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Thread: New DNA Papers

  1. #1421
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    Caiyong Yin, Kaiyuan Su, Ziwei He, Dian Zhai, Kejian Guo, Xueyun Chen, Li Jin, and Shilin Li, "Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs." Genes 2020, 11, 743; doi:10.3390/genes11070743.

    Received: 21 May 2020; Accepted: 2 July 2020; Published: 3 July 2020

    Abstract: Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic
    applications, such as pedigree source searching from public security databases and male identification
    from male–female mixed samples. For various populations, databases composed of Y-STR
    haplotypes have been built to provide investigating leads for solving difficult or cold cases.
    Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide
    polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR
    haplotypes for 27 markers typed by the Yfiler™— Plus kit and Y-SNP haplogroups defined by 24 loci
    within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565)
    populations. The genetic backgrounds of these two populations were explicitly characterized by
    the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on
    27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies
    and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution
    spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia
    alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR
    allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network
    was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation
    event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of
    the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic
    backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering
    detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs
    in population differentiation and male pedigree discrimination.

    Keywords: population investigation; Y-STR; Y-SNP; population differentiation

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  3. #1422
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    origins of the present Malagasy population

    Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population
    Margit Heiske, Omar Alva, Veronica Pereda-Loth, Matthew Van Schalkwyk, Chantal Radimilahy, Thierry Letellier, Jean-Aimé Rakotarisoa, Denis Pierron

    Abstract
    The origin of the Malagasy population has been a subject of speculation since the 16th century. Contributions of African, Asian, Indian, Melanesian, Arabic, Persian populations have been suggested based on physical and cultural anthropology, oral tradition, linguistics and later also by archaeology. In the mid-20th century, increased knowledge of heredity rules and technical progress enabled the identification of African and Asian populations as main contributors. Recent access to the genomic landscape of Madagascar demonstrated pronounced regional variability in the relative contributions of these two ancestries, yet with significant presence of both African and Asian components throughout Madagascar. This article reviews the extent to which genetic results have settled historical questions concerning the origin of the Malagasy population. After an overview of the early literature, the genetic results of the 20th and 21th centuries are discussed and then complemented by the latest results in genome-wide analyses. While there is still much uncertainty regarding when, how and the circumstances under which the ancestors of the modern Malagasy population arrived on the island, we propose a scenario based on historical texts and genomic results.
    YFull: YF14620 (Dante Labs 2018)

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  5. #1423
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    Decomposing the admixture statistic, D, suggests a negligible contribution due to archaic introgression into humans.

    Abstract:It is widely accepted that non-African humans carry a few percent of Neanderthal DNA due to historical inter-breeding. However, methods used to infer a legacy all assume that mutation rate is constant and that back-mutations can be ignored. Here I decompose the widely used admixture statistic, D, in a way that allows the overall signal to be apportioned to different classes of contributing site. I explore three main characteristics: whether the putative Neanderthal allele is likely derived or ancestral; whether an allele is fixed in one of the two human populations; and the type of mutation that created the polymorphism, defined by the base that mutated and immediately flanking bases. The entire signal used to infer introgression can be attributed to a subset of sites where the putative Neanderthal base is common in Africans and fixed in non-Africans. Moreover, the four triplets containing highly mutable CpG motifs alone contribute 29%. In contrast, sites expected to dominate the signal if introgression has occurred, where the putative Neanderthal allele is absent from Africa and rare outside Africa, contribute negligibly. Together, these observations show that D does not capture a signal due to introgression but instead they support an alternative model in which a higher mutation rate in Africa drives increased divergence from the ancestral state.

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    Comparision Study of Iraqi populations In Middle-Euphrates with Haplotype reference

    Comparision Study of Iraqi populations In Middle-Euphrates with Haplotype reference Database (YHRD) and study their Haplogroups
    Mohammed zuhair Naji, Ali Hmood Al-Saadi. Biology department of science in University of Babylon, Babylon, Iraq. - (Sep 2020)

    Abstract:
    In this study, a sample of 144 persons lived in middle-Euphrates of Iraq population was analyzed using 5 Y-chromosome short tandem repeat (STR) polymorphisms. The results Comparison with (YHRD) showed that there are 44 match with 307,169 Haplotypes, the highest match was in haplotype H13 it record 4707 match with 83 countries. In study Analysis of AMOVA and MDS plots show the Kuwait (from Arabia population) and Japan (over world population) were more closed to Iraqi population with same cluster plot. The sixty two haplotypes sorted in six main haplogroups (E, G, I, J, Q and R). haplogroup J was the biggest one in compare with other haplogroup and include all Hashemites sub-population.

