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Thread: New DNA Papers

  1. #1521
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    C4a1a-a2

    Canada China
    Genetic Polymorphism Analysis of Mitochondrial DNA from Chinese Guangdong Liannan Yao ethnic group

    Shiyu Sun, Jinpeng Chen, Mingqi Zhang, Huang Huang, Xihong Lin, Weian Du, Huilin Sun

    DOI: 10.21203/rs.3.rs-58135/v1

    Abstract

    Background

    Genetic polymorphism and haplotype distribution characteristics analysis of mitochondrial DNA in Chinese Guangdong Liannan Yao group was conducted in this study, to provide genetic basis for tracing the origin and historical migration of Liannan Yao people.

    Results

    46 mutation sites were found, and among which single nucleotide transition was the most commonly observed variant (86.17%). Multiple (sub)haplogroups were detected in Liannan Yao ethnic group, among which haplogroup D was the most common haplogroup (29.80%), and the least were C and Y (0.48% respectively).

    Conclusions

    The Liannan Yao population had the commonalities of the ethnic groups in southern China, but it was significantly different from other Chinese ethnic populations. The present results revealed that Liannan Yao ethnic group was genetically closer related to Fujian She ethnic population, Yunnan Yao population, and Hunnan Miao population. The data enriched the Chinese mtDNA database and provided a reference for forensic identification and screening for potential pathogenic mutations.

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  3. #1522
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    Canada China
    Genetic characterization of the North-West Indian populations: analysis of mitochondrial DNA control region variations

    Gagandeep Singh, Srinivas Yellapu, Harkirat Singh Sandhu, Indu Sharma, Varun Sharma & A. J. S. Bhanwer

    https://doi.org/10.1080/03014460.2021.1879933

    Background

    Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history, and forensic science.

    Aim

    The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient.

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  5. #1523
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    Indigenous ancestry and admixture in the Uruguayan population

    Abstract

    The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in 'Charrúas' and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.

    https://www.biorxiv.org/content/10.1...9.447750v1?ct=

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  7. #1524
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    United States of America Star of David Israel
    Evidence of the interplay of genetics and culture inEthiopia
    Saioa López

    https://doi.org/10.1038/s41467-021-23712-w


    The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with–and shape–genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals’ birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geo-graphic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.

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  9. #1525
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    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil
    Genetic characterization of a collection of Tsantsas from Ecuadorian museums
    Verónica Baquero-Méndez et al.
    https://doi.org/10.1016/j.forsciint.2021.110879
    https://www.sciencedirect.com/scienc...79073821001997

    Highlights
    • 14 shrunken heads from national museums in Ecuador were examined using molecular techniques

    • Sex was determined by high resolution melting analysis of AMEL gene; one female and thirteen males were identified.

    • Analysis of a fragment of HVR-1 region (16209-16402) of the mitochondrial DNA showed that most tsantsas presented haplogroups from Native American populations

    Abstract
    Tsantsas are shrunken human heads originally made for ceremonial purposes by Amazonian indigenous groups of the Shuar and Achuar family, previously called Jivaroan tribes. A significant demand of these objects during the first half of the 20th century led to the manufacture of counterfeit shrunken heads for commercial purposes. For museums where these collections are held, as well as for the indigenous groups who claim their ownership, it is important to identify the origin and authenticity of these tsantsas. We hypothesized that a collection of 14 tsantsas from 3 different museum collections in Ecuador are human and aimed to characterize their sex and potential origin. We amplified the amelogenin gene and performed a high resolution melting analysis to determine their human origin and characterize their sex. We also analyzed a fragment (16209-16402) from the HVR-1 region to identify the mtDNA haplogroups present in the tsantsa collection. Our exploratory results show that all the tsantsas are human and that the collection is comprised of 13 males and 1 female. A total of seven mtDNA haplogroups were found among the tsantsa collection using the mtDNA EMPOP database. These results show a predominance of the Amerindian mtDNA haplogroups B, C and D. Additional principal component analysis, genetic distance tree and haplotype network analyses suggest a relationship between the tsantsa specimens and Native American groups.
    mtDNA Haplogroup composition The tsantsas were genotyped for a fragment (16209-16402) of the HVR-1 region for mtDNA haplogroup assignment and identification of polymorphic variations between individuals (Table 1). The distribution of mtDNA haplogroups were as follows: Haplogroup C and D were the most representative (each of them with a 29%), followed by haplogroup B (21%). These mtDNA haplogroups (B, C and D) are highly representative from Native American populations. The haplogroup M80 was found on individuals T8 and T11 (14%). This haplogroup is found in Negritos from Palawan in the Philippines. Finally, individual T1 showed the European haplogroup U (7%).

