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Gretzinger J, Schmitt F, Mötsch A, Carlhoff S, Lamnidis TC, Huang Y, Ringbauer H, Knipper C, Francken M, Mandt F, Hansen L, Freund C, Posth C, Rathmann H, Harvati K, Wieland G, Granehäll L, Maixner F, Zink A, Schier W, Krausse D, Krause J, Schiffels S. Evidence for dynastic succession among early Celtic elites in Central Europe. Nat Hum Behav 2024:10.1038/s41562-024-01888-7. [PMID: 38831077 DOI: 10.1038/s41562-024-01888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
The early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the 'West-Hallstattkreis', stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as 'early Celtic', suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felicitas Schmitt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Angela Mötsch
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Selina Carlhoff
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Corina Knipper
- Curt Engelhorn Zentrum Archäometrie gGmbH, Mannheim, Germany
| | - Michael Francken
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Franziska Mandt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Leif Hansen
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Hannes Rathmann
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Katerina Harvati
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
- DFG Center for Advanced Studies in the Humanities 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Günther Wieland
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Lena Granehäll
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Wolfram Schier
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Dirk Krausse
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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2
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Hodișan R, Zaha DC, Jurca CM, Petchesi CD, Bembea M. Genetic Diversity Based on Human Y Chromosome Analysis: A Bibliometric Review Between 2014 and 2023. Cureus 2024; 16:e58542. [PMID: 38887511 PMCID: PMC11182565 DOI: 10.7759/cureus.58542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2024] [Indexed: 06/20/2024] Open
Abstract
The Y chromosome has gained significant importance in the examination of genetic studies of populations because of its non-recombinant character and its form of uniparental inheritance. This work seeks to offer a comprehensive review of the specialty literature in the field of population genetics, focusing specifically on the analysis of the human Y chromosome using a bibliometric approach and knowledge mapping. This involves establishing worldwide structural networks by identifying the primary research themes, authors, and papers that have had a significant impact on the academic community. The objective is to examine global publications by analyzing citations at both the document and country level. This will involve conducting co-citation analysis for references with a high number of citations, examining bibliographic coupling through journal analysis, analyzing the co-occurrence of keywords, and investigating collaboration between authors from a country perspective. The research papers have been extracted from the Web of Science database. The bibliometric analysis was performed using the Bibliometrix and VOSviewer software tools. The purpose of this article is to serve as a starting point for future research dedicated to the analysis of the diversity of human Y chromosome haplotypes. The objectives of the study were to identify and present the most cited publications and references with the highest number of citations, and to highlight current publications at the national level.
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Affiliation(s)
- Ramona Hodișan
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Dana C Zaha
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Claudia M Jurca
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Codruta D Petchesi
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Marius Bembea
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
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3
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Yanus GA, Sokolenko AP, Imyanitov EN. Northern origin of the BRCA2 c.5286 T > G founder allele. Breast Cancer Res Treat 2024; 204:191. [PMID: 38062337 DOI: 10.1007/s10549-023-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 01/24/2024]
Affiliation(s)
- Grigory A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Litovskaya, 2, Russia, 194100
| | - Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758.
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Litovskaya, 2, Russia, 194100.
