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

  1. #3211
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    https://www.ebi.ac.uk/ena/browser/view/PRJEB42866

    The origin and legacy of the Etruscans through a 2,000-year archeogenomic time transect

    Max Planck Institute for the Science of Human History

    The origin, development and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria has been the subject of scholarly debate for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE – 1,000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European-associated steppe ancestry and the lack of recent Anatolian admixture among the putative non-Indo-European-speaking Etruscans. Despite comprising diverse individuals of central European, northern African and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This continuity drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Finally, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

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  3. #3212
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    Quote Originally Posted by Genarh View Post
    Researchers find Highland East Asian origin for prehistoric Himalayan populations
    http://phys.org/news/2016-06-highlan...himalayan.html
    ...Warinner and colleagues sequenced the nuclear and mitochondrial genomes of eight high-altitude Himalayan individuals dating to three distinct cultural periods spanning 3150 to 1250 years before present. The authors compared these ancient DNA sequences to genetic data from diverse modern humans, including four Sherpa and two Tibetans from Nepal.

    All eight prehistoric individuals across the three time periods were most closely related to contemporary highland East Asian populations, i.e., the Sherpa and Tibetans, strengthening evidence that the diverse material culture of prehistoric Himalayan populations is the result of acculturation or culture diffusion rather than large-scale gene flow or population replacement from outside highland East Asia.

    Even more revealing, both prehistoric individuals and contemporary Tibetan populations shared beneficial mutations in two genes, EGLN1 and EPAS1, which are implicated in adaptation to low-oxygen conditions found at high altitudes, but EGLN1 adaptations were observed earlier.

    Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc
    http://www.pnas.org/content/113/27/7485.full
    Mitochondrial and Y Chromosome Haplogroup Identification. Using high-coverage, consensus full mtDNA genome sequences (SI Appendix, Table S1), we next inferred haplogroup assignment for each ACA individual. All eight individuals are assigned to haplogroups reported to be present in contemporary Nepalis and/or Tibetans (SI Appendix, Table S3) (21, 40) and rare or absent in present-day Indian and Pakistani populations (41). The oldest sample in our study, C1, belongs to haplogroup D4, a major maternal lineage among Tibetans. Interestingly, Tibetan D4 has a deep divergence time from other East Asian populations (26–27 kya), further supporting genetic affinity between the ACA individuals and contemporary high-altitude East Asians (21). Four male individuals with >2× coverage were determined to belong to Y chromosome haplogroups O-M117 and D (SI Appendix, Table S4), which are among the most frequent haplogroups in contemporary Tibetans (21) based on haplogroup-tagging SNPs from the cleantree program (42).
    Quote Originally Posted by parasar View Post
    Posted by Dienekes at his blog:
    Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
    Huerta-Sánchez et. al.

    http://www.nature.com/nature/journal...ture13408.html
    https://www.pnas.org/content/118/22/e2020803118
    "The discovery of the archaic Denisovan hominins is one of the most significant findings in human evolutionary biology in the last decade. However, as of today, we have more questions than answers regarding this mysterious hominin group. This study leverages the information from the well-known example of adaptive introgression on the EPAS1 gene in Tibetans, to gain insight on the history of our species’ interaction with Denisovans. We show that the Tibetan-EPAS1 haplotype came from the East Asian-specific Denisovan introgression event, and it remained selectively neutral for a long time in the population before positive selection occurred, which may be concurrent with the permanent inhabitation of the Tibetan Plateau after the Last Glacial Maximum (LGM) ...

    The Denisovan Introgression Introducing the Tibetan EPAS1 Haplotype Occurred More than 48,000 y Ago.
    "

    Last edited by parasar; 06-04-2021 at 05:52 PM.