    A long story short:
    This population (n=144) was separated to two sub-population Hashemites (n=72) with results arranged as Haplotypes (H1 - H10) and Commoners (Non- Hashemites) sub-population (n=72), the study provided the first detailed Haplogroup downstreams for Iraqi's using NevGen predictor. It's also noted the absence of J-FGC11 and any J-Z2331 lineages among the Hashemites and general Iraqis in exception of H19 representing a non Hashemite sample. Here is another version for the paper.

    Attached Images Attached Images
    Last edited by The Saite; 01-23-2021 at 02:58 PM.
    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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  9. #1425
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    Atif Adnan, Kaidirina Kasimu, Allah Rakha, Guanglin He, Tongya Yang, Chuan-Chao Wang, Jie Lu, and Jin-feng Xuan, "Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs." Mol Genet Genomic Med. 2020;8:e1149. DOI: 10.1002/mgg3.1149.

    Abstract

    Background: Dalian is a city formed in the 1880s in Liaoning province, Northeastern
    China with a population of 6.69 million now. Han is the largest ethnic group not only
    across Mainland China (92%) and Taiwan (97%) but also considered to be the largest
    ethnic group of the world contributing to above 18% of world's population.

    Methods: In the current study, we genotyped Goldeneye® 20Y System loci in 879
    unrelated male individuals from the Han ethnic group in Dalian city and calculated
    the forensic parameters of the 20 Y-STR loci.

    Results: In total, we observed 855 haplotypes, among which 835 (94.99%) were
    unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is
    97.27% and it slightly reduces to 96.93% when only Y-filer® set of 17 Y-STRs were
    used, which mitigates using the extended set of markers in this population. We found
    DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed
    the highest gene diversity (0.7621) in single copy Y-STR, and DYS385 showed the
    highest gene diversity (0.9683) among all.

    Conclusion: Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic
    distance showed difference among Han population from the east to the west and
    from the north to the south. We also predicted haplogroups using Y-STR haplotypes,
    which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup
    C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a
    null allele at the DYS448 in our samples. We also performed linear discriminatory
    analysis (LDA) between Han and other prominent Chinese minority ethnic groups.
    We presented Y-STRs data in the Y-Chromosome Haplotype Reference Database
    (YHRD) for the future forensic and other usage.

    KEYWORDS
    Dalian, forensic genetics, Han, O haplogroup, Y-Chromosome Haplotype Reference Database (YHRD), Y-STRs

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  11. #1426
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    Quote Originally Posted by The Saite View Post
    Comparision Study of Iraqi populations In Middle-Euphrates with Haplotype reference Database (YHRD) and study their Haplogroups
    Mohammed zuhair Naji, Ali Hmood Al-Saadi. Biology department of science in University of Babylon, Babylon, Iraq. - (Sep 2020)

    Abstract:
    In this study, a sample of 144 persons lived in middle-Euphrates of Iraq population was analyzed using 5 Y-chromosome short tandem repeat (STR) polymorphisms. The results Comparison with (YHRD) showed that there are 44 match with 307,169 Haplotypes, the highest match was in haplotype H13 it record 4707 match with 83 countries. In study Analysis of AMOVA and MDS plots show the Kuwait (from Arabia population) and Japan (over world population) were more closed to Iraqi population with same cluster plot. The sixty two haplotypes sorted in six main haplogroups (E, G, I, J, Q and R). haplogroup J was the biggest one in compare with other haplogroup and include all Hashemites sub-population.

    A long story short:
    This population (n=144) was separated to two sub-population Hashemites (n=72) with results arranged as Haplotypes (H1 - H10) and Commoners (Non- Hashemites) sub-population (n=72), the study provided the first detailed Haplogroup downstreams for Iraqi's using NevGen predictor. It's also noted the absence of J-FGC11 and any J-Z2331 lineages among the Hashemites and general Iraqis in exception of H19 representing a non Hashemite sample. Here is another version for the paper.

