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

  1. #2981
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    More from the EAA Virtual Abstract book posted by blackflash:

    LATE BRONZE AGE KUCKENBURG: A UNIQUE WINDOW INTO THE URNFIELD CULTURE IN CENTRAL EUROPE
    Abstract author(s): Orfanou, Eleftheria - Himmel, Marie (Max Planck Institute for the Science of Human History, Department of Archaeogenetics) - Paust, Enrico (Institut für Ur- und Frühgeschichte, Friedrich-Schiller-Universität Jena) - Roberts, Patrick - Zach, Barbara - Spengler, Robert (Max Planck Institute for the Science of Human History, Department of Archaeology) - Ettel, Peter (Institut für Ur- und Frühgeschichte, Friedrich-Schiller-Universität Jena) - Haak, Wolfgang (Max Planck Institute for the Science of Human History, Department of Archaeogenetics)
    The coexistence of different mortuary practices within a given site offers the possibility of studying the intersection of demograph-ic, social, and cultural variability. This study focuses on the Late Bronze Age (LBA) site of Kuckenburg located in Central Germany. The site is unique because it has both inhumations and cremations ascribed to the Urnfield period, a time period when cremations were, elsewhere, usually the main form of mortuary practice. It has also been continuously occupied from the Late Paleolithic until the Early Middle Ages, enabling comparison of inhumations from different time periods.We apply a multidisciplinary approach, including ancient DNA, stable isotope analysis, osteoarchaeology, and material culture analy-sis to get a better understanding of the Urnfield related groups in the LBA of Central Europe. Ancient DNA analyses shed new light on the different mortuary practices, including the relationship of kinship and population affinity to burial location.Analysis of genome-wide data from 18 inhumated individuals show that these individuals share the same genetic profile with indi-viduals of the preceding periods of Early Bronze Age (EBA), indicating genetic continuity over time. Meanwhile, stable carbon and nitrogen isotope analysis suggest a similarity of diet to this earlier period, with some subtle variation. We are also able to determine that three out of 18 individuals are first-degree relations: a mother with two daughters. This triple burial, like most burials at Kuckenburg, points to a multi-phase burial rite. Overall, our findings indicate that different mortuary practices at Kuckenburg were not the result of a new genetic group coming in but rather increasing cultural variation within a local population. Our study shows that combination of multiple lines of evidence, such as ancient DNA, archaeology, and isotope studies, is necessary if our aim is to reconstruct a more complete picture of the past.

    UNIPARENTAL GENETIC DATA EXPAND THE ARCHAEOLOGICAL AND HISTORICAL KNOWLEDGE OF THE AVAR ELITE POPULATION
    Abstract author(s): Csáky, Veronika (Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences Centre of Excellence) - Gerber, Dániel - Szeifert, Bea (Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences Centre of Excellence; Department of Genetics, ELTE Eötvös Loránd University) - Koncz, István (Institute of Archaeological Sciences, ELTE Eötvös Loránd University) - Mende, Balázs - Csiky, Gergely (Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences Centre of Excellence) - Jeong, Choongwon (Department of Archaeogenetics, Max Planck Institute for the Science of Human History; School of Biological Sciences, Seoul National Universi-ty) - Krause, Johannes (Department of Archaeogenetics, Max Planck Institute for the Science of Human History) - Vida, Tivadar (Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences Centre of Excellence; Institute of Archaeological Sciences, ELTE Eötvös Loránd University) - Szécsényi-Nagy, Anna (Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences Centre of Excellence)
    The Avars arrived in the Carpathian Basin in 568 AD and founded their empire (Avar Qaganate) which played an important geopolitical role in Central European history. The Asian origin of Avars is supported by written sources as well as archaeological findings, howev-er, localisation of their homeland is still questionable and controversial. With our study, we try to answer the research questions of
    102103archaeologists and historians regarding to the social organization and origin of Avar elite stratum.We investigated genetic variability of twenty-six individuals belonging to the high-ranking Avar elite group excavated from ten dif-ferent cemeteries at the centre of the Carpathian Basin more than a century after the Avar conquest. Seven out of ten are located in the Danube-Tisza Interfluve, probably in the primarily power centre, where also the eight members of the highest elite Avar group were found.The maternal genetic data of the studied Avar group is heterogenous compared to the paternal gene pool, which is mostly composed of N1a1 M46 haplotypes detected uniquely in the Danube-Tisza Interfluve. The mitochondrial lineages belong to a wide range of Eurasian haplogroups with dominance of Asian haplotypes.We determined paternal kinship of four and nine individuals buried inside and between cemeteries belonged mostly to the “Kun-bábony group”. Furthermore, we found some maternal kinship based on identical mitochondrial haplotypes between six individuals. Based on population genetic and phylogenetic analyses the results suggest East-Central Asian origin of Avar period elite society (i.e. Southern Siberia and Mongolia), which is supported also by nuclear genomic data and some of archaeological findings. Moreover, we assume, that the Avars migrated rather as closed society with endogamous group of families than military corps, because the Asian maternal and paternal genetic composition of the Avar elite was preserved through several generations after the Avar conquest in the Carpathian Basin.

