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

  1. #3751
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    Kyrgyzstan
    https://www.sciencedirect.com/scienc...511?via%3Dihub

    Available online 18 May 2023

    In Press, Corrected Proof

    Historical genomes elucidate European settlement and the African diaspora in Delaware

    Raquel E. Fleskes, 1,2,7,9,* Douglas W. Owsley, 3,* Karin S. Bruwelheide, 3 Kathryn G. Barca,3 Daniel R. Griffith, 4
    Graciela S. Cabana, 5,6 and Theodore G. Schurr 2

    Received 16 September 2022, Revised 1 February 2023, Accepted 24 April 2023, Available online 18 May 2023.

    https://doi.org/10.1016/j.cub.2023.04.069

    Highlights

    • Genomic data indicate eight individuals of European and three of African ancestry
    • Individuals were interred in separate burial groupings based on genomic ancestry
    • Paternally related parent and child of African descent were identified
    • Maternally related grandparent, parent, and child of European descent were found

    Summary

    The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery’s Rest archaeological site (circa 1675–1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15–20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America.

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  3. #3752
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    Rivollat et al, Neolithic kinship at Gurgy, France

    Extensive pedigrees reveal the social organisation of a Neolithic community

    Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations. However, for prehistoric societies these systems can only be studied indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local vs. non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which allows for the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here, we report ancient DNA, strontium isotope and contextual data from >100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic ~4850-4500 BCE. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, which were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The micro-demographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and high number of adult full siblings suggest stable health conditions and a supportive social network, facilitating high fertility and low mortality. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.

    Data is available:

    https://www.ebi.ac.uk/ena/browser/view/PRJEB61818

    So it is this paper finally.

    https://submissions.e-a-a.org/eaa202...?Abstract=3000

    Started a thread:

    https://anthrogenica.com/showthread....rance&p=931896
    Last edited by teepean47; 05-22-2023 at 07:38 PM.

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  5. #3753
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    Ancient Human Mitochondrial Genome of the Beagle Channel (Tierra Del Fuego, Argentina

    Abstract

    The increasing use of massively parallel sequencing in the study of current and ancient human populations has enabled new approaches to bioanthropological and archaeological issues, although its application on archaeological samples requires the use of technologies that are not easily accessible outside of USA and European research centers. In order to obtain an ancient mitogenome in Argentina, several institutions collaborated to apply massively parallel sequencing and bioinformatic methodologies on an enriched aDNA library of an individual from the Beagle Channel (dated 1,504 ± 46 years BP), a region of particular interest for this line of inquiry. The mitogenome was obtained with an average depth of 8X and its haplotype was assigned to haplogroup D1g. Phylogenetic reconstruction showed a close relationship with a Yámana from Navarino Island and an individual from Hoste Island (Chilean Antarctic Province), the three sharing an ancestor 203-4,439 years ago. These have mutations reported only for current and ancient individuals from the Beagle Channel, and their relationship with the rest of the D1g subhaplogroups is unclear. The results obtained here are consistent with the reduction of mobility in the Fuegian archipelago around ~4,500 years BP that has been proposed based on archaeological evidence.

    Data is available:

    https://www.ebi.ac.uk/ena/browser/view/PRJEB58193

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  7. #3754
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    Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe

    Abstract

    The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show the same patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We also found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4,000 years, from the Mesolithic to the end of Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.

    Data is available:

    https://www.ebi.ac.uk/ena/browser/view/PRJEB59598

    EDIT: Looks like this one is still at preprint stage.

    https://www.researchsquare.com/article/rs-1966812/v1

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    Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights in

    Abstract

    Thailand is a country where over 60 languages from five language families (Austroasiatic, Austronesian, Hmong-Mien, Kra-Dai, and Sino-Tibetan) are spoken. The Kra-Dai language family is the most prevalent, and Thai, the official language of the country, belongs to it. Previous genome-wide studies on Thailand populations revealed a complex population structure and put some hypotheses forward concerning the population history of the country. However, many published populations have not been co-analyzed, and some aspects of population history were not explored adequately. In this study, we employ new methods to re-analyze published genome-wide genetic data on Thailand populations, with a focus on 14 Kra-Dai-speaking groups. Our analyses reveal South Asian ancestry in Kra-Dai-speaking Lao Isan and Khonmueang, and in Austroasiatic-speaking Palaung, in contrast to a previous study in which the data were generated. We support the admixture scenario for the formation of Kra-Dai-speaking groups from Thailand who harbor both Austroasiatic-related ancestry and Kra-Dai-related ancestry from outside of Thailand. We also provide evidence of bidirectional admixture between Southern Thai and Nayu, an Austronesian-speaking group from Southern Thailand. Challenging some previously reported genetic analyses, we reveal a close genetic relationship between Nayu and Austronesian-speaking groups from Island Southeast Asia (ISEA).