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  5. #3213
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    The earliest herders of East Asia: Examining Afanasievo entry to Central Mongolia

    William Honeychurch, Leland Rogers, Chunag Amartuvshin, Erdenebaatar Diimaajav, Nasan-OchirErdene-Ochir, Mark E.Hall, Michelle Hrivnyak

    https://doi.org/10.1016/j.ara.2021.100264

    Abstract

    The Afanasievo world reportedly overlaps the borders of five nations including two countries of East Asia: Mongolia and China. Across these several regions, the first appearance of domestic herd animals (sheep, goat, cattle) and the initial practice of copper and bronze metallurgy are associated with Afanasievo communities. Since mobile pastoralism has long been a significant part of the Mongolian cultural tradition the question of when, where, and how Afanasievo groups entered Mongolia is of extreme interest to archaeologists. Over the past 50 years several important sites have been reported and analyzed but these are still little known among Western scholars. In this study we provide a brief overview of Afanasievo archaeology, its peripheries, and its recent analytical breakthroughs and then develop a unique perspective on the Afanasievo world from its farthest eastern edge in central Mongolia. We assess the different roles of migration and diffusion in the process of herd animal introduction and present two current hypotheses explaining the intensification of pastoralism in this region during the late 3rd and early 2nd millennium BC. We argue that the impact of Afanasievo entry into East Asia was a transformative process but must be understood in the context of significant innovations made by East Asian indigenous communities, eventually leading to a unique form of eastern steppe pastoralism in Mongolia.

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  7. #3214
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    Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes

    Summary

    The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic, mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings, household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük, and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.

    https://www.sciencedirect.com/scienc...60982221004231

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  9. #3215
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    https://www.preprints.org/manuscript/202106.0124/v1

    Through 40.000 years of human presence in Southern Europe: the Italian case study

    Serena Aneli1*, Matteo Caldon1, Tina Saupe2, Francesco Montinaro2,3, Luca Pagani1,2
    1 Department of Biology, University of Padova, Padova, Italy 2 Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia 3 Department of Biology, Aldo Moro University of Bari, Bari, Italy
    *corresponding author. Email: [email protected]


    Abstract

    The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area has been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) repeopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern i) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; ii) the role of Sicily and Sardinia before LGM; iii) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; iv) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
    Last edited by etrusco; 06-09-2021 at 10:52 PM.

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  11. #3216
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    Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 )

    Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 CE) indicates the first known case of late-onset Pompe disease
    @article {Iadarola2021.06.08.21258201,
    author = {Iadarola, Barbara and Lavezzari, Denise and Modi, Alessandra and Degli Esposti, Chiara and Beltrami, Cristina and Rossato, Marzia and Zaro, Valentina and Napione, Ettore and Latella, Leonardo and Lari, Martina and Caramelli, David and Salviati, Alessandro and Delledonne, Massimo},
    title = {Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 CE) indicates the first known case of late-onset Pompe disease},
    elocation-id = {2021.06.08.21258201},
    year = {2021},
    doi = {10.1101/2021.06.08.21258201},
    publisher = {Cold Spring Harbor Laboratory Press},
    abstract = {Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard "clinical exome analysis" conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder.

    The WES variants data are available for download from our public repository using the provided link (VCF file with associated BED files of callable regions).http://ddlab.sci.univr.it/files/Cangrande/Cangrande.tar.gz},
    URL = {https://www.medrxiv.org/content/early/2021/06/09/2021.06.08.21258201},
    eprint = {https://www.medrxiv.org/content/early/2021/06/09/2021.06.08.21258201.full.pdf},
    journal = {medRxiv}
    }
    Last edited by pmokeefe; 06-10-2021 at 05:27 AM.
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  13. #3217
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    Significant admixture with a ancient Wusun observed in contemporary Bulgarians

    Significant (Z|−4|) admixture signal with a source from ancient Wusun observed in contemporary Bulgarians
    Svetoslav Stamov
    Abstract
    We report the presence of significant Central Asian ancestry in both contemporary Bulgarians and in early medieval population from SMC (Saltovo Mayaky Culture).

    The existence of Chalcolithic-Iran (Hajj-Fruz) and Wusun related ancestral component in contemporary Bulgarians comes as a surprise and sheds light on both migration route and ethnic origins of Proto-Bulgarians. We interpret these results as an evidence for a Central –Asian connection for the tribes, constituting the population of SMC and Kubrat’s Old Great Bulgaria in Pontic steppe from 6th-7th century AD.

    We identify Central Asian Wusun tribes as carriers of this component on the base from the results from f3 and f4 statistics. We suggest that Wusun-related tribes must have played role (or might have even been the backbone) in what became known as the Hunnic migration to Europe during 3rd-5th century AD. Same population must have taken part in the formation of the SMC (Saltovo-Mayaki Culture) and Great Old Bulgarian during 6th-9th century AD in Pontic – Caspian steppe.