    THE ANGLO-SAXON MIGRATION AND FORMATION OF THE EARLY ENGLISH GENE POOL
    Abstract author(s): Gretzinger, Joscha (Max Planck Institute for the Science of Human History) - Altena, Eveline (Leiden Uni-versity Medical Center, University of Leiden) - Papac, Luka (Max Planck Institute for the Science of Human History) - Krause, Johannes (Max Planck Institute for the Science of Human History; Faculty of Biosciences, University of Jena) - Sayer, Duncan (School of Forensic and Applied Sciences, University of Central Lancashire) - Schiffels, Stephan (Max Planck Institute for the Science of Human History)
    A series of migrations and accompanied cultural changes has formed the peoples of Britain and still represents the foundations of the English national identity. For the most prominent of these, the Anglo-Saxon migration, the traditional view, resting upon historical sources and derived concepts of ethnic and national origins from the 19th century, outlined that the indigenous Romanised British population was forcibly replaced by invading Germanic tribes, starting in the 5th century AD. However, to which extent this historic event coincided with factual immigration that affected the genetic composition of the British population was focus of generations of scientific and social controversy. To better understand this key period, we have so far generated genome-wide sequences from 80 individuals from eight cemeteries in East and South England. We combined this data with previously published genome-wide data to a total dataset of more than 200 ancient British genomes spanning from the Early Bronze Age to the Early Middle Ages, allowing us to investigate shifts and affinities in British fine-scale population structure during this phase of transformation. Here we present two preliminary results: First, we detect a substantial increase in continental Northern European ancestry akin to the extant Danish and Northern German populations during the Early Anglo-Saxon period, replacing approximately 80% of the indigenous British ancestry during that time period. Second, we nevertheless highlight the continuous presence of ancestry identified in Pre-Saxon Iron Age and Roman individuals during the Early and Middle Anglo-Saxon period, originating in the Early British Bronze Age and closely resembling present-day Celtic-speaking populations from Ireland and Scotland. Therefore, our study suggests that the early English population was the outcome of long-term ethnogenetic processes in which the acculturation and assimilation of native Britons into the immigrating Anglo-Saxon society played a key role.
    Ελευθερία ή θάνατος.

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  3. #2982
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    Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

    Abstract

    During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods.

    https://genomebiology.biomedcentral....59-020-02160-7

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  5. #2983
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    The evolutionary history of Neanderthal and Denisovan Y chromosomes

    Abstract

    Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

    https://science.sciencemag.org/content/369/6511/1653

    Supplementary:

    https://science.sciencemag.org/conte....6511.1653.DC1
    Last edited by teepean47; 09-24-2020 at 06:13 PM.

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  7. #2984
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    Oriente B from Sicily is not of mitochondrial haplogroup HV1 but U2′3′4′7′8′9:
    AlessandraModi et al. : Paleogenetic and morphometric analysis of a Mesolithic individual from Grotta d’Oriente: An oldest genetic legacy for the first modern humans in Sicily
    Abstract:
    Grotta d’Oriente, a coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. Inside the cave, during different field excavations, three burials attributable to the Late Upper Palaeolithic and Mesolithic were found. The Mesolithic Oriente B individual, directly dated at 9,377 ± 25 uncal BP, was previously assigned to HV1 haplogroup using a traditional approach. However, it is well known that PCR based methods are prone to erroneous haplotype or haplogroup determination. In order to redefine the mitochondrial lineage of this Mesolithic hunter-gatherer and explore its phylogenetic position, we target-enriched and sequenced the complete mitochondrial genome of Oriente B. Moreover, we conducted a morphometric analysis to assess its phenetic affinities.

    Oriente B individual was classified into U2′3′4′7′8′9 haplogroup. In Sicily, this lineage has also been found on the Upper Palaeolithic Oriente C and Early Mesolithic individuals from Grotta dell’Uzzo. Our results show significant genetic and morphological similarities in Sicilian Early Mesolithic hunter-gatherers, presumably because of genetic drift processes. Furthermore, dating the emergence of the “Sicilian clade”, we speculate that Epigravettian hunter-gatherers carrying U2′3′4′7′8′9 haplogroup might be the first settlers of Sicily arrived from the Italian peninsula by the crossing of a temporary land-bridge around the Last Glacial Maximum.

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  9. #2985
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    Quote Originally Posted by Bernard View Post
    Oriente B from Sicily is not of mitochondrial haplogroup HV1 but U2′3′4′7′8′9:
    AlessandraModi et al. : Paleogenetic and morphometric analysis of a Mesolithic individual from Grotta d’Oriente: An oldest genetic legacy for the first modern humans in Sicily
    Abstract:
    Very good to see that this was done partly by the co-authors that actually made the original paper.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509116/
    Last edited by epoch; 09-30-2020 at 04:02 PM.

