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Thread: New DNA Papers

  1. #611
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    Another superfical and misleading "work" on modern North African populations:

    Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa
    Lara R. Arauna, Javier Mendoza-Revilla, Alex Mas-Sandoval, Hassan Izaabel, Asmahan Bekada, Soraya Benhamamouch, Karima Fadhlaoui-Zid, Pierre Zalloua, Garrett Hellenthal and David Comas.

    Abstract

    North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates. We analyze genome-wide autosomal data in five Berber and six Arab groups, and compare them to Middle Easterns, sub-Saharans, and Europeans. Haplotype-based methods show a lack of correlation between geographical and genetic populations, and a high degree of genetic heterogeneity, without strong differences between Berbers and Arabs. Berbers enclose genetically diverse groups, from isolated endogamous groups with high autochthonous component frequencies, large homozygosity runs and low effective population sizes, to admixed groups with high frequencies of sub-Saharan and Middle Eastern components. Admixture time estimates show a complex pattern of recent historical migrations, with a peak around the 7th century C.E. coincident with the Arabization of the region; sub-Saharan migrations from in the 1st century B.C. in agreement with Roman slave trade; and a strong migration in the 17th century C.E., coincident with a huge impact of the trans-Atlantic and trans-Saharan trade of sub-Saharan slaves in the Modern Era. The genetic complexity found should be taken into account when selecting reference groups in population genetics and biomedical studies.
    It seems they forgot some very basic concepts like drift, homogeneous/heterogeneous, outlier...
    Here is my very basic and illustrated answer using their very own PCA, it's pretty straight-forward:
    2016_Arauna_Figure1.jpg
    Paternal Y-DNA haplogroup: E-M35>E-Z827>L19>M81>M183
    Maternal [grandfather] Y-DNA: E-M35>E-Z827>L19>M81>M183>PF2477>PF2546
    Hidden Content

    Lactase Persistence (LP)
    13910: TT (rs4988235 AA)
    22018: AA (rs182549 TT)

    (my mother's LP: same results)

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  3. #612
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    Boattini A, Sarno S, Bini C, Pesci V, Barbieri C, De Fanti S, et al. (2016) Mutation Rates and Discriminating Power for 13 Rapidly-Mutating Y-STRs between Related and Unrelated Individuals. PLoS ONE 11(11): e0165678. doi:10.1371/journal.pone.0165678

    Rapidly Mutating Y-STRs (RM Y-STRs) were recently introduced in forensics in order to increase the differentiation of Y-chromosomal profiles even in case of close relatives. We estimate RM Y-STRs mutation rates and their power to discriminate between related individuals by using samples extracted from a wide set of paternal pedigrees and by comparing RM Y-STRs results with those obtained from the Y-filer set. In addition, we tested the ability of RM Y-STRs to discriminate between unrelated individuals carrying the same Y-filer haplotype, using the haplogroup R-M269 (reportedly characterised by a strong resemblance in Y-STR profiles) as a case study. Our results, despite confirming the high mutability of RM Y-STRs, show significantly lower mutation rates than reference germline ones. Consequently, their power to discriminate between related individuals, despite being higher than the one of Y-filer, does not seem to improve significantly the performance of the latter. On the contrary, when considering R-M269 unrelated individuals, RM Y-STRs reveal significant discriminatory power and retain some phylogenetic signal, allowing the correct classification of individuals for some R-M269-derived sub-lineages. These results have important implications not only for forensics, but also for molecular anthropology, suggesting that RM Y-STRs are useful tools for exploring subtle genetic variability within Y-chromosomal haplogroups.

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  5. #613
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    H4a1-T152C!

    United States of America Italy 1861-1946 Spain
    Genomic continuity of Argentinean Mennonites
    http://www.nature.com/articles/srep36392

    Abstract
    Mennonites are Anabaptist communities that originated in Central Europe about 500 years ago. They initially migrated to different European countries, and in the early 18th century they established their first communities in North America, from where they moved to other American regions. We aimed to analyze an Argentinean Mennonite congregation from a genome-wide perspective by way of investigating >580.000 autosomal SNPs. Several analyses show that Argentinean Mennonites have European ancestry without signatures of admixture with other non-European American populations. Among the worldwide datasets used for population comparison, the CEU, which is the best-subrogated Central European population existing in The 1000 Genome Project, is the dataset showing the closest genome affinity to the Mennonites. When compared to other European population samples, the Mennonites show higher inbreeding coefficient values. Argentinean Mennonites show signatures of genetic continuity with no evidence of admixture with Americans of Native American or sub-Saharan African ancestry. Their genome indicates the existence of an increased endogamy compared to other Europeans most likely mirroring their lifestyle that involve small communities and historical consanguineous marriages.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  7. #614
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    United States of America United States Tree Flag Bermuda United Kingdom France Italy
    (Juric 2016)
    Juric 2016.png
    Citation: Juric I, Aeschbacher S, Coop G (2016) The Strength of Selection against Neanderthal Introgression. PLoS Genet 12(11): e1006340. doi:10.1371/journal.pgen.1006340

    Editor: David Reich, Broad Institute of MIT and Harvard, UNITED STATES

    Received: December 22, 2015; Accepted: September 6, 2016; Published: November 8, 2016

    Copyright: © 2016 Juric et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    dp :-)
    Last edited by dp; 11-09-2016 at 04:59 PM. Reason: thanks joe
    Grace and good eure and long prosperitee. [Lydg. Mum. Goldsmiths]

    ysearch/mitosearch id: atr94 GENBANK/ENA mtDNA id: KF703542 member ISOGG

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  9. #615
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    United States of America Italy 1861-1946 Spain
    Reconstructing Druze population history
    http://www.nature.com/articles/srep35837

    Abstract: The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern–Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze.

