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Thread: Filling Important Gaps in the Genomic History of Southwest Asia

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    Filling Important Gaps in the Genomic History of Southwest Asia

    Filling Important Gaps in the Genomic History of Southwest Asia
    Ludovic Orlando
    Many crucial developments in human prehistory occurred in Southwest Asia, including the transition to agriculture as well as the emergence of writing and of the earliest civilization. Two new studies in this issue of Cell map the genetic composition of human groups inhabiting the region during the sixth and first millennia Before Common Era (BCE) and uncover periods of significant population turnover.

    Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus
    Eirini Skourtanioti,Yilmaz S. Erdal, Marcella Frangipane, Francesca Balossi Restelli, K. Aslıhan Yener, Frances Pinnock, Paolo Matthiae, Rana Özbal, Ulf-Dietrich Schoop, Farhad Guliyev, Tufan Akhundov, Bertille Lyonnet, Emily L. Hammer, Selin E. Nugent, Marta Burri, Gunnar U. Neumann, Sandra Penske, Tara Ingman, Murat Akar, Rula Shafiq, Giulio Palumbi, Stefanie Eisenmann, Marta D’Andrea, Adam B. Rohrlach, Christina Warinner, Choongwon Jeong, Philipp W. Stockhammer, Wolfgang Haak, Johannes Krause
    Highlights
    Genome-wide analysis of 110 ancient individuals from the Near East
    Gene pools of Anatolia and Caucasus were biologically connected ∼6500 BCE
    Gene flow from neighboring populations in Northern Levant during 3rd millennium BCE
    One individual of likely Central Asian origin in 2nd millennium BCE Northern Levant
    Summary
    Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today’s Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age.

    The Genomic History of the Bronze Age Southern Levant
    Lily Agranat-Tamir, Shamam Waldman, Mario A.S. Martin, David Gokhman, Nadav Mishol, Tzilla Eshel, Olivia Cheronet, Nadin Rohland, Swapan Mallick, Nicole Adamski, Ann Marie Lawson, Matthew Mah, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Francesca Candilio, Denise Keating, Beatriz Gamarra, Shay Tzur, Mario Novak, Rachel Kalisher, Shlomit Bechar, Vered Eshed, Douglas J. Kennett, Marina Faerman, Naama Yahalom-Mack, Janet M. Monge, Yehuda Govrin, Yigal Erel, Benjamin Yakir, Ron Pinhasi, Shai Carmi, Israel Finkelstein, Liran Carmel, David Reich

    Highlights
    Analysis of genome-wide data for nine sites from the Bronze Age Southern Levant
    Contemporaneous samples from multiple sites are genetically similar
    Migration from the Zagros and/or Caucasus to the Levant between 2500–1000 BCE
    People related to these individuals contributed to all present-day Levantine populations
    Summary
    We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the “Canaanite” material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different “Canaanite” groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.

    A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years
    Marc Haber, Joyce Nassar, Mohamed A. Almarri, Tina Saupe, Lehti Saag, Samuel J. Griffith, Claude Doumet-Serhal, Julien Chanteau, Muntaha Saghieh-Beydoun, Yali Xue, Christiana L. Scheib , Chris Tyler-Smith
    The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world’s great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.
    Third paper courtesy of Rozenfeld

    Press Release from Max Planck Institute
    Human Mobility and Western Asia’s Early State-Level Societies
    Archaeogenomic analysis of Anatolia, Northern Levant and the Southern Caucasus sheds light on population dynamics from the Neolithic to Bronze Age, as peoples transitioned from farming to pastoralist communities and early state-level societies.

    MAY 28, 2020
    The regions of Anatolia, the Northern Levant and the Caucasus played important roles in the development of complex social and cultural models during the Chalcolithic and Bronze Age. Through genomic analysis of 110 individuals ranging from 7500 to 3000 years ago, this study sheds light on how human mobility accompanied the spread of ideas and material culture prior to and during the emergence of some of the world’s earliest state-level societies.
    Last edited by pmokeefe; 05-28-2020 at 04:22 PM.
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    First paper seems to be paywalled.

