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Thread: New DNA Papers

  1. #1541
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    Paternal genetic structure of Kyrgyz ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs

    Feng Song, Mengyuan Song, Haibo Luo, Mingkun Xie, Xindi Wang, Hao Dai, Yiping Hou

    https://doi.org/10.1002/elps.202100142

    Abstract

    Kyrgyz ethnic group is one of the nomads in China, with the majority in Xinjiang and a small part of them living in Heilongjiang province. Historically, they have went through five migrations westward due to the wars. The name “Kyrgyz” means 40 tribes, originating from the primary groups of Kyrgyz. However, it is a largely understudied population, especially from the Y chromosome. In this study, we used a previously validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) system to study Kyrgyz ethnic group. A total of 314 male samples of Kyrgyz ethnic group were genotyped by 173 Y-SNPs and 27 Y-STRs. After data analysis, the results unveiled that Kyrgyz ethnic group was a population with high percentage of both haplogroup C2a1a3a1d∼-F10091 (91/134) and R1a1a1b2a2-Z2124 (109/134), which has never been reported. This implied that Kyrgyz ethnic group might have gone through bottleneck effects twice, with these two main lineages left. Mismatch analysis indicated that the biggest mismatch number in haplogroup C2a1a3a1d∼-F10091 was 10, while that of haplogroup R1a1a1b2a2-Z2124 was 20. This huge difference reflected the different substructure in two lineages, suggesting that haplogroup C2a1a3a1d∼-F10091 might have the least admixture compared to the other two lineages. After admixture modelling with other datasets, the conclusion could be drawn that Kyrgyz ethnic group had great genetic affinity with Punjabi from Lahore, Pakistan, which supported that Kyrgyz ethnic group in China was close to central Asian.
    Last edited by Shuzam87; 07-15-2021 at 04:44 AM.

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  3. #1542
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    Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system

    May Thi Anh Ta, Nam Ngoc Nguyen, Duc Minh Tran, Trang Hong Nguyen, Tuan Anh Vu, Dung Thi Le, Phuong Thi Le, Thu Thi Hong Do, Ha Hoang & Hoang Ha Chu

    https://doi.org/10.1007/s00414-021-02649-1

    Abstract

    Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system — an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.

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  5. #1543
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    Genomic insights into the demographic history of North East Asians

    Genomic insights into the differentiated population admixture structure and demographic history of North East Asians
    Guanglin He, Mengge Wang, Xing Zou, Renkuan Tang, Hui-Yuan Yeh, Zheng Wang, Xiaomin Yang, Ziyang Xia, Yingxiang Li, Jianxin Guo, Rui Wang, Jing Liu, Kongyang Zhu, Jing Chen, Meiqing Yang, Qu Shen, Jinwen Chen, Jing Zhao, Hao Ma, Lanhai Wei, Ling Chen, Changhui Liu, Chao Liu, Gang Chen, Yiping Hou, Chuan-Chao Wang

    Abstract
    North China and South Siberia, mainly populated by Altaic-speaking populations, possess extensive ethnolinguistic diversity and serve as the crossroad for the initial peopling of America and western-eastern trans-continental communication. Yet, the complex scenarios of genetic origin, population structure, and admixture history of North-East Asia remain to be fully characterized, especially for Mongolic people in China with a genome-wide perspective. Thus, we genotyped genome-wide SNPs for 510 individuals from 38 Chinese Mongolic, Tungusic, and Sinitic populations to explore the sharing alleles and haplotypes within the studied groups and following merged it with 3508 modern and ancient Eurasian individuals to reconstruct the deep evolutionary and natural selection history of northern East Asians. We identified significant substructures within Altaic-speaking populations with the primary common ancestry linked to the Neolithic northern East Asians: Western Turkic people harbored more western Eurasian ancestry; Northern Mongolic people in Siberia and eastern Tungusic people in Amur River Basin (AR possessed dominant Neolithic Mongolian Plateau (MP) or ARB ancestry; Southern Mongolic people in China owned obvious genetic impact from Neolithic Yellow River Basin (YR farmers. Additionally, we found the differentiated admixture history between western and eastern Mongolians and geographically close Northeast Hans: the former received a genetic impact from western Eurasians and the latter retained the dominant YRB and ARB Neolithic ancestry. Moreover, we demonstrated that Kalmyk people from the northern Caucasus Mountain possessed a strong genetic affinity with Neolithic MP people, supporting the hypothesis of their eastern Eurasian origin and long-distance migration history. We also illuminated that historic pastoral empires in the MP contributed considerably to the gene pool of northern Mongolic people but rarely to southern ones. We finally found natural signatures in Mongolians associated with alcohol metabolism. Generally, our results not only illuminated that complex population migration and admixture of Neolithic ancestral sources from the MP or ARB played an important role in the spread of Altaic-speaking populations and Proto-Altaic language, which partly supported the Northeast Asia-origin hypothesis, but also demonstrated that the observed multi-sources of genetic diversity contributed significantly to the modern existing extensive ethnolinguistic diversity in North-East Asia.
    YFull: YF14620 (Dante Labs 2018)

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  7. #1544
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    Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels

    Mengge Wang, Guanglin He, Xing Zou, Jing Liu Ziwei Ye, Tianyue Ming, Weian Du, Zheng Wang, Yiping Hou

    https://doi.org/10.1016/j.fsigen.2021.102565

    Highlights

    • Two high-resolution C-M130 Y-SNP SNaPshot panels were constructed
    • A Chinese population high-resolution phylogenetic tree containing 215 Y-SNPs was built
    • Some detected microvariants are associated with specific haplogroups
    • The studied Mongolian populations possessed major East Asian-dominant haplogroups

    Abstract

    The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2low asterisk-M217 and incoming lineages from other regions of southern East Asia (O2low asterisk-M122, O1blow asterisk-P31, and N1low asterisk-CTS3750) and western Eurasia (R1low asterisk-M173). We also observed DE-M145, D1low asterisk-M174, C1low asterisk-F3393, Glow asterisk-M201, I-M170, Jlow asterisk-M304, L-M20, O1alow asterisk-M119, and Qlow asterisk-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.

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  9. #1545
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    Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina

    Naida Babić Jordamović, Tamara Kojović, Serkan Dogan, Larisa Bešić, Lana Salihefendić, Rijad Konjhodžić, Vedrana Škaro, Petar Projić, Vesna Hadžiavdić, Adna Ašić and Damir Marjanović

    https://doi.org/10.3389/fgene.2021.671467

    Abstract

    Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-single nucleotide polymorphism (SNP) markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-short tandem repeat (STR) markers using different software packages, and this method gained much attention recently due to its labor-, time-, and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43.13, 14.79, and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.

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     Andour (07-29-2021),  David Bush (08-03-2021),  JMcB (07-26-2021),  parasar (07-27-2021),  pmokeefe (07-26-2021),  RCO (07-26-2021),  Riverman (07-28-2021),  sheepslayer (07-27-2021),  teepean47 (07-27-2021)

  11. #1546
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    The effective family size ... from Quebec settlers to their 20th-century descendants

    The effective family size of immigrant founders predicts their long-term demographic outcome: from Quebec settlers to their 20th-century descendants
    Tommy Harding, Emmanuel Milot, Helene Vezina, Damian Labuda

    Abstract
    Human evolution involves population splits, size fluctuations, founder effects, and admixture. Population history reconstruction based on genetic diversity data routinely relies on simple demographic models while projecting the past. Yet, no specific demographic assumptions are needed to understand the genetic structure of the founder population of Quebec. Because genealogy and genetics are intimately related, we used descending genealogies of this population to pursue the fate of its founder lineages. Maternal and paternal lines reflect the transmission of mtDNA and the Y-chromosome, respectively. We followed their transmission in real-time, from the 17th century down to its 20th-century population. We counted the number of married children of immigrants (i.e., their effective family size, EFS), estimated the proportion of successful immigrants in terms of their survival ratio, and assessed net growth rates and extinction. Likewise, we evaluated the same parameters for their Quebec-born descendants. The survival ratio of the first immigrants was the highest and declined over time in association with the decreasing immigrants EFS. Parents with high EFS left plentiful married progeny, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. The 17th and 18th-century immigrants bear the most remarkable demographic and genetic impact on the 20th-century population of Quebec. Lessons learned from Quebec genealogies can teach us about the consequences of founder effects and migrations through real peoples history. The effective family size of immigrant founders predicts their long-term demographic outcome.
    YFull: YF14620 (Dante Labs 2018)

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  13. #1547
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    Genetic continuity of Bronze Age ancestry with increased Steppe-related ancestry in Late Iron Age Uzbekistan

    Vikas Kumar, E Andrew Bennett, Dongyue Zhao, Yun Liang, Yunpeng Tang, Meng Ren, Qinyan Dai, Xiaotian Feng, Peng Cao, Ruowei Yang, Feng Liu, Wanjing Ping, Ming Zhang, Manyu Ding, Melinda A Yang, Berdimurodov Amridin, Hasanov Muttaliu, Jianxin Wang, Qiaomei Fu

    https://doi.org/10.1093/molbev/msab216

    Abstract

    While Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of Bactria-Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events which impacted the demography and population structure of this region, we generated 27 genome-wide SNP capture datasets of Late Iron Age individuals around the Historical Kushan time period (∼2100-1500 BP) from three sites in South Uzbekistan. Overall, Bronze Age ancestry persists into the Iron Age in Uzbekistan, with no major replacements of populations with Steppe-related ancestry. However, these individuals suggest diverse ancestries related to Iranian farmers, Anatolian farmers and Steppe herders, with a small amount of West European Hunter Gatherer, East Asian and South Asian Hunter Gatherer ancestry as well. Genetic affinity towards the Late Bronze Age Steppe herders and a higher Steppe-related ancestry than that found in BMAC populations suggest an increased mobility and interaction of individuals from Northern Steppe in a Southward direction. In addition, a decrease of Iranian farmers and an increase of Anatolian farmer-like ancestry in Uzbekistan Iron Age individuals were observed compared to the BMAC populations from Uzbekistan. Thus, despite continuity from the Bronze Age, increased admixture played a major role in the shift from the Bronze to the Iron Age in southern Uzbekistan. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting more widespread admixture among local populations.