    https://www.nature.com/articles/s41598-023-35507-8

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  11. #3756
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    On the genes, genealogies, and geographies of Quebec

    SCIENCE
    VOL. 380, NO. 6647
    25 May 2023
    pp. 849-855
    DOI: 10.1126/science.add5300
    Abstract

    Population genetic models only provide coarse representations of real-world ancestry. We used a pedigree compiled from 4 million parish records and genotype data from 2276 French and 20,451 French Canadian individuals to finely model and trace French Canadian ancestry through space and time. The loss of ancestral French population structure and the appearance of spatial and regional structure highlights a wide range of population expansion models. Geographic features shaped migrations, and we find enrichments for migration, genetic, and genealogical relatedness patterns within river networks across regions of Quebec. Finally, we provide a freely accessible simulated whole-genome sequence dataset with spatiotemporal metadata for 1,426,749 individuals reflecting intricate French Canadian population structure. Such realistic population-scale simulations provide opportunities to investigate population genetics at an unprecedented resolution.
    https://www.science.org/doi/10.1126/science.add5300
    Sample: Kapisa ► Kapisa scaled
    Fit: 2.290209772
    Results: Ganj Dareh N 45.2
    CG CentralSteppeMLBA 21.8
    Simulated AASI NW by DMXX 19.2
    Marmara Barcin N 6
    TTK Neolithic 5.8
    Chokhopani 2700BP 2

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  13. #3757
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    https://www.mdpi.com/2313-5778/7/2/28

    Genetics Unveil the Genealogical Ancestry and Physical Appearance of an Unknown Historical Figure: Lady Leonor of Castile (Spain) (1256–1275)


    by Sara Palomo-Díez
    1,2,* [ORCID] , Cláudia Gomes
    1,2 [ORCID] , María Sonia Fondevila
    3, Ángel Esparza-Arroyo
    4, Ana María López-Parra
    1,2 [ORCID] , María Victoria Lareu
    3, Eduardo Arroyo-Pardo
    1,2 [ORCID] and Juan Francisco Pastor
    5 [ORCID]
    1
    Health Legislation, Psychiatry, and Pathology Department, Medicine Faculty, The Complutense University of Madrid, 28040 Madrid, Spain
    2
    Forensic Sciences Group, Genetics and Toxicology, San Carlos Research Institute (IdISSC), Clínico San Carlos Hospital, 28040 Madrid, Spain
    3
    Medicine and Odontology Faculty, Santiago de Compostela University, 15705 Santiago de Compostela, Spain
    4
    GIR ‘PrehUSAL’, Department of Prehistory, Ancient History and Archaeology, University of Salamanca, 37007 Salamanca, Spain
    5
    Anatomy and Embriology Department, Medicine Faculty, Valladolid University, 47003 Valladolid, Spain
    *
    Author to whom correspondence should be addressed.
    Genealogy 2023, 7(2), 28; https://doi.org/10.3390/genealogy7020028
    Received: 2 March 2023 / Revised: 15 April 2023 / Accepted: 18 April 2023 / Published: 20 April 2023
    (This article belongs to the Special Issue Family Identities: How Genetics Is Contributing to Genealogical (Re)search)
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    Abstract
    Through this study, it has been possible to establish an accurate prediction of the physical characteristics, biogeographical origin, and genealogical ancestry of a previously obscured historical figure: The Princess Lady Leonor of Castile (1256–1275), one of the legitimate daughters of the Spanish King Alfonso X “The Wise”. The genetic analysis of External Visible Characteristics in the mummified remains attributed to this Princess has allowed determining her origin by mitochondrial and nuclear DNA analysis, and her physical appearance for hair, eyes, and skin color by autosomal SNPs. The results show that the mummified remains correspond to a young European woman with black hair, green-hazel eyes, and white skin. Her physical appearance has not been possible to be compared with any pictorial source, but the biogeographical analysis results are consistent with the historiographic genealogical information.
    Keywords:
    ancient DNA; biogeographical origin; mitochondrial DNA (mtDNA); Alfonso X of Castile “The Wise”; external visible characteristics (EVCs); History of Spanish royalty; genealogy

