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Thread: New DNA Papers

  1. #1601
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    T1a2b- SK1480
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    Australia Italy Veneto Friuli Italy Trentino Alto Adige Italy Ladinia Austria Tirol
    Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina

    https://www.frontiersin.org/articles...21.671467/full


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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  3. #1602
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    Thousands of Qatari genomes inform human migration history and improve imputation of

    Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes

    Abstract

    Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East.

    https://www.nature.com/articles/s41467-021-25287-y

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  5. #1603
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    H2a5b

    Russian Federation
    The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

    Abstract
    The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15–30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4–9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.

    https://www.nature.com/articles/s41467-021-26188-w

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  7. #1604
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    United States of America England
    What appear to be novel ideas about Y-DNA in Ireland: https://www.irishorigenes.com/conten...NdaRZggkXxEiH8

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  9. #1605
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    Genomic insights into the population history and biological adaptation of Southwester

    Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people

    Abstract

    Hmong-Mien-speaking (HM) populations, widely distributed in South China, North of Thailand, Laos and Vietnam, have experienced different settlement environments, dietary habits and pathogen exposure. However, their specific biological adaptation also remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations and also identified one new ancestral lineage specifically exited in HM people, which spatially distributed from Sichuan and Guizhou in the North to Thailand in the South and temporally dated to at least 500 years. The sharing patterns of the newly-identified homogeneous ancestry component combined the estimated admixture times via the decay of Linkage Disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward recently, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically-informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese population genomic diversity project (CPGDP), especially in the ethnolinguistic regions.

    https://www.biorxiv.org/content/10.1...6.463767v1?ct=

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  11. #1606
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    United States of America Italy 1861-1946 Spain
    Not sure if this was posted last year. No surprise to anyone... U152 is most frequent in all sampled Swiss populations with a peak of 53% in Ticino.

    The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration
    https://www.sciencedirect.com/scienc...301186#tbl0005

    Abstract
    A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.
    Last edited by R.Rocca; 10-18-2021 at 01:09 AM.
    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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  13. #1607
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    H37

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    Quote Originally Posted by R.Rocca View Post
    Not sure if this was posted last year. No surprise to anyone... U152 is most frequent in all sampled Swiss populations with a peak of 53% in Ticino.

    The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration
    https://www.sciencedirect.com/scienc...301186#tbl0005

    Abstract
    A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.
    https://anthrogenica.com/showthread....l=1#post748616
    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. #1608
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    United States of America China
    Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

    Juan Esteban Rodriguez-Rodriguez, Alexander G Ioannidis, Erika Landa-Chavarria, Javier Blanco-Portillo, Consuelo D. Quinto-Cortes, Rosenda I Penaloza-Espinosa, Karla Sandoval, Andres Moreno-Estrada

    doi: https://doi.org/10.1101/2021.10.09.463780
    (This article is a preprint and has not been certified by peer review)

    https://www.biorxiv.org/content/10.1...10.09.463780v1

    Abstract
    Mexico has considerable population substructure due to pre-Columbian diversity and subsequent variation in admixture levels from trans-oceanic migrations, primarily from Europe and Africa, but also, to a lesser extent, from Asia. Detailed analyses exploring sub-continental structure remain limited and post-Columbian demographic dynamics within Mexico have not been inferred with genomic data. We analyze the distribution of ancestry tracts to infer the timing and number of pulses of admixture in ten regions across Mexico, observing older admixture timings in the first colonial cities and more recent timings moving outward into southern and southeastern Mexico. We characterize the specific origin of the heterogeneous Native American ancestry in Mexico: a widespread western-central Native Mesoamerican component in northern Aridoamerican states and a central-eastern Nahua contribution in Guerrero (southern Mexico) and Veracruz to its north. Yucatan shows lowland Mayan ancestry, while Sonora exhibits a unique northwestern native Mexican ancestry matching no sampled reference, each consistent with localized indigenous cultures. Finally, in Acapulco, Guerrero a notable proportion of East Asian ancestry was observed, an understudied heritage in Mexico. We identified the source of this ancestry within Southeast Asia--specifically western Indonesian and non-Negrito Filipino--and dated its arrival to approximately thirteen generations ago (1620 CE). This points to a genetic legacy from the 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico. Although this piece of the colonial Spanish trade route from China to Europe appears in historical records, it has been largely ignored as a source of genetic ancestry in Mexico, neglected due to slavery, assimilation as "Indios" and incomplete historical records.

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  17. #1609
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    United States of America India Hyderabad State Dutch East India Company Chola Empire
    The Y chromosome ancestry marker R1b1b2: a surrogate of the SARS-CoV-2 population affinity
    Muntaser Ibrahim & Abdalhameed Salih
    Human Genome Variation volume 8, Article number: 11 (2021)

    Abstract
    Individual and population susceptibilities to disease remain a murky area of investigation, clouded by past bias based on ideological differences and wars. The current SARS-CoV-2 pandemic, the largest in living memory, brought this matter to forefront as the disparity in disease burden became apparent. A timeline analysis of the pandemic revealed the presence of country clusters that display a marked preponderance of disease among populations carrying the ancestry marker R1b1b2, notably associated with both infection and mortality. This marker is a relic of past human expansions from western Asia and subsequently Europe and the rest of the world, which may have been accompanied by peculiar biological events rendering these populations vulnerable to SARS-CoV-2.