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    Quote Originally Posted by rozenfeld View Post
    First paper seems to be paywalled.
    There might be something at the magical place where "all barriers in the way of science" are removed.

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    Both of these sound very exciting. Lots of new papers lately, 2020 not so deadbeat after all.
    YDNA: R1b-BY50830 Stepney, London, UK George Wood b. 1782 English <-> Bavarian cluster
    maternal-gf YDNA: ?? Gurr, James ~1740, Smarden, Kent, England.
    maternal-gm YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    maternal-ggf YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    paternal-ggf YDNA: R1b-Z17901. Gould, John Somerset England 1800s.
    paternal-ggf YDNA: R1b-L48. Scott, William Hamilton Ireland(?) 1800s

    other:
    Welch: early 1800s E-M84 Kent, England.

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    Haplogroups for The Genomic History of the Bronze Age Southern Levant here:
    https://www.cell.com/cms/10.1016/j.c...b12aa70d4/mmc2
    One of the samples is R1b:
    I10768 Megiddo_MLBA 1600-1500 BCE J2a2a2 R1b1a1a2
    Last edited by pmokeefe; 05-28-2020 at 04:11 PM.
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    Quote Originally Posted by Pribislav View Post
    There might be something at the magical place where "all barriers in the way of science" are removed.
    I already tried it, it gives me almost blank PDF.

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    Also, there is third paper published today:

    Quote Originally Posted by rozenfeld View Post
    https://www.cell.com/ajhg/fulltext/S...297(20)30155-5

    A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

    Marc Haber
    Joyce Nassar
    Mohamed A. Almarri
    Tina Saupe
    Lehti Saag
    Samuel J. Griffith
    Claude Doumet-Serhal
    Julien Chanteau
    Muntaha Saghieh-Beydoun
    Yali Xue
    Christiana L. Scheib
    Chris Tyler-Smith
    Show less

    Open Access Published:May 28, 2020
    DOI:https://doi.org/10.1016/j.ajhg.2020.05.008

    The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world’s great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

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    delete
    Last edited by Pribislav; 05-28-2020 at 03:57 PM.

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    Supplemental Information for Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus
    Does not appear to be behind a paywall

    Document S1. Tables S2, S6–S8, and S10

    Table S1
    Details of AMS Radiocarbon Dating on Selected 95 Individuals after Quality Filtering, Related to Figure 2

    Table S3
    List of Ancient Populations Published by Previous Studies which Are Used in Our Analyses, Related to STAR Methods Grouping of individuals and nomenclature; Dataset.


    Table S4
    Outgroup f3-Statistics, Related to Figure 6 Shared genetic drift between each of the Late Chalcolithic/Bronze Age (LC-LBA) groups of the present study and a panel of Test populations compared to the distal population Mbuti. Test populations consist of 300 ancient and modern worldwide populations. f3-statistics were estimated on autosomal portion of the Human Origins (HO) SNPs with a minimum total Nº SNP per test of 50,000. The highest 40 f3-statistics are presented per LC-LBA group.


    Table S5
    Genetic Differences between Neolithic-Early Chalcolithic (N-EC) Populations and the Late Chalcolithic-Late Bronze Age (LC-LBA) with Respect to a Test Population Measured by f4(Mbuti,Test;Barcın_N/Büyükkaya_EC/TellKurdu_EC, LC-LBA), Related to Figure 6 Test populations include European and West Asians ancient populations. f4-statistics were estimated on the on the autosomal portion of the 1240K SNP panel and standard errors were estimated by 5 cM block jack-knifing. Significant values (|z-score| ≥ 3) indicate that Test shares more alleles with the LC-LBA than N-EC (positive sign) or vice versa (negative sign) and are annotated in bold. Results important for our interpretations are annotated in Italics.


    Table S9
    Assignment of Y Chromosome and Mitochondrial Haplogroups, Related to STAR Methods Sex determination and uniparental haplotypes.
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