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  15. #3758
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    The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa
    https://www.pnas.org/doi/10.1073/pna...b%20%200pubmed
    Abstract:
    The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
    We analyze the functional and spatiotemporal properties of 57 hard sweeps inferred in ancient human genomes to reconstruct human evolution during the poorly understood Out of Africa migration. Our analyses reveal a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in Arabia or surrounding regions, prior to a rapid dispersal across the rest of Eurasia as far as Australia. Functional targets include multiple interacting loci involved in fat storage, neural development, skin physiology, and cilia function, with associations with multiple modern Western diseases. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, indicating that cold environments were a prominent historical selection pressure that potentially facilitated the successful peopling of Eurasia.

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    https://www.nature.com/articles/s41467-023-38393-w

    Yersinia pestis genomes reveal plague in Britain 4000 years ago

    Pooja Swali, Rick Schulting, Alexandre Gilardet, Monica Kelly, Kyriaki Anastasiadou, Isabelle Glocke, Jesse McCabe, Mia Williams, Tony Audsley, Louise Loe, Teresa Fernández-Crespo, Javier Ordoño, David Walker, Tom Clare, Geoff Cook, Ian Hodkinson, Mark Simpson, Stephen Read, Tom Davy, Marina Silva, Mateja Hajdinjak, Anders Bergström, Thomas Booth & Pontus Skoglund

    Nature Communications volume 14, Article number: 2930 (2023)

    Abstract

    Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Eurasia between 5000 and 2500 years before present (BP). One of these, termed the ‘LNBA lineage’ (Late Neolithic and Bronze Age), has been suggested to have spread into Europe with human groups expanding from the Eurasian steppe. Here, we show that the LNBA plague was spread to Europe’s northwestern periphery by sequencing three Yersinia pestis genomes from Britain, all dating to ~4000 cal BP. Two individuals were from an unusual mass burial context in Charterhouse Warren, Somerset, and one individual was from a single burial under a ring cairn monument in Levens, Cumbria. To our knowledge, this represents the earliest evidence of LNBA plague in Britain documented to date. All three British Yersinia pestis genomes belong to a sublineage previously observed in Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Eastern Asia ~3200 cal BP. While the severity of the disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.

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  19. #3760
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    A weakly structured stem for human origins in Africa

    Abstract:
    Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2,3,4,5,6,7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1–4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.
    This paper produces some interesting results. It proposes that Humans actually descend from two ancestral lineages of the genus Homo which split apart 1 Million years ago, which explains some of the variation in modern humans. Correspondingly, they move the date of Human diversification closer to the present, positing that the Khoe-San split off only around 120K years ago rather than 250K

    Screenshot_2023-06-03_204221_1_50.jpg

    Stem populations merge with varying proportions to form the different contemporary groups. We observe a sharp bottleneck in stem 1 down to Ne = 100 after the split of the Neanderthal branch. This represents the lower bound allowed in our optimization (an Ne of 100), although the size of this bottleneck is poorly constrained (95% confidence interval 100–851). After a long period of exchange with stem 2, stem 1 then fractures into stem 1E and stem 1S at 478 ka. The timing of this divergence was also poorly constrained (95% confidence interval 276– 478 ka). These populations evolve independently until 119 ka (101−125 ka) when stem 1S and stem 2 combine to form the ancestors of the Nama, with proportions of 30% and 70%, respectively. Similarly, stem 1E and stem 2 combine in equal proportions (50% each) to form the ancestors of the western and eastern Africans (and thus also all individuals who later disperse during the out-of-Africa event). Finally, the Mende receive a large additional pulse of gene flow from stem 2, replacing 19% (18–21%) of their population 25 ka (22−26 ka). The later stem 2 contribution to the western African Mende resulted in better model fits (∆LL ≈ 60,000). This may indicate that an ancestral stem 2 population occupied western or central Africa, broadly speaking. The differing proportions in the Nama and eastern Africans may also indicate a geographical separation of stem 1S in southern Africa and stem 1E in eastern Africa.

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