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Thread: New DNA Papers

  1. #901
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    https://www.biorxiv.org/content/earl...medium=twitter

    MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians

    Zoltan Maroti, Tibor Torok, Endre Neparaczki, Istvan Rasko, Istvan Nagy, Miklos Maroti, Tamas Varga, Peter Bihari, Zsolt Boldogkoi, Dora Tombacz, Tibor Kalmar

    doi: https://doi.org/10.1101/247395

    Abstract

    By making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FST calculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXth Hungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.

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  3. #902
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    https://www.nature.com/articles/s41588-017-0031-6

    Reconstructing an African haploid genome from the 18th century

    Anuradha Jagadeesan, Ellen D. Gunnarsdóttir, S. Sunna Ebenesersdóttir, Valdis B. Guðmundsdóttir, Elisabet Linda Thordardottir, Margrét S. Einarsdóttir, Hákon Jónsson, Jean-Michel Dugoujon, Cesar Fortes-Lima, Florence Migot-Nabias, Achille Massougbodji, Gil Bellis, Luisa Pereira, Gísli Másson, Augustine Kong, Kári Stefánsson & Agnar Helgason

    Nature Genetics (2018)
    doi:10.1038/s41588-017-0031-6

    Received: 01 March 2017
    Accepted: 18 December 2017
    Published online: 15 January 2018

    Abstract

    A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ’s maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon.


    UPD: In addition, we used WGS data from a sixth-generation patrilineal descendant of HJ to determine that his Y chromosome belongs to haplogroup I2a2a3a2 (according to the ISOGG 2013 classification system), which has a frequency of 0.15% in Iceland.
    Last edited by rozenfeld; 01-15-2018 at 08:34 PM.

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  5. #903
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    https://www.nature.com/articles/s41598-017-18893-8

    Article | Open

    Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively

    Indu Sharma, Varun Sharma, Akbar Khan, Parvinder Kumar, Ekta Rai, Rameshwar N. K. Bamezai, Miguel Vilar & Swarkar Sharma

    Scientific Reports 8, Article number: 851 (2018)
    doi:10.1038/s41598-017-18893-8

    Received: 23 June 2017
    Accepted: 19 December 2017
    Published online: 16 January 2018

    Abstract

    Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.

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    Estimating time to the common ancestor for a beneficial allele

    Joel Smith1,*, Graham Coop2, Matthew Stephens3,4, and John Novembre3

    Abstract

    The haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele’s age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the sur- rounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to ap- proaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to estimate the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.

    https://watermark.silverchair.com/ms...W_fcBIHfryzczg

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  9. #905
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    Quote Originally Posted by Chad Rohlfsen View Post
    Estimating time to the common ancestor for a beneficial allele

    Joel Smith1,*, Graham Coop2, Matthew Stephens3,4, and John Novembre3

    Abstract

    The haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele’s age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the sur- rounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to ap- proaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to estimate the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.

    https://watermark.silverchair.com/ms...W_fcBIHfryzczg
    That link would not work for me.
    This one does https://www.biorxiv.org/content/early/2016/08/24/071241
    But this is a pre-print from August 2016.
    Could not locate formal publication. Chad, is that what your link connected to?

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    AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs

    AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimisation can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimisation objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.

    https://www.biorxiv.org/content/early/2018/01/20/250837


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    Quote Originally Posted by rozenfeld View Post
    https://www.biorxiv.org/content/earl...medium=twitter

    MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians

    Zoltan Maroti, Tibor Torok, Endre Neparaczki, Istvan Rasko, Istvan Nagy, Miklos Maroti, Tamas Varga, Peter Bihari, Zsolt Boldogkoi, Dora Tombacz, Tibor Kalmar

    doi: https://doi.org/10.1101/247395

    Abstract

    By making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FST calculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXth Hungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.
    Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors

    https://www.biorxiv.org/content/bior...50688.full.pdf
    The possible genetic relation of modern Hungarians to Finno-Ugric groups was tested in several studies [6–8], however all these found Hungarians being genetically unrelated to Uralic people. One of the latest studies [9] reported that a Y-chromosome haplogroup (N-L1034) is shared between 4% of the Hungarian Seklers (Hungarian-speaking ethnic group living in Transylvania) and 15% of the closest language relatives the Mansis, though the same marker is also present in Central Asian Uzbeks and has been detected just in one Hungarian [10]. These results indicated that Uralic genetic links hardly exist in modern Hungarians.

