    Three individuals, three stories, three burials from medieval Trondheim, Norway

    Stian Suppersberger Hamre , Geir Atle Ersland, Valérie Daux, Walther Parson, Caroline Wilkinson

    PLOS
    Published: July 3, 2017
    https://doi.org/10.1371/journal.pone.0180277

    Abstract

    This article presents the life stories of three individuals who lived in Trondheim, Norway, during the 13th century. Based on skeletal examinations, facial reconstructions, genetic analyses, and stable oxygen isotope analyses, the birthplace, mobility, ancestry, pathology, and physical appearance of these people are presented. The stories are discussed within the relevant historical context. These three people would have been ordinary citizens, without any privileges out of the ordinary, which makes them quite rare in the academic literature. Through the study of individuals one gets a unique look into the Norwegian medieval society.

    Note: they only sequenced control region of mtDNA and some Y-STRs for male sample.

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    http://journals.plos.org/plosone/art...l.pone.0179742

    Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice

    Alice Beau , Maïté Rivollat , Hélène Réveillas, Marie-Hélène Pemonge, Fanny Mendisco, Yohann Thomas, Philippe Lefranc , Marie-France Deguilloux

    PLOS
    Published: July 5, 2017
    https://doi.org/10.1371/journal.pone.0179742

    Abstract

    In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in “non-conventional” positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

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    Quote Originally Posted by rozenfeld View Post
    http://journals.plos.org/plosone/art...l.pone.0179742

    Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice

    Alice Beau , Maïté Rivollat , Hélène Réveillas, Marie-Hélène Pemonge, Fanny Mendisco, Yohann Thomas, Philippe Lefranc , Marie-France Deguilloux

    PLOS
    Published: July 5, 2017
    https://doi.org/10.1371/journal.pone.0179742

    Abstract

    In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in “non-conventional” positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.
    At least they tried:

    Nevertheless, no Y chromosome SNP profile could be determined, questioning the conservation of nuclear DNA in the region. Consequently, the multi-scale analyses conducted stood on the maternal gene pool characterized for the Gougenheim group.
     


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    rs182549 TT (22018 AA)

    Red Hair Carrier:
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    Dad's mtDNA: K1a1

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    https://hms.harvard.edu/news/decoding-brain-evolution

    Decoding Brain Evolution

    New center asks: What genetic changes gave us the human brain?

    By NANCY FLIESLER
    July 6, 2017

    How did our distinctive brains evolve? What genetic changes, coupled with natural selection, gave us language? What allowed modern humans to form complex societies, pursue science, create art?

    While we have some understanding of the genes that differentiate us from other primates, that knowledge cannot fully explain human brain evolution. But with a $10 million grant to some of Boston’s most highly evolved minds in genetics, genomics, neuroscience and human evolution, some answers may emerge in the coming years.

    The Seattle-based Paul G. Allen Frontiers Group has announced the creation of an Allen Discovery Center for Human Brain Evolution at Boston Children’s Hospital and Harvard Medical School. It will be led by Christopher A. Walsh, the Bullard Professor of Pediatrics and Neurology at HMS and chief of the Division of Genetics and Genomics at Boston Children’s. Michael Greenberg, the Nathan Marsh Pusey Professor of Neurobiology and head of the Department of Neurobiology at HMS, and David Reich, professor of genetics at HMS, will co-lead the center.

    “Unraveling the mysteries of the human brain will propel our understanding of brain development, brain evolution and human behavior,” said George Q. Daley, dean of HMS. “It also will help us understand what makes us unique as a species.

    “The research conducted by these three remarkable scientists spans the gamut from molecule to organism to system and underscores the cross-pollination among basic, translational and clinical discovery as well as across neurobiology, genetics, evolutionary biology and neurology,” Daley said.

    The center’s agenda is a bold one: to catalogue the key genes required for human brain evolution, to analyze their roles in human behavior and cognition and to study their functions to discover evolutionary mechanisms.

    “To understand when and how our modern brains evolved, we need to take a multi-pronged approach that will reflect how evolution works in nature and identify how experience and environment affect the genes that gave rise to modern human behavior,” Walsh said.

    “The launch of this center is a wonderful opportunity for three laboratories that have been working independently to come together and study the genetic, molecular and evolutionary forces that have given rise to the spectacular capacities of the human brain,” said Greenberg.

    The funding “will allow us to use ancient DNA analysis to track changes in the frequency of genetic mutations over time, which will in turn illuminate our understanding of the nature of human adaptation,” added Reich.

    An evolving understanding

    We already know some basics of human brain evolution. First came the enlargement of the primate brain, culminating perhaps 2 million years ago with the emergence of our genus, Homo, and the use of crude stone tools and fire. Next came a tripling of brain size during the 500,000 years before Homo sapiens arose. Finally, just over 50,000 years ago, there was a great leap forward in human behavior, with archaeological evidence of more efficient manufacturing of stone tools and a rich aesthetic and spiritual life.

    What transpired genetically? Prior research has taken a piecemeal approach to occasional genes that have different structures in humans versus non-humans. For example, Walsh’s lab has identified several genes that regulate cerebral cortical size and patterning, some of them through the study of brain abnormalities. The lab recently found a gene involved in brain folding—thanks to a brain malformation called polymicrogyria—that may have enhanced our language ability.

    But such findings only scratch the surface of the cognitive, behavioral and cultural strides humans have made over the past 50,000 years. That’s a blink of the eye in evolutionary terms. What enabled us to invent money, develop agriculture, build factories, write symphonies, tell jokes?

    Rosetta Stone(s) to decode brain evolution

    The researchers think not one but multiple mechanisms of evolution helped form the modern human brain. Such mechanisms include:

    Gene addition, duplication or deletion
    Alteration in the protein-coding sequence of genes to create new or modified biochemical functions
    Changes in noncoding DNA sequences altering patterns of gene expression, allowing an existing gene to be “re-purposed”
    Polygenic changes (changes in many genes working together)

    Accordingly, the center’s research methods will include, in varying combinations:

    Sequencing of ancient DNA recovered from bones and teeth
    Genomic studies of large populations to identify regions that correlate with human traits

    Genetic studies to test functional effects of mutations in the evolutionarily important genomic sequences
    Functional studies in neurons to determine the roles of these evolutionarily important sequences in the brain

    No genetic stone unturned

    All these approaches will be supported by powerful computational data analysis—reaching across genomes, across populations, across hundreds of thousands of years.

    The project leaders summed it up: “This group will provide the most rigorous possible examination of how, when and where the unique features of the amazing human brain came about.”

    The $10 million grant will be distributed over four years, with the potential for $30 million over eight years.

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    http://www.sciencemag.org/news/2017/...s-swept-across

    First big efforts to sequence ancient African DNA reveal how early humans swept across the continent

    By Elizabeth PennisiJul. 6, 2017 , 12:45 PM

    Review article about two recent works on aDNA from Africa, however both are unpublished: one was posted on biorxiv, another was announced at SMBE17.

    Also: "Early Europeans and Asians have had portions of their genomes sequenced by the hundreds over the past decade, rewriting Eurasian history in the process. " - really? Where I can see hundreds of ancient genomes from Asia?

    UPD: the article about the same in Nature:
    http://www.nature.com/news/ancient-g...s&sf95854851=1
    Last edited by rozenfeld; 07-06-2017 at 08:39 PM.

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