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Thread: New DNA Papers

  1. #931
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    Last edited by vettor; 02-20-2018 at 04:44 PM.

    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .......T2b17
    Grandfather mtdna .......T1a1e
    Sons Mtdna .....K1a4
    Grandfather-Maternal ......I1d-P109...CTS6009
    Wife's Ydna .....R1a-M512

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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  3. #932
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    Population turnover in Remote Oceania shortly after initial settlement - preprint

    Ancient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania ("First Remote Oceanians") were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.

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  5. #933
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    https://www.nature.com/articles/s41431-017-0012-3

    Lan-Hai Wei et al., Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan, European Journal of Human Genetics, volume 26, pages230–237 (2018)

    The Y-chromosome haplogroup C3*-Star Cluster (revised to C2*-ST in this study) was proposed to be the Y-profile of Genghis Khan. Here, we re-examined the origin of C2*-ST and its associations with Genghis Khan and Mongol populations. We analyzed 34 Y-chromosome sequences of haplogroup C2*-ST and its most closely related lineage. We redefined this paternal lineage as C2b1a3a1-F3796 and generated a highly revised phylogenetic tree of the haplogroup, including 36 sub-lineages and 265 non-private Y-chromosome variants. We performed a comprehensive analysis and age estimation of this lineage in eastern Eurasia, including 18,210 individuals from 292 populations. We discovered that the origin of populations with high frequencies of C2*-ST can be traced to either an ancient Niru’un Mongol clan or ordinary Mongol tribes. Importantly, the age of the most recent common ancestor of C2*-ST (2576 years, 95% CI = 1975–3178) and its sub-lineages, and their expansion patterns, are consistent with the diffusion of all Mongolic-speaking populations, rather than Genghis Khan himself or his close male relatives. We concluded that haplogroup C2*-ST is one of the founder paternal lineages of all Mongolic-speaking populations, and direct evidence of an association between C2*-ST and Genghis Khan has yet to be discovered.

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  7. #934
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    Data on haplotype diversity in the hypervariable region I, II and III of mtDNA amongst the Brahmin population of Haryana
    Author Kapil Verma Sapna Sharma Arun Sharma Jyoti Dalal Tapeshwar Bhardwaja
    Data in Brief
    Volume 17, April 2018, Pages 305-313
    open access
    Open acess https://www.sciencedirect.com/scienc...52340918300143
    Abstract
    Human mitochondrial DNA (mtDNA) is routinely analysed for pathogenic mutations, evolutionary studies, estimation of time of divergence within or between species, phylogenetic studies and identification of degraded remains. The data on various regions of human mtDNA has added enormously to the knowledge pool of population genetics as well as forensic genetics. The displacement-loop (D-loop) in the control region of mtDNA is rated as the most rapidly evolving part, due to the presence of variations in this region. The control region consists of three hypervariable regions. These hypervariable regions (HVI, HVII and HVIII) tend to mutate 5–10 times faster than nuclear DNA. The high mutation rate of these hypervariable regions is used in population genetic studies and human identity testing. In the present data, potentially informative hypervariable regions of mitochondrial DNA (mtDNA) i.e. HVI (np 16024–16365), HVII (np 73–340) and HVIII (np 438–576) were estimated to understand the genetic diversity amongst Brahmin population of Haryana. Blood samples had been collected from maternally unrelated individuals from the different districts of Haryana. An array of parameters comprising of polymorphic sites, transitions, transversions, deletions, gene diversity, nucleotide diversity, pairwise differences, Tajima's D test, Fu's Fs test, mismatch observed variance and expected heterozygosity were estimated. The observed polymorphisms with their respective haplogroups in comparison to rCRS were assigned.
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal

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  9. #935
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    10 months old, but I have not seen it before

    https://digitalcommons.wayne.edu/cgi...biol_preprints

    Y chromosome haplogroups in the Bosnian-Herzegovinian population based on 23 Y-STR loci

    the 49% of I2a is slightly less that the 51% of I2a in the croatian islands .............could this be the original haplogroup for the region?

    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .......T2b17
    Grandfather mtdna .......T1a1e
    Sons Mtdna .....K1a4
    Grandfather-Maternal ......I1d-P109...CTS6009
    Wife's Ydna .....R1a-M512

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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  11. #936
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    https://www.nature.com/articles/s41467-018-03342-5

    Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

    Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-loth, Jazmin Sanchez, Omar Alva, Amal Arachiche, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Francois-Xavier Ricaut, Jean-Aimé Rakotoarisoa, Chantal Radimilahy, Mark Stoneking & Thierry Letellier

    Nature Communicationsvolume 9, Article number: 932 (2018)
    doi:10.1038/s41467-018-03342-5

    Received: 22 June 2017
    Accepted: 06 February 2018
    Published online: 02 March 2018

    Abstract

    While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

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  13. #937
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    https://www.biorxiv.org/content/early/2018/03/12/250191

    Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

    Clare Bycroft,Ceres Fernández-Rozadilla, Clara Ruiz-Ponte, Iéns Quintela-García, Ángel Carracedo, Peter Donnelly, Simon Myers

    doi: https://doi.org/10.1101/250191

    Abstract

    Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian Peninsula is linguistically diverse, has a complex demographic history, and is unique among European regions in having a centuries-long period of Muslim rule. Previous genetic studies of Spain have examined either a small fraction of the genome or only a few Spanish regions. Thus, the overall pattern of fine-scale population structure within Spain remains uncharacterised. Here we analyse genome-wide genotyping array data for 1,413 Spanish individuals sampled from all regions of Spain. We identify extensive fine-scale structure, down to unprecedented scales, smaller than 10 Km in some places. We observe a major axis of genetic differentiation that runs from east to west of the peninsula. In contrast, we observe remarkable genetic similarity in the north-south direction, and evidence of historical north-south population movement. Finally, without making particular prior assumptions about source populations, we show that modern Spanish people have regionally varying fractions of ancestry from a group most similar to modern north Moroccans. The north African ancestry results from an admixture event, which we date to 860 - 1120 CE, corresponding to the early half of Muslim rule. Our results indicate that it is possible to discern clear genetic impacts of the Muslim conquest and population movements associated with the subsequent Reconquista.

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  15. #938
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    http://www.pnas.org/content/pnas/ear...80115.full.pdf

    Population genomic analysis of elongated skulls
    reveals extensive female-biased immigration
    in Early Medieval Bavaria


    Modern European genetic structure demonstrates strong corre-
    lations with geography, while genetic analysis of prehistoric
    humans has indicated at least two major waves of immigration
    from outside the continent during periods of cultural change.
    However, population-level genome data that could shed light
    on the demographic processes occurring during the intervening
    periods have been absent. Therefore, we generated genomic data
    from 41 individuals dating mostly to the late 5th/early 6th century
    AD from present-day Bavaria in southern Germany, including
    11 whole genomes (mean depth 5.56×). In addition we developed
    a capture array to sequence neutral regions spanning a total of 5
    Mb and 486 functional polymorphic sites to high depth (mean 72×)
    in all individuals. Our data indicate that while men generally had
    ancestry that closely resembles modern northern and central Eu-
    ropeans, women exhibit a very high genetic heterogeneity; this
    includes signals of genetic ancestry ranging from western Europe
    to East Asia

    http://www.pnas.org/content/pnas/sup...80115.sapp.pdf
    Last edited by vettor; 03-13-2018 at 05:43 AM.

    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .......T2b17
    Grandfather mtdna .......T1a1e
    Sons Mtdna .....K1a4
    Grandfather-Maternal ......I1d-P109...CTS6009
    Wife's Ydna .....R1a-M512

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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  17. #939
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    Quote Originally Posted by vettor View Post
    http://www.pnas.org/content/pnas/ear...80115.full.pdf

    Population genomic analysis of elongated skulls
    reveals extensive female-biased immigration
    in Early Medieval Bavaria


    Modern European genetic structure demonstrates strong corre-
    lations with geography, while genetic analysis of prehistoric
    humans has indicated at least two major waves of immigration
    from outside the continent during periods of cultural change.
    However, population-level genome data that could shed light
    on the demographic processes occurring during the intervening
    periods have been absent. Therefore, we generated genomic data
    from 41 individuals dating mostly to the late 5th/early 6th century
    AD from present-day Bavaria in southern Germany, including
    11 whole genomes (mean depth 5.56×). In addition we developed
    a capture array to sequence neutral regions spanning a total of 5
    Mb and 486 functional polymorphic sites to high depth (mean 72×)
    in all individuals. Our data indicate that while men generally had
    ancestry that closely resembles modern northern and central Eu-
    ropeans, women exhibit a very high genetic heterogeneity; this
    includes signals of genetic ancestry ranging from western Europe
    to East Asia

    http://www.pnas.org/content/pnas/sup...80115.sapp.pdf
    There is an Ancient DNA Paper and it was already been posted in the forum "Genetic Genealogy and Ancient DNA in the News"
    Paternal: R1b-U152+ L2+ ZZ48+ FGC10543+, Pietro della Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: Haplogroup H4a1-T152C!, Maria Coto, b. ~1864, Asturias, Spain
    Mother's Paternal: Haplogroup J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: Haplogroup T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain

    Avatar: Bell Beaker East Group Warrior circa 2500 BC. (after Heyd 2000; drawing B. Richter)

  18. #940
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    Quote Originally Posted by R.Rocca View Post
    There is an Ancient DNA Paper and it was already been posted in the forum "Genetic Genealogy and Ancient DNA in the News"
    thanks

    I thought all new papers only had to go in the thread I choose

    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .......T2b17
    Grandfather mtdna .......T1a1e
    Sons Mtdna .....K1a4
    Grandfather-Maternal ......I1d-P109...CTS6009
    Wife's Ydna .....R1a-M512

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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