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St. Petersburg, Russia, 197758
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Litovskaya, 2, Russia, 194100
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4
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Reščenko R, Brīvība M, Atava I, Rovīte V, Pečulis R, Silamiķelis I, Ansone L, Megnis K, Birzniece L, Leja M, Xu L, Shi X, Zhou Y, Slaitas A, Hou Y, Kloviņš J. Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation. Int J Mol Sci 2023; 24:15345. [PMID: 37895026 PMCID: PMC10607061 DOI: 10.3390/ijms242015345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Despite rapid improvements in the accessibility of whole-genome sequencing (WGS), understanding the extent of human genetic variation is limited by the scarce availability of genome sequences from underrepresented populations. Developing the population-scale reference database of Latvian genetic variation may fill the gap in European genomes and improve human genomics research. In this study, we analysed a high-coverage WGS dataset comprising 502 individuals selected from the Genome Database of the Latvian Population. An assessment of variant type, location in the genome, function, medical relevance, and novelty was performed, and a population-specific imputation reference panel (IRP) was developed. We identified more than 18.2 million variants in total, of which 3.3% so far are not represented in gnomAD and dbSNP databases. Moreover, we observed a notable though distinct clustering of the Latvian cohort within the European subpopulations. Finally, our findings demonstrate the improved performance of imputation of variants using the Latvian population-specific reference panel in the Latvian population compared to established IRPs. In summary, our study provides the first WGS data for a regional reference genome that will serve as a resource for the development of precision medicine and complement the global genome dataset, improving the understanding of human genetic variation.
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Affiliation(s)
- Raimonds Reščenko
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivanna Atava
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Vita Rovīte
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Raitis Pečulis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivars Silamiķelis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Līga Birzniece
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Mārcis Leja
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia;
- Institute of Clinical and Preventive Medicine, University of Latvia, LV-1079 Riga, Latvia
| | - Liqin Xu
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Xulian Shi
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yan Zhou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Andis Slaitas
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yong Hou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
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5
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Kloska A, Giełczyk A, Grzybowski T, Płoski R, Kloska SM, Marciniak T, Pałczyński K, Rogalla-Ładniak U, Malyarchuk BA, Derenko MV, Kovačević-Grujičić N, Stevanović M, Drakulić D, Davidović S, Spólnicka M, Zubańska M, Woźniak M. A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe. Int J Mol Sci 2023; 24:15095. [PMID: 37894775 PMCID: PMC10606184 DOI: 10.3390/ijms242015095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used-Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846-1.000 for all classes.
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Affiliation(s)
- Anna Kloska
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland
- Faculty of Medical Sciences, Bydgoszcz University of Science and Technology, 85796 Bydgoszcz, Poland
| | - Agata Giełczyk
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85796 Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, 02106 Warsaw, Poland
| | - Sylwester M. Kloska
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland
- Faculty of Medical Sciences, Bydgoszcz University of Science and Technology, 85796 Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85796 Bydgoszcz, Poland
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85796 Bydgoszcz, Poland
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland
| | - Boris A. Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, 685000 Magadan, Russia
| | - Miroslava V. Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, 685000 Magadan, Russia
| | - Nataša Kovačević-Grujičić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
| | - Milena Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
- Serbian Academy of Sciences and Arts, 11000 Belgrade, Serbia
| | - Danijela Drakulić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
| | - Slobodan Davidović
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | | | - Magdalena Zubańska
- Faculty of Law and Administration, Department of Criminology and Forensic Sciences, University of Warmia and Mazury, 10726 Olsztyn, Poland
| | - Marcin Woźniak
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland
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6
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Stolarek I, Zenczak M, Handschuh L, Juras A, Marcinkowska-Swojak M, Spinek A, Dębski A, Matla M, Kóčka-Krenz H, Piontek J, Figlerowicz M. Genetic history of East-Central Europe in the first millennium CE. Genome Biol 2023; 24:173. [PMID: 37488661 PMCID: PMC10364380 DOI: 10.1186/s13059-023-03013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). RESULTS To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. CONCLUSIONS The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe.
