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      Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia

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          Abstract

          Hungarians who live in Central Europe today are one of the westernmost Uralic speakers. Despite of the proposed Volga-Ural/West Siberian roots of the Hungarian language, the present-day Hungarian gene pool is highly similar to that of the surrounding Indo-European speaking populations. However, a limited portion of specific Y-chromosomal lineages from haplogroup N, sometimes associated with the spread of Uralic languages, link modern Hungarians with populations living close to the Ural Mountain range on the border of Europe and Asia. Here we investigate the paternal genetic connection between these spatially separated populations. We reconstruct the phylogeny of N3a4-Z1936 clade by using 33 high-coverage Y-chromosomal sequences and estimate the coalescent times of its sub-clades. We genotype close to 5000 samples from 46 Eurasian populations to show the presence of N3a4-B539 lineages among Hungarians and in the populations from Ural Mountain region, including Ob-Ugric-speakers from West Siberia who are geographically distant but linguistically closest to Hungarians. This sub-clade splits from its sister-branch N3a4-B535, frequent today among Northeast European Uralic speakers, 4000–5000 ya, which is in the time-frame of the proposed divergence of Ugric languages.

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          Most cited references 48

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Primer3—new capabilities and interfaces

            Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
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              Bayesian Phylogenetics with BEAUti and the BEAST 1.7

              Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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                Author and article information

                Contributors
                helen2po@ut.ee
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                24 May 2019
                24 May 2019
                2019
                : 9
                Affiliations
                [1 ]ISNI 0000 0001 0943 7661, GRID grid.10939.32, Institute of Genomics, Estonian Biocentre, , University of Tartu, ; Tartu, 51010 Estonia
                [2 ]ISNI 0000 0001 1498 9209, GRID grid.424755.5, Hungarian Natural History Museum, Department of Anthropology, ; Budapest, 1083 Hungary
                [3 ]ISNI 0000 0001 2294 6276, GRID grid.5591.8, Eötvös Loránd University Budapest, Department of Finno-Ugric Studies, ; Budapest, 1088 Hungary
                [4 ]ISNI 0000 0001 0807 2090, GRID grid.425397.e, Pázmány Péter Catholic University, Faculty of Humanities and Social Sciences, Department of Early Hungarian and Migration Period Archaeology, ; Piliscsaba, 2087 Hungary
                [5 ]ISNI 0000 0004 0451 5175, GRID grid.429238.6, Laboratory of Ethnogenomics, Institute of Molecular Biology of National Academy of Sciences, ; Yerevan, 0014 Armenia
                [6 ]Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054 Russia
                [7 ]ISNI 0000 0001 1015 7624, GRID grid.77269.3d, Department of Genetics and Fundamental Medicine, , Bashkir State University, ; Ufa, 450054 Russia
                [8 ]ISNI 0000 0001 0943 7661, GRID grid.10939.32, Department of Evolutionary Biology, Institute of Molecular and Cellular Biology, , University of Tartu, ; Tartu, 51010 Estonia
                Article
                44272
                10.1038/s41598-019-44272-6
                6534673
                31127140
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: FundRef https://doi.org/10.13039/501100002301, Eesti Teadusagentuur (Estonian Research Council);
                Award ID: PRG243
                Award ID: PRG243
                Award ID: PRG243
                Award ID: PRG243
                Award ID: PUT1217
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100008530, EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj);
                Award ID: 2014-2020.4.01.16-0125
                Award ID: 2014-2020.4.01.16-0771
                Award ID: 2014-2020.4.01.16-0030
                Award ID: 2014-2020.4.01.16-0030
                Award ID: 2014-2020.4.01.15-0012
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100005189, Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council);
                Award ID: IUT24-1
                Award ID: IUT24-1
                Award ID: IUT24-1
                Award ID: IUT24-1
                Award ID: IUT24-1
                Award ID: IUT24-1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100003443, Ministry of Education and Science of the Russian Federation (Minobrnauka);
                Award ID: №АААА-А16-116020350032-1
                Award Recipient :
                Categories
                Article
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                © The Author(s) 2019

                Uncategorized

                evolution, population genetics

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