    Note: Modern Druze were compared to ancient DNA samples, but the ancients are from Lazaridis et al. (2016).
    Last edited by R.Rocca; 11-16-2016 at 04:28 PM.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  11. #616
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    Genetic trail for the early migrations of Aisin Gioro, the imperial house of the Qing dynasty
    Abstract
    The House of Aisin Gioro, the imperial clan of Qing dynasty (1644–1911), affected the history of China and the formation of Manchu ethnicity greatly. However, owing to the lack of historical records and archeological evidences, the origin of the House of Aisin Gioro remains ambiguous. To clarify the origin of Aisin Gioro clan, we conducted whole Y-chromosome sequencing on three samples and Y-single-nucleotide polymorphism (Y-SNP) genotyping on other four samples beside those reported in previous work. We confirmed that the paternal lineage of the Aisin Gioro clan belongs to haplogroup C3b1a3a2-F8951, a brother branch of C3*-Star Cluster (currently named as C3b1a3a1-F3796, once linked to Genghis Khan), which is quite different from the predominant lineage C3c-M48 in other Tungusic-speaking populations. We also determined a series of unique Y-SNP markers for the Aisin Gioro clan. Diversity analyses of haplogroup C3b1a3a2-F8951 revealed the early migration of the ancestors of the Aisin Gioro clan from the middle reaches of Amur River to their later settlement in southeastern Manchuria. Hence, our results suggest that the Aisin Gioro clan may be descendants of ancient populations in Transbaikal region and closely related to origin of current Daur populations. Our research indicated that detailed research of stemma and deep sequencing of Y chromosomes are helpful to explore the prehistoric activities of populations lacking historical records and archeological evidences

    http://www.nature.com/jhg/journal/va...g2016142a.html

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  13. #617
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    U152>L2>Z49>Z142>
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    I2a2a1b2a1b1>Y4925
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    H37

    England Scotland Wales Germany Palatinate Ireland Leinster Sweden Finns
    DNA tests prove Scots clan are Viking not Irish

    http://www.deadlinenews.co.uk/2015/0...ing-not-irish/
    Last edited by MitchellSince1893; 11-20-2016 at 05:15 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    35% English, 15% Scottish, 14% Welsh, 14% German, 11% Ulster Scot, 5% Ireland, 3% Scandinavian, 2% French/Dutch, 1% India
    Hidden Content

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  15. #618
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    Kyrgyzstan
    https://www.academia.edu/30025626/%D..._%D0%A1._86-96

    Paper in Russian with summary in English, the data is not yet published.

    GENE POOL OF TURKMENS FROM KARAKALPAKSTAN IN THEIR CENTRAL ASIAN CONTEXT (Y-CHROMOSOME POLYMORPHISM)

    R.A. Skhalyakho 1,2, M.K. Zhabagin 3, Yu.M. Yusupov 4, A.T. Agdzhoyan 2,1, Zh.M. Sabitov 5, V.M. Gurianov 2, O.A. Balaganskaya 2, D.A. Dalimova 6, D.Kh. Davletchurin 6, Sh.U. Turdikulova
    7, M.I. Chukhryaeva 1,2, R.R. Asilgujin 4, A.R. Akilzhanova 3, O.P. Balanovsky 2,1, E.V. Balanovska 1

    Turkmens represent one of the least studied population of Central Asia due to lack of international scientific integration of Turkmenistan into the gene pool studies. Preserving in Turkmens the memory of thetribal affiliation allows the parallel study of tribal structure and Y-chromosome which are both transmitted along the paternal line.The panel of Y-chromosome markers highly informative for genetic studies (41 SNP and 17 STR markers)has been used for the study of the gene pool of the northern Turkmen population – Turkmens in Karakalpakstan(N=83). Sample of Turkmens from Xojeyli and Shumanay districts of Karakalpakstan included mainly (88%)one of the largest Turkmen’ tribe (Yomud) and only a few representatives of other clans (Gochak, Oliz, Uker,Yagly). Among 12 identified haplogroups the major haplogroup Q composed three-quarters of the gene pool.The remaining quarter of the gene pool consisted of haplogroups H, R1b, R1a, and G2a(with frequenciesfrom 4 to 7 per cent) and variants of haplogroups C2, J1, J2a, N1*, N1c met in 1-2 individuals each. Pronounced similarity of gene pools of the Turkmens in Central Asia - Karakalpakstan, Iran and Afghanistan – has allowed to hypothesize that haplogroup Q is typical for the gene pool of the Turkmen ethnic group as a whole.The genetic distance between the gene pools of Turkmens and other Central Asian populations showed no appreciable effects on the gene pool of the Turkmen in Karakalpakstan by its geographical neighbors – Uzbeks, Dungans, and Karakalpaks. Analysis of Y-chromosome haplogroup Q fast mutating STR markershas also confirmed this conclusion. The estimated date of STR cluster of Turkmens in Karakalpakstan onhaplogroup Q phylogenetic network was 900±300 years (date by ASD method was 1090±430).

    Keywords:
    ethnogenesis, gene pool, gene geography, Y-chromosome, haplogroup, Turkmens, clan,Yomud, Central Asia

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  17. #619
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    J1a1 FGC6064+ M365+
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    H1ao1

    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil
    Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations
    Marc Habe et al.
    AJHG - Published Online: November 23, 2016 - Open Article

    Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

    http://www.cell.com/ajhg/abstract/S0002-9297(16)30448-7
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  19. #620
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    Italy European Union
    Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean

    Abstract:
    Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
    http://journals.plos.org/plosone/art...l.pone.0167065

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