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Affiliation(s)
- Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | | | - Anna Spinek
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Artur Dębski
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Marzena Matla
- Department of History, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Hanna Kóčka-Krenz
- Department of Archaeology, Collegium Historicum, Adam Mickiewicz University, Poznan, Poland
| | - Janusz Piontek
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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7
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Wilke F, Herrick N, Matthews H, Hoskens H, Singh S, Shaffer JR, Weinberg SM, Shriver MD, Claes P, Walsh S. Exploring regional aspects of 3D facial variation within European individuals. Sci Rep 2023; 13:3708. [PMID: 36879022 PMCID: PMC9988837 DOI: 10.1038/s41598-023-30855-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Facial ancestry can be described as variation that exists in facial features that are shared amongst members of a population due to environmental and genetic effects. Even within Europe, faces vary among subregions and may lead to confounding in genetic association studies if unaccounted for. Genetic studies use genetic principal components (PCs) to describe facial ancestry to circumvent this issue. Yet the phenotypic effect of these genetic PCs on the face has yet to be described, and phenotype-based alternatives compared. In anthropological studies, consensus faces are utilized as they depict a phenotypic, not genetic, ancestry effect. In this study, we explored the effects of regional differences on facial ancestry in 744 Europeans using genetic and anthropological approaches. Both showed similar ancestry effects between subgroups, localized mainly to the forehead, nose, and chin. Consensus faces explained the variation seen in only the first three genetic PCs, differing more in magnitude than shape change. Here we show only minor differences between the two methods and discuss a combined approach as a possible alternative for facial scan correction that is less cohort dependent, more replicable, non-linear, and can be made open access for use across research groups, enhancing future studies in this field.
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Affiliation(s)
- Franziska Wilke
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Noah Herrick
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Sylvia Singh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA.
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8
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Albert EA, Kondratieva OA, Baranova EE, Sagaydak OV, Belenikin MS, Zobkova GY, Kuznetsova ES, Deviatkin AA, Zhurov AA, Karpulevich EA, Volchkov PY, Vorontsova MV. Transferability of the PRS estimates for height and BMI obtained from the European ethnic groups to the Western Russian populations. Front Genet 2023; 14:1086709. [PMID: 36726807 PMCID: PMC9885218 DOI: 10.3389/fgene.2023.1086709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Genetic data plays an increasingly important role in modern medicine. Decrease in the cost of sequencing with subsequent increase in imputation accuracy, and the accumulation of large amounts of high-quality genetic data enable the creation of polygenic risk scores (PRSs) to perform genotype-phenotype associations. The accuracy of phenotype prediction primarily depends on the overall trait heritability, Genome-wide association studies cohort size, and the similarity of genetic background between the base and the target cohort. Here we utilized 8,664 high coverage genomic samples collected across Russia by "Evogen", a Russian biomedical company, to evaluate the predictive power of PRSs based on summary statistics established on cohorts of European ancestry for basic phenotypic traits, namely height and BMI. We have demonstrated that the PRSs calculated for selected traits in three distinct Russian populations, recapitulate the predictive power from the original studies. This is evidence that GWAS summary statistics calculated on cohorts of European ancestry are transferable onto at least some ethnic groups in Russia.
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Affiliation(s)
- E. A. Albert
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia,*Correspondence: E. A. Albert,
| | - O. A. Kondratieva
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | | - A. A. Deviatkin
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - A. A. Zhurov
- National Medical Research Center for Endocrinology, Moscow, Russia
| | - E. A. Karpulevich
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
| | - P. Y. Volchkov
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - M. V. Vorontsova
- National Medical Research Center for Endocrinology, Moscow, Russia
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9
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Peltola S, Majander K, Makarov N, Dobrovolskaya M, Nordqvist K, Salmela E, Onkamo P. Genetic admixture and language shift in the medieval Volga-Oka interfluve. Curr Biol 2023; 33:174-182.e10. [PMID: 36513080 DOI: 10.1016/j.cub.2022.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.1,2,3 A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9th century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.4,5,6 In the 10th-11th centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.3 This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.
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Affiliation(s)
- Sanni Peltola
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Kerttu Majander
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Kerkko Nordqvist
- Department of Cultures, Archaeology, University of Helsinki, 00014 Helsinki, Finland
| | - Elina Salmela
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Biology, University of Turku, 20014 Turku, Finland
| | - Päivi Onkamo
- Department of Biology, University of Turku, 20014 Turku, Finland.