    Individual mtDNA Haplogroup* HVR-1 variable nucleotides
    T1 U8b1b C16234T T16324C
    T2 B2k T16217C A16240G C16291T T16362C
    T3 C1 C16223T T16298C T16325C C16327T
    T4 C1 C16223T T16298C T16325C C16327T A16331G
    T5 D1G1a1 C16223T C16260T T16325C T16362C
    T6 D1G1a1 C16223T T16325C T16362C
    T7 D4h3a C16223T A16241G C16301T T16342C T16362C
    T8 M80 C16223T T16325C A16331G
    T9 D1 C16223T T16325C T16362C
    T10 B4a1+16311 T16217C T16362C
    T11 M80 C16223T T16325C
    T12 B4 T16217C C16223T C16260T C16266T
    T13 C1 C16223T T16298C T16325C C16327T A16331G G16398A
    T14 C1 C16223T T16298C T16325C C16327T A16331G
    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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  11. #1526
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    Australia Italy Veneto Friuli Italy Trentino Alto Adige Italy Ladinia Austria Tirol
    Establishing the Middle Sea: The Late Bronze Age of Mediterranean Europe (1700–900 BC)

    https://link.springer.com/article/10...14-021-09165-1

    The Late Bronze Age (1700–900 BC) represents an extremely dynamic period for Mediterranean Europe. Here, we provide a comparative survey of the archaeological record of over half a millennium within the entire northern littoral of the Mediterranean, from Greece to Iberia, incorporating archaeological, archaeometric, and bioarchaeological evidence. The picture that emerges, while certainly fragmented and not displaying a unique trajectory, reveals a number of broad trends in aspects as different as social organization, trade, transcultural phenomena, and human mobility. The contribution of such trends to the processes that caused the end of the Bronze Age is also examined. Taken together, they illustrate how networks of interaction, ranging from the short to the long range, became a defining aspect of the “Middle Sea” during this time, influencing the lives of the communities that inhabited its northern shore. They also highlight the importance of research that crosses modern boundaries for gaining a better understanding of broad comparable dynamics.


    My Path = ( K-M9+, TL-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

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  13. #1527
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    United States of America India Hyderabad State Dutch East India Company Chola Empire
    The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3, f4, qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1–1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei’s genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.

    Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians
    Yan Liu1 †, Mengge Wang2*†, Pengyu Chen3,4†, Zheng Wang2, Jing Liu2, Lilan Yao3,4, Fei Wang2, Renkuan Tang5, Xing Zou2* and Guanglin He2,6*

    https://www.frontiersin.org/articles...21.582357/full
    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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  15. #1528
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    Y-chromosome lineages in São Tomé e Príncipe and Cabo Verde islands: Different input of European influence