    Shows high correlation between mortality rate of Covid with R1b1b2


    https://www.nature.com/articles/s41439-021-00141-1
    Y: H1a1a4b3b1a8 Yfull id-> YF83218
    Medals->Hidden Content
    mtDNA:U2a1a2
    G25 Ancients Dist 1.0 IRN_Shahr_I_Sokhta_BA2 88.4 MAR_Taforalt 2.6NPL_Mebrak 5
    VK2020_SWE_Gotland_VA 4 Hidden Content

    Lactose Persistence rs3213871 rs4988243 rs4988183 rs3769005 rs2236783
    found -> DA125, Kangju

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  19. #1610
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    U2a1a2
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    HM69 (<-J2b2 <-L1a)

    United States of America India Hyderabad State Dutch East India Company Chola Empire

    Sebastiano Schillaci∗

    Another paper on correlation between R1b and covid in Italy by Sebastiano Schillaci∗


    https://osf.io/yv8kc/download

    Here we develop some of the ideas we have first proposed in [1]. In particular, the linear correlation between the initial
    growth rate of COVID-19 contagion and the average Y-DNA haplogroup percentages in different countries is computed.
    In the case of haplogroup R1b, a positive correlation with high confidence level is found. Utilizing the maximum R1b
    percentages in place of the average ones, a more significant result is obtained. Considering an extended R1b data set,
    correlations with even higher confidence level are found (p-values 3.94 × 10−7
    and 2.40 × 10−9
    , respectively). Repeating the
    same procedure for the initial growth rate of deaths, similar results are obtained (p-values 9.17 × 10−11 and 2.18 × 10−12
    ,
    respectively). Furthermore, the correlation of haplogroup R1b with cases and deaths per capita is calculated over a
    five-month period, obtaining comparable results (e.g. p-value 2.45 × 10−17 on April 10th). The difference between the
    correlation with maximum R1b percentages and the correlation with average ones is decreasing over time. Finally, assuming
    the possible involvement of R1b carriers, three scenarios are outlined according to their passive or active role in the spread
    of the virus.

    Conclusion
    In this work, first, a coefficient α representing the growth
    rate of the contagion is obtained for 56 countries, using an
    exponential fit of the number of cases in the first days of
    spreading. Then, the Pearson’s linear correlation coefficient
    between the rates α and the average Y-DNA haplogroup
    percentages in the corresponding countries is calculated, obtaining a highly significant correlation with haplogroup R1b.
    Lastly, the correlation between the same rates α and the
    maximum haplogroup R1b percentages in the corresponding
    countries is calculated, obtaining an even more highly significant correlation. A similar calculation is repeated with the
    number of deaths in the initial days of spreading, obtaining
    again highly significant correlation with haplogroup R1b.
    The same procedure is then repeated with an extended R1b
    data set of 84 countries, strengthening the results.
    Moreover, it has been studied how the correlation of average and maximum haplogroup R1b percentages with cases
    per capita varies over a five-month period. The same procedure has been applied to the deaths per capita. Comparing
    the results, it emerges that at the beginning the correlation is
    stronger with the maximum R1b percentages than with the
    average ones, but over time the difference decreases. This
    could be explained supposing that the effects of contagion
    become evident first in areas with higher R1b frequency.
    Three possible scenarios are then outlined, according to
    the passive or active involvement of R1b carriers in the diffusion of the virus. They could develop more severe symptoms,
    be more susceptible to infection, be more contagious, or one
    of their combinations. In particular, R1b carriers being
    asymptomatic (or pre-symptomatic) spreaders seems to be
    the most likely option.
    Given those results, it could be useful to take into consideration the ideas here presented when confronting the current
    pandemic struggle. Our findings should warrant further
    epidemiological observational studies, such as case-control
    studies, to confirm or disprove the possible involvement of
    R1b carriers in the spread of the virus. A positive result
    could speed up the discovery of a treatment, help to make
    more reliable quantitative forecasting models or, at least,
    help to better tune the social distancing measures and to
    inform future vaccination campaign priorities.

    http://sxs.altervista.org/coronaviru...43658447265625

    Italy
    http://sxs.altervista.org/wp-content/uploads/Italy-overlay.png

    Europe
    http://sxs.altervista.org/wp-content/uploads/Red_COVID-19_Outbreak_Cases_per_capita_in_Europe.png
    Y: H1a1a4b3b1a8 Yfull id-> YF83218
    Medals->Hidden Content
    mtDNA:U2a1a2
    G25 Ancients Dist 1.0 IRN_Shahr_I_Sokhta_BA2 88.4 MAR_Taforalt 2.6NPL_Mebrak 5
    VK2020_SWE_Gotland_VA 4 Hidden Content

    Lactose Persistence rs3213871 rs4988243 rs4988183 rs3769005 rs2236783
    found -> DA125, Kangju

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