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10
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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11
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Yanus GA, Savonevich EL, Sokolenko AP, Romanko AA, Ni VI, Bakaeva EK, Gorustovich OA, Bizin IV, Imyanitov EN. Founder vs. non-founder BRCA1/2 pathogenic alleles: the analysis of Belarusian breast and ovarian cancer patients and review of other studies on ethnically homogenous populations. Fam Cancer 2023; 22:19-30. [PMID: 35596902 DOI: 10.1007/s10689-022-00296-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/08/2022] [Indexed: 01/13/2023]
Abstract
The spectrum of BRCA1/2 mutations demonstrates significant interethnic variations. We analyzed for the first time the entire BRCA1/2 coding region in 340 Belarusian cancer patients with clinical signs of BRCA1/2-related disease, including 168 women with bilateral and/or early-onset breast cancer (BC), 104 patients with ovarian cancer and 68 subjects with multiple primary malignancies involving BC and/or OC. BRCA1/2 pathogenic alleles were detected in 98 (29%) women, with 67 (68%) of these being represented by founder alleles. Systematic comparison with other relevant studies revealed that the founder effect observed in Belarus is among the highest estimates observed worldwide. These findings are surprising, given that the population of Belarus did not experience geographic or cultural isolation throughout history.
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Affiliation(s)
- G A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E L Savonevich
- Department of Obstetrics and Gynecology, Grodno State Medical University, Grodno, Belarus
| | - A P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia. .,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.
| | - A A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| | - V I Ni
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E Kh Bakaeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - O A Gorustovich
- Department of Obstetrics and Gynecology, Grodno State Medical University, Grodno, Belarus
| | - I V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - E N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.,Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia
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12
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Maréchal L, Dumoncel J, Santos F, Astudillo Encina W, Evteev A, Prevost A, Toro-Ibacache V, Venter RG, Heuzé Y. New insights into the variability of upper airway morphology in modern humans. J Anat 2022; 242:781-795. [PMID: 36585765 PMCID: PMC10093156 DOI: 10.1111/joa.13813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 01/01/2023] Open
Abstract
The biological adaptation of the human lineage to its environment is a recurring question in paleoanthropology. Particularly, how eco-geographic factors (e.g., environmental temperature and humidity) have shaped upper airway morphology in hominins have been subject to continuing debate. Nasal shape is the result of many intertwined factors that include, but are not limited to, genetic drift, sexual selection, or adaptation to climate. A quantification of nasal airway (NA) morphological variation in modern human populations is crucial to better understand these multiple factors. In the present research, we study 195 in vivo CT scans of adult individuals collected in five different geographic areas (Chile, France, Cambodia, Russia, and South Africa). After segmentation of the nasal airway, we reconstruct 3D meshes that are analyzed with a landmark-free geometric morphometrics method based on surface deformation. Our results highlight subtle but statistically significant morphological differences between our five samples. The two morphologically closest groups are France and Russia, whose NAs are longer and narrower, with an important protrusion of the supero-anterior part. The Cambodian sample is the most morphologically distinct and clustered sample, with a mean NA that is wider and shorter. On the contrary, the Chilean sample form the most scattered cluster with the greatest intra-population variation. The South African sample is morphologically close to the Cambodian sample, but also partially overlaps the French and Russian variation. Interestingly, we record no correlation between NA volume and geographic groups, which raises the question of climate-related metabolic demands for oxygen consumption. The other factors of variation (sex and age) have no influence on the NA shape in our samples. However, NA volume varies significantly according both to sex and age: it is higher in males than in females and tends to increase with age. In contrast, we observe no effect of temperature or humidity on NA volume. Finally, we highlight the important influence of asymmetries related to nasal septum deviations in NA shape variation.