    5 STRs...Wow.

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  13. #1427
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    A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution

    A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
    Douyue Li, Saichao Pan, Hongxi Zhang, Yongzhuo Fu, Zhuli Peng, Liang Zhang, Shan Peng, Fei Xu, Hanrou Huang, Ruixue Shi, Heping Zheng, Yousong Peng, Zhongyang Tan

    Abstract
    Background: Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences.

    Results: The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA.

    Conclusions: These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.
    YFull: YF14620 (Dante Labs 2018)

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  15. #1428
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    Accurate and fast familial relationship inference in large scale biobank studies

    RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID
    Ardalan Naseri ,Junjie Shi,Xihong Lin,Shaojie Zhang,Degui Zhi

    Abstract
    Inference of relationships from whole-genome genetic data of a cohort is a crucial prerequisite for genome-wide association studies. Typically, relationships are inferred by computing the kinship coefficients (ϕ) and the genome-wide probability of zero IBD sharing (π0) among all pairs of individuals. Current leading methods are based on pairwise comparisons, which may not scale up to very large cohorts (e.g., sample size >1 million). Here, we propose an efficient relationship inference method, RAFFI. RAFFI leverages the efficient RaPID method to call IBD segments first, then estimate the ϕ and π0 from detected IBD segments. This inference is achieved by a data-driven approach that adjusts the estimation based on phasing quality and genotyping quality. Using simulations, we showed that RAFFI is robust against phasing/genotyping errors, admix events, and varying marker densities, and achieves higher accuracy compared to KING, the current leading method, especially for more distant relatives. When applied to the phased UK Biobank data with ~500K individuals, RAFFI is approximately 18 times faster than KING. We expect RAFFI will offer fast and accurate relatedness inference for even larger cohorts.

    Author summary
    Inferring familial relationships has a wide range of applications. Family-based genome-wide association studies and population-based GWAS both require genetic relationships. Inferring relationship is essential for unknown familial structures and can be used to correct pedigree information due to false paternity, sample switches, or unregistered adoption. Current approaches for inferring relationships are not scalable for large cohorts comprising millions of individuals. Here, we present a fast and flexible method, called RAFFI, using Identical by Descent (IBD) segments. IBD segments are uninterrupted DNA segments inherited from a common ancestor. Relationships are usually inferred by computing the kinship coefficients and the genome-wide probability of zero IBD sharing among all pairs of individuals. In the first step, we search for IBD segments using RaPID which avoids a pairwise comparison of all individuals in a haplotype panel. In the second step, we compute the kinship coefficients to infer the relationships. To make our method robust against genotyping and phasing error, the thresholds of kinship coefficients for different degrees of relatedness are adjusted. As a result, the lower detection power of IBD segments due to phasing errors or misspecification of the genotyping error rate will not comprise the inference of relationships.
    YFull: YF14620 (Dante Labs 2018)

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  17. #1429
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    Estimating divergence times from DNA sequences

    Estimating divergence times from DNA sequences
    Per Sjödin, James McKenna, Mattias Jakobsson
    Abstract
    The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the ‘Two-Two (TT)’ and the ‘Two-Two-outgroup (TTo)’ methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split-times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo-method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.
    YFull: YF14620 (Dante Labs 2018)

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  19. #1430
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    Medieval Super-Grandfather founder of Western Kazakh Clans from Haplogroup C2a1a2-M48

    Abstract

    Western Kazakhstan is populated by three clans totaling 2 million people. Since the clans are patrilineal, the Y-chromosome is the most informative genetic system for tracing their origin. We genotyped 40 Y-SNP and 17 Y-STR markers in 330 Western Kazakhs. High phylogenetic resolution within haplogroup C2a1a2-M48 was achieved by using additional SNPs. Three lines of evidence indicate that the Alimuly and Baiuly clans (but not the Zhetiru clan) have a common founder placed 700 ± 200 years back by the STR data and 500 ± 200 years back by the sequencing data. This supports traditional genealogy claims about the descent of these clans from Emir Alau, who lived 650 years ago and whose lineage might be carried by two-thirds of Western Kazakhs. There is accumulation of specific haplogroups in the subclans representing other lineages, confirming that the clan structure corresponds with the paternal genetic structure of the steppe population.

    https://www.nature.com/articles/s10038-021-00901-5

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