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  15. #1548
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    Insights into the Middle Eastern paternal genetic pool in Tunisia

    Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population.
    Sarra Elkamel, Sofia L. Marques, Luis Alvarez, Veronica Gomes, Sami Boussetta, Soufia Mourali-Chebil, Houssein Khodjet-El-Khil, Lotfi Cherni, Amel Benammar-Elgaaied & Maria J. Prata.

    Abstract:
    To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages (Y-DNA) ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.

    Highlights:
    Considering Tunisian populations as a whole, the majority part of their paternal haplogroups are of autochthonous Berber origin (71.67%), which co-exists with others assumedly from the Middle East (18.35%) and to a lesser extent from Sub-Saharan Africa (5.2%), Europe (3.45%) and Asia (1.33%) Most of Tunisian populations here analysed exhibited high levels of Y-STR diversity, reflecting the wealth of demographic histories underlying current-day populations. This finding is in agreement with previous studies using different types of markers that reported the highest genetic diversities in North African populations.

    1.PNG
    2.PNG
    Autosomal using ancient populations :
    93% Late Period Ancient Egyptian, 4% JOR_EBA, 3% GRC_Minoan_Lassithi (Just another G25's Scaled results with a Suitable fit).

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  17. #1549
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    Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype and haplogroup lineages

    Guanglin He, Mengge Wang, Yuan Didi, Xing Zou, Zheng Wang, Hui-Yuan Yeh, Jing Liu, Lan-Hai Wei, Chuan-Chao Wang, Bofeng Zhu and Chao Liu

    https://www.frontiersin.org/articles...27821/abstract

    Abstract

    The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers (e.g., STRs, low-density SNPs). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns haven’t been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou province, one of the most ethnolinguistically diverse regions and merged it with over 3000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup-f3/f4 statistics. QpGraph-based phylogenies and f4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans respectively from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes and paternal and maternal lineages.

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     Nebuchadnezzar II (08-04-2021),  okarinaofsteiner (08-05-2021),  Piquerobi (08-08-2021),  pmokeefe (08-04-2021),  Riverman (08-05-2021),  sheepslayer (08-04-2021),  teepean47 (08-04-2021)

  19. #1550
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    The genomic history of the Middle East

    Population structure and admixture
    Uncovering population structure and past admixture events is important for understanding population history and for designing and interpreting medical studies. We explored the structure and diversity of our dataset using both single-variant and haplotype-based methods. After merging our dataset with global populations, fineSTRUCTURE (Lawson et al., 2012) identified genetic clusters that are concordant with geography and showed that self-labeled populations generally formed distinct clusters (Figure 1C). Populations from the Levant and Iraq (Lebanese, Syrians, Jordanians, Druze, BedouinA, and Iraqi-Arabs) clustered together, while Iraqi-Kurds clustered with Central Iranian populations. Arabian populations (EmiratiA, Saudis, Yemenis, and Omanis) clustered with BedouinB from the HGDP. Within the Emirati population, we identified subpopulations with excess Iranian and South Asian ancestries (EmiratiB and EmiratiC; Figure 1. We also found subpopulations harboring relatively higher African ancestry (SaudiB, EmiratiD; Figure 1.
    We next analyzed our samples in the context of ancient regional and global populations. Principal component analysis (Figures 1D and S1) shows that present-day Middle Easterners are positioned between ancient Levantine hunter-gatherers (Natufians), Neolithic Levantines (Levant_N), Bronze Age Europeans, and ancient Iranians. Arabians and Bedouins are positioned close to ancient Levantines, while present-day Levantines are drawn toward Bronze Age Europeans. Iraqi-Arabs, Iraqi-Kurds, and Assyrians appear relatively closer to ancient Iranians. We found that most present-day Middle Easterners can be modeled as deriving their ancestry from four ancient populations (Table 1): Levant_N, Neolithic Iranians (GanjDareh_N), Eastern Hunter Gatherers (EHG), and an ∼4,500-year-old East African (Mota). We observed a contrast between the Levant and Arabia: Levantines have excess EHG ancestry (Figure 1E), which we showed previously had arrived in the Levant after the Bronze Age along with people carrying ancient south-east European and Anatolian ancestry (Haber et al., 2017, Haber et al., 2020). Our results here show this ancestry is much higher in the Levant compared to Arabia (Table 1). Another contrast between the Levant and Arabia is the excess of African ancestry in Arabian populations. We found that the closest source of African ancestry for most populations in our dataset is Bantu Speakers from Kenya, in addition to contributions from Nilo-Saharan speakers from Ethiopia. We estimate that African admixture in the Middle East occurred within the last 2,000 years, with most populations showing signals of admixture around 500–1,000 years ago (Figure S1; Table S1), in agreement with previous studies (Hellenthal et al., 2014).

    https://www.cell.com/cell/fulltext/S...674(21)00839-4

    gr1_lrg.jpg
    Last edited by VladimirTaraskin; 08-04-2021 at 02:51 PM.

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