    [https://www.fsigeneticssup.com/artic...168-6/fulltext


    Abstract

    The Y-chromosome haplogroup composition of the population of São Tomé e Príncipe and Cabo Verde Archipelagos was profiled by using 24 biallelic markers, and compared with populations from Europe, Africa and the Middle East. According to the traditional view, these archipelagos colonized by the Portuguese in the 15th century were settled mainly by West African slaves, with the addition of a minor fraction of male colonizers from Europe. Although the major proportion of the founding population of São Tomé e Príncipe cluster in haplogroup E3a (84.2%), very common among sub-Saharans, this lineage was observed at a frequency of only 15.9% in Cabo Verde. Haplogroups I, J and R1, characterized of populations of Europe and the Middle East account for more than half of the paternal lineages of Cabo Verdeans (53.5%). These West Eurasian haplogroups are found at a frequency of only 12.5% in the population of São Tomé e Príncipe. Our findings suggest that despite the sub-Saharan genetic background of these archipelagos, a relevant contribution of European paternal lineages is present in nowadays populations indicating that gene flow from multiple sources have been important in the formation of the diversity of the islanders, nevertheless with a different degree of admixture.

    Mitochondrial portraits of the Madeira and Açores archipelagos witness different genetic pools of its settlers

    https://www.researchgate.net/publica...f_its_settlers

    Abstract

    We have studied the matrilineal genetic composition of the Madeira and Açores north Atlantic archipelagos, which were settled by the Portuguese in the 15th century. Both archipelagos, and particularly Madeira, were involved in a complex commercial network established by the Portuguese, which included the trading of slaves across the Atlantic. One hundred and fifty-five mtDNAs sampled from the Madeira and 179 from the Açores archipelagos were analysed for the hypervariable segment I (HVS-I), and for haplogroup-diagnostic coding-region RFLPs. The different settlement histories of both groups of islands are well reflected in their present day mtDNA pool. Although both archipelagos show identical diversity values, they are clearly different in their haplogroup content. Madeira displays a stronger sub-Saharan imprint, with haplogroups L1-L3 constituting about 13% of the lineages. Also, the relative frequencies of L sub-clusters in Madeira and mainland Portugal suggests that, at least in part, African presence in Madeira can be attributed to a direct gene flow from West Africa and not via Portugal. A comparison of the genetic composition of these two archipelagos with the Canary Islands, specially taking into account that their European source population was essentially from the Iberian Peninsula, testifies the stronger impact of the North African U6 cluster in the Canaries. This group is present in Madeira at a moderate frequency, but very reduced in the Açores. Nevertheless the recorded introduction of Canary native Guanches, who are characterized by the presence of particular sub-clade U6b1, has left no detectable imprints in the present day population of Madeira.

    The highest frequency of mtDNA L in Europe (22%) in southern Portugal paddies:

    Genetic characterization of uniparental lineages in populations from Southwest Iberia with past malaria endemicity

    https://pubmed.ncbi.nlm.nih.gov/20737604/

    Abstract

    Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD--Coruche, Pias, and Alcacer do Sal--to evaluate if their present-day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty-five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y-chromosome markers. Results were then compared with data from other Portuguese and non-Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub-Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub-Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia.

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  17. #1529
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    Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

    https://www.nature.com/articles/s41467-018-07748-z

    Abstract

    Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.


    In the paper, converso means, East/South Mediterranean ancestry, people converted to Catholic Christianity, normally considered to be of Jewish origin, but also Islamic, or more rarely other.
    Last edited by jose luis; 06-21-2021 at 11:43 AM. Reason: In response to Mr. Targum, add the meaning of the word "convert" in the paper.

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  19. #1530
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    istribution and diversity of Central African hunter-gatherers

    Population inter-connectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers
    Cecilia Padilla-Iglesias, Lane Atmore, Jesus Olivero, Karen Lupo, Andrea Manica, Lucio Vinicius, Andrea Migliano
    Abstract
    The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density is explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also predicted hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by dated archaeological sites. Finally, we show that genomic estimates of separation times between CAHG groups match our ecological estimates of periods favouring population splits, and that recoveries of connectivity would have facilitated subsequent gene-flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.
    YFull: YF14620 (Dante Labs 2018)

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