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Affiliation(s)
- Laura Maréchal
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
| | - Jean Dumoncel
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
| | - Frédéric Santos
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
| | | | - Andrej Evteev
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Alice Prevost
- Plastic and Maxillo-facial Surgery Department, University Hospital Center of Toulouse, Toulouse, France
| | - Viviana Toro-Ibacache
- Centro de Análisis Cuantitativo en Antropología Dental, Universidad de Chile, Santiago, Chile
| | - Rudolph G Venter
- Division of Orthopaedic Surgery, Department of Surgical Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - Yann Heuzé
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
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13
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Gretzinger J, Sayer D, Justeau P, Altena E, Pala M, Dulias K, Edwards CJ, Jodoin S, Lacher L, Sabin S, Vågene ÅJ, Haak W, Ebenesersdóttir SS, Moore KHS, Radzeviciute R, Schmidt K, Brace S, Bager MA, Patterson N, Papac L, Broomandkhoshbacht N, Callan K, Harney É, Iliev L, Lawson AM, Michel M, Stewardson K, Zalzala F, Rohland N, Kappelhoff-Beckmann S, Both F, Winger D, Neumann D, Saalow L, Krabath S, Beckett S, Van Twest M, Faulkner N, Read C, Barton T, Caruth J, Hines J, Krause-Kyora B, Warnke U, Schuenemann VJ, Barnes I, Dahlström H, Clausen JJ, Richardson A, Popescu E, Dodwell N, Ladd S, Phillips T, Mortimer R, Sayer F, Swales D, Stewart A, Powlesland D, Kenyon R, Ladle L, Peek C, Grefen-Peters S, Ponce P, Daniels R, Spall C, Woolcock J, Jones AM, Roberts AV, Symmons R, Rawden AC, Cooper A, Bos KI, Booth T, Schroeder H, Thomas MG, Helgason A, Richards MB, Reich D, Krause J, Schiffels S. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 2022; 610:112-119. [PMID: 36131019 PMCID: PMC9534755 DOI: 10.1038/s41586-022-05247-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | | | - Maria Pala
- University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- University of Huddersfield, Huddersfield, UK
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ceiridwen J Edwards
- University of Huddersfield, Huddersfield, UK
- University of Oxford, Oxford, UK
| | | | - Laura Lacher
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susanna Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Åshild J Vågene
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Haak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Rita Radzeviciute
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Martina Abenhus Bager
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luka Papac
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Frank Both
- Landesmuseum Natur und Mensch, Oldenburg, Germany
| | | | | | - Lars Saalow
- Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany
| | - Stefan Krabath
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK
- Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Neil Faulkner
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Chris Read
- The Atlantic Technological University, Sligo, Ireland
| | | | | | | | | | | | - Verena J Schuenemann
- University of Zurich, Zurich, Switzerland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | - Andrew Richardson
- Canterbury Archaeological Trust, Canterbury, UK
- Isle Heritage CIC, Sandgate, UK
| | | | | | | | | | - Richard Mortimer
- Oxford Archaeology East, Cambridge, UK
- Cotswold Archaeology, Needham Market, UK
| | - Faye Sayer
- University of Birmingham, Birmingham, UK
| | - Diana Swales
- Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK
| | | | | | - Robert Kenyon
- East Dorset Antiquarian Society (EDAS), West Bexington, UK
| | - Lilian Ladle
- Department of Archaeology and Anthropology, Bournemouth University, Poole, UK
| | - Christina Peek
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | | | | | | | | | | | | | | | | | - Anooshka C Rawden
- Fishbourne Roman Palace, Fishbourne, UK
- South Downs Centre, Midhurst, UK
| | - Alan Cooper
- BlueSkyGenetics, Adelaide, South Australia, Australia
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Agnar Helgason
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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14
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Štular B, Lozić E, Belak M, Rihter J, Koch I, Modrijan Z, Magdič A, Karl S, Lehner M, Gutjahr C. Migration of Alpine Slavs and machine learning: Space-time pattern mining of an archaeological data set. PLoS One 2022; 17:e0274687. [PMID: 36121819 PMCID: PMC9484688 DOI: 10.1371/journal.pone.0274687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 09/01/2022] [Indexed: 11/18/2022] Open
Abstract
The rapid expansion of the Slavic speakers in the second half of the first millennium CE remains a controversial topic in archaeology, and academic passions on the issue have long run high. Currently, there are three main hypotheses for this expansion. The aim of this paper was to test the so-called “hybrid hypothesis,” which states that the movement of people, cultural diffusion and language diffusion all occurred simultaneously. For this purpose, we examined an archaeological Deep Data set with a machine learning method termed time series clustering and with emerging hot spot analysis. The latter required two archaeology-specific modifications: The archaeological trend map and the multiscale emerging hot spot analysis. As a result, we were able to detect two migrations in the Eastern Alps between c. 500 and c. 700 CE. Based on the convergence of evidence from archaeology, linguistics, and population genetics, we have identified the migrants as Alpine Slavs, i.e., people who spoke Slavic and shared specific common ancestry.
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Affiliation(s)
- Benjamin Štular
- Znanstvenoraziskovalni Center Slovenske Akademije Znanosti in Umetnosti, Ljubljana, Slovenia
- * E-mail:
| | - Edisa Lozić
- Znanstvenoraziskovalni Center Slovenske Akademije Znanosti in Umetnosti, Ljubljana, Slovenia
- Institute of Classics, University of Graz, Graz, Austria
| | - Mateja Belak
- Znanstvenoraziskovalni Center Slovenske Akademije Znanosti in Umetnosti, Ljubljana, Slovenia
| | - Jernej Rihter
- Znanstvenoraziskovalni Center Slovenske Akademije Znanosti in Umetnosti, Ljubljana, Slovenia
| | - Iris Koch
- Institute of Classics, University of Graz, Graz, Austria
| | - Zvezdana Modrijan
- Znanstvenoraziskovalni Center Slovenske Akademije Znanosti in Umetnosti, Ljubljana, Slovenia
| | - Andrej Magdič
- Območna Enota Maribor, Javni Zavod Republike Slovenije za Varstvo Kulturne Dediščine, Maribor, Slovenia
| | - Stephan Karl
- Institute of Classics, University of Graz, Graz, Austria
| | - Manfred Lehner
- Institute of Classics, University of Graz, Graz, Austria
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15
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Mroczek M, Inashkina I, Stavusis J, Zayakin P, Khrunin A, Micule I, Kenina V, Zdanovica A, Zídková J, Fajkusová L, Limborska S, van der Kooi AJ, Brusse E, Leonardis L, Maver A, Pajusalu S, Õunap K, Puusepp S, Dobosz P, Sypniewski M, Burnyte B, Lace B. CAPN3 c.1746-20C>G variant is hypomorphic for LGMD R1 calpain 3-related. Hum Mutat 2022; 43:1347-1353. [PMID: 35731190 DOI: 10.1002/humu.24421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]
Abstract
The investigated intronic CAPN3 variant NM_000070.3:c.1746-20C>G occurs in the Central and Eastern Europe with a frequency of >1% and there are conflicting interpretations on its pathogenicity. We collected data on 14 patients carrying the CAPN3 c.1746-20C>G variant in trans position with another CAPN3 pathogenic/likely pathogenic variant. The patients compound heterozygous for the CAPN3 c.1746-20C>G variant presented a phenotype consistent with calpainopathy of mild/medium severity. This variant is most frequent in the North/West regions of Russia and may originate from that area. Molecular studies revealed that different splicing isoforms are produced in the muscle. We hypothesize that c.1746-20C>G is a hypomorphic variant with a reduction of RNA and protein expression and only individuals having a higher ratio of abnormal isoforms are affected. Reclassification of the CAPN3 variant c.1746-20C>G from variant with a conflicting interpretation of pathogenicity to hypomorphic variant explains many