    Our genetic data support the Hun-Conqueror connection which could have been the basis of the historical-cultural Hungarian Hun tradition [3].
    https://www.biorxiv.org/content/early/2018/01/19/250688

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  14. #908
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    https://www.nature.com/articles/s41431-017-0012-3

    Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan

    Lan-Hai Wei, Shi Yan, Yan Lu, Shao-Qing Wen, Yun-Zhi Huang, Ling-Xiang Wang, Shi-Lin Li, Ya-Jun Yang, Xiao-Feng Wang, Chao Zhang, Shu-Hua Xu, Da-Li Yao, Li Jin & Hui Li

    European Journal of Human Genetics (2018)
    doi:10.1038/s41431-017-0012-3

    Received: 17 January 2017
    Revised: 27 July 2017
    Accepted: 23 August 2017
    Published online: 22 January 2018

    Abstract

    The Y-chromosome haplogroup C3*-Star Cluster (revised to C2*-ST in this study) was proposed to be the Y-profile of Genghis Khan. Here, we re-examined the origin of C2*-ST and its associations with Genghis Khan and Mongol populations. We analyzed 34 Y-chromosome sequences of haplogroup C2*-ST and its most closely related lineage. We redefined this paternal lineage as C2b1a3a1-F3796 and generated a highly revised phylogenetic tree of the haplogroup, including 36 sub-lineages and 265 non-private Y-chromosome variants. We performed a comprehensive analysis and age estimation of this lineage in eastern Eurasia, including 18,210 individuals from 292 populations. We discovered that the origin of populations with high frequencies of C2*-ST can be traced to either an ancient Niru’un Mongol clan or ordinary Mongol tribes. Importantly, the age of the most recent common ancestor of C2*-ST (2576 years, 95% CI = 1975–3178) and its sub-lineages, and their expansion patterns, are consistent with the diffusion of all Mongolic-speaking populations, rather than Genghis Khan himself or his close male relatives. We concluded that haplogroup C2*-ST is one of the founder paternal lineages of all Mongolic-speaking populations, and direct evidence of an association between C2*-ST and Genghis Khan has yet to be discovered.

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    Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance

    Juan C. Chacon-Duque, View ORCID ProfileKaustubh Adhikari, Macarena Fuentes-Guajardo, Javier Mendoza-Revilla, Victor Acuna-Alonzo, Rodrigo Barquera Lozano, Mirsha Quinto-Sanchez, Jorge Gomez-Valdes, Paola Everardo Martinez, Hugo Villamil-Ramirez, Tabita Hunemeier, Virginia Ramallo, Caio C. Silva de Cerqueira, Malena Hurtado, Valeria Villegas, Vanessa Granja, Mercedes Villena, Rene Vasquez, Elena Llop, Jose R. Sandoval, Alberto A. Salazar-Granara, Maria-Laura Parolin, Karla Sandoval, Rosenda I. Penaloza-Espinosa, Hector Rangel-Villalobos, Cheryl Winkler, William Klitz, Claudio Bravi, Julio Molina, Daniel Corach, Ramiro Barrantes, Veronica Gomes, Carlos Resende, Leonor Gusmao, Antonio Amorim, Yali Xue, Jean-Michel Dugoujon, Pedro Moral, Rolando Gonzalez-Jose, Lavinia Schuler-Faccini, Francisco M. Salzano, Maria-Catira Bortolini, Samuel Canizales-Quinteros, Giovanni Poletti, Carla Gallo, Gabriel Bedoya, Francisco Rothhammer, David Balding, Garrett Hellenthal, Andres Ruiz-Linares
    doi: https://doi.org/10.1101/252155

    Abstract

    Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry on the physical appearance of these individuals. We find that pre-Columbian Native genetic structure is mirrored in Latin Americans 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 from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that Central Andean ancestry impacts on variation of facial features in Latin Americans, particularly nose morphology, possibly relating to environmental adaptation during the evolution of Native Americans.

    https://www.biorxiv.org/content/early/2018/01/23/252155

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  18. #910
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    http://onlinelibrary.wiley.com/doi/1...jpa.23374/full

    Residence rule flexibility and descent groups dynamics shape uniparental genetic diversities in South East Asia

    First published: 23 January 2018
    DOI: 10.1002/ajpa.23374

    Abstract

    Objectives

    Social organization plays a major role in shaping human population genetic diversity. In particular, matrilocal populations tend to exhibit less mitochondrial diversity than patrilocal populations, and the other way around for Y chromosome diversity. However, several studies have not replicated such findings. The objective of this study is to understand the reasons for such inconsistencies and further evaluate the influence of social organization on genetic diversity.

    Materials and Methods

    We explored uniparental diversity patterns using mitochondrial HV1 sequences and 17 Y-linked short tandem repeats (STRs) in 12 populations (n = 619) from mainland South–East Asia exhibiting a wide range of social organizations, along with quantitative ethno-demographic information sampled at the individual level.

    Results

    MtDNA diversity was lower in matrilocal than in multilocal and patrilocal populations while Y chromosome diversity was similar among these social organizations. The reasons for such asymmetry at the genetic level were understood by quantifying sex-specific migration rates from our ethno-demographic data: while female migration rates varied between social organizations, male migration rates did not. This unexpected lack of difference in male migrations resulted from a higher flexibility in residence rule in patrilocal than in matrilocal populations. In addition, our data suggested an impact of clan fission process on uniparental genetic patterns.

    Conclusions

    The observed lack of signature of patrilocality on Y chromosome patterns might be attributed to the higher residence flexibility in the studied patrilocal populations, thus providing a potential explanation for the apparent discrepancies between social and genetic structures. Altogether, this study highlights the need to quantify the actual residence and descent patterns to fit social to genetic structures.

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