    We also explore the genomic origins of Thracians and their relations to contemporary Europeans. We conclude that contemporary Bulgarians do not harbor Thracian-specific ancestry, since ancient Thracian samples share more SNPs with contemporary Greeks and even contemporary Icelanders than with contemporary Bulgarians.
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  15. #3218
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    How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture

    Abstract

    Ancient human remains have the potential to explain a great deal about the prehistory of humankind. Due to recent technological and bioinformatics advances, their study, at the palaeogenomic level, can provide important information about population dynamics, culture changes, and the lifestyles of our ancestors. In this study, mitochondrial and nuclear genome data obtained from human bone remains associated with the Neolithic Globular Amphorae culture, which were recovered in the Megalithic barrow of Kierzkowo (Poland), were reanalysed to gain insight into the social organisation and use of the archaeological site and to provide information at the individual level. We were able to successfully estimate the minimum number of individuals, sex, kin relationships, and phenotypic traits of the buried individuals, despite the low level of preservation of the bone samples and the intricate taphonomic conditions. In addition, the evaluation of damage patterns allowed us to highlight the presence of “intruders”—that is, of more recent skeletal remains that did not belong to the original burial. Due to its characteristics, the study of the Kierzkowo barrow represented a challenge for the reconstruction of the biological profile of the human community who exploited it and an excellent example of the contribution that ancient genomic analysis can provide to archaeological reconstruction.

    https://www.mdpi.com/2073-4425/12/6/910

    Last edited by Waldemar; 06-12-2021 at 05:40 AM.

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  17. #3219
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    Population dynamics in the Japanese Archipelago since the Pleistocene ...

    Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome
    Fuzuki Mizuno, Jun Gojobori, Masahiko Kumagai, Hisao Baba, Yasuhiro Taniguchi, Osamu Kondo, Masami Matsushita, Takayuki Matsushita, Fumihiko Matsuda, Koichiro Higasa, Michiko Hayashi, Li Wang, Kunihiko Kurosaki & Shintaroh Ueda
    2021/06/13
    Abstract
    The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.
    Last edited by pmokeefe; 06-13-2021 at 03:47 PM.
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  19. #3220
    Registered Users
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    Ethnicity
    Venetharum natio populosa
    Nationality
    Polish
    Y-DNA (P)
    R-L1029>YP263>Y2912*
    mtDNA (M)
    H141,U5a1b1j(W)

    Poland Poland Pomerania
    Genetic analysis of the human remains of the burials of the 17th–18th centuries of the Corpus Christi Church in Nesvizh (Belarus)

    ABSTRACT
    During archaeological excavation in the territory of the Corpus Christi Church in Nesvizh, the regular burials dated to the 17th–18th centuries were discovered. The genetic material extracted from the bones of seven unidentified individuals was analyzed using the forensic genetics approaches, including STR profiling and DNA phenotyping. The genetic examination revealed that the remains of three samples (#1, #2, #6) belonged to women, and the four others (#3, #4, #5, and #7) belonged to men. Autosomal STR-data and Y-chromosomal profiles were obtained for five samples. The kinship analysis excluded that woman #1 and men #3, #4, #5, #7 were first-degree relatives. According to the Y-STR profiles, men #3, #4, #7 referred to the haplogroup R1a, the haplotype of individual #5 corresponded to I2. The both haplogroups are widely represented in Eastern Europe, which, with a high degree of probability, suggests the Slavic origin of the individuals under investigation. To predict eye and hair color, we used the HIrisPlex DNA phenotyping system. The analysis gave the satisfactory results for woman #1 and man #7. In correspondence to the allelic variants of the 24 SNP system, woman #1 had an intermediate type of iris pigmentation and dark blond hair (p = 0.635) with dark shade (0.639), light skin tone, low tendency to sunburn, and a high probability of freckles and pigmented spots of the skin. For male #7, the HIrisPlex model predicted blue eye color with a high probability (p = 0.915), as well as blond hair color (p = 0.915) and light hair color shade (p = 0.962). Our data allow us to conclude that the unknown individuals under investigation have significant genetical and phenotypical similarity with the modern Belarusian population.

    https://doklady.belnauka.by/jour/art...?locale=en_US#

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