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  11. #2986
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    Investigating the demographic history of Japan using ancient oral microbiota

    Abstract
    While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.

    https://royalsocietypublishing.org/d...rstb.2019.0578

    Note: the data should have human aDNA but I could not access the paper.

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  13. #2987
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    Looks like there are several potential aDNA studies in the current issue of Philosophical Transactions of the Royal Society B: Biological Sciences

    https://royalsocietypublishing.org/t.../2020/375/1812

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    Ancestry, health, and lived experiences of enslaved Africans in 18th century Charleston: An osteobiographical analysis

    Abstract

    Objectives
    In 2013, the burials of 36 individuals of putative African ancestry were discovered during renovation of the Gaillard Center in downtown Charleston, South Carolina. The Charleston community facilitated a bioarchaeological and mitogenomic study to gain insights into the lives of these unknown persons, referred to as the Anson Street Ancestors, including their ancestry, health, and lived experiences in the 18th century.

    Methods
    Metric and morphological assessments of skeletal and dental characteristics were recorded, and enamel and cortical bone strontium stable isotope values generated. Whole mitochondrial genomes were sequenced and analyzed.

    Results
    Osteological analysis identified adults, both females and males, and subadults at the site, and estimated African ancestry for most individuals. Skeletal trauma and pathology were infrequent, but many individuals exhibited dental decay and abscesses. Strontium isotope data suggested these individuals mostly originated in Charleston or sub‐Saharan Africa, with many being long‐term residents of Charleston. Nearly all had mitochondrial lineages belonging to African haplogroups (L0‐L3, H1cb1a), with two individuals sharing the same L3e2a haplotype, while one had a Native American A2 mtDNA.

    Discussion
    This study generated detailed osteobiographies of the Anson Street Ancestors, who were likely of enslaved status. Our results indicate that the Ancestors have diverse maternal African ancestries and are largely unrelated, with most being born locally. These details reveal the demographic impact of the trans‐Atlantic slave trade. Our analysis further illuminates the lived experiences of individuals buried at Anson Street, and expands our understanding of 18th century African history in Charleston.

    https://onlinelibrary.wiley.com/doi/...002/ajpa.24149

    The samples from this project:

    https://www.ncbi.nlm.nih.gov/biosamp...rom_uid=658314
    Last edited by teepean47; 10-07-2020 at 12:30 PM.

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    Brunel's thesis is at least available: http://theses.md.univ-paris-diderot....d_20181114.pdf



    Paleogenomics of human population dynamics on the French territory between 7000 and 2000 before present
    edit: Why did I write "at least", and not "finally"? Do not ask me, it is a curious slip, perhaps revealing of the little that I expect from this text.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  19. #2990
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    Paleogenetic evidence of a Pyrenean Neolithic family: Kinship, physical appearance and biogeography multidisciplinary analysis

    Abstract

    One of the most important Neolithic necropolises in the north-east of the Iberian Peninsula is La Feixa del Moro (3975-3790 cal. BC), located at 1335 mamsl in the Pyrenees (Juberri, Sant Julia de Lňria, Andorra). Within the scarcity of multiple simultaneous Neolithic burials, the main importance of La Feixa del Moro lies in the fact that it is one of the very few cases to suggest a biological family burial, comprising two adults and a newborn baby.

    Accordingly, the purpose of the present work was the multidisciplinary interpretation of the necropolis in the Neolithic context of the Pyrenees, on a potential route between the Iberian Peninsula and Europe. Therefore, kinship and biogeographic analyses were performed, as well as external visible characteristics phenotyping.

    Our results suggest the possibility of a traditional nuclear family, pointing to a very probable relation between the newborn and both adults. First, two mitochondrial haplotypes and two lineages were determined: H1, for the presumable mother and newborn, and U5, for the presumed father. Second, regarding their physical appearance, they all had brown eyes, the adult female and the neonate had dark brown hair, while the adult male's hair was dark red-brown. Finally, it was possible to confirm the sex of two of the individuals, as the newborn baby gender was also confirmed by the High Troughoutput Sequencing analysis.

    The multidisciplinary analysis of the La Feixa del Moro burial place envisions a very probable familial burial. Not only does the genetic evidence point to biological kinship, but also the archaeological record indicates a habitational area surrounding the burial site. The similar artefacts and the care shown during the funerary ritual suggest a probable biological Neolithic family.


    https://www.sciencedirect.com/scienc...cid=rss_sd_all


    Individual 1 haplogroup U5b frequency on AmtDB, considering the Neolithic period, in Europe: 26 /337 (searched on 14th May 2020)

    Individual 2 and 3 haplogroup H1 frequency on AmtDB, considering the Neolithic period, in Europe: 18/337 (searched on 14th May 2020)


    Capture.PNG
    Last edited by teepean47; 10-09-2020 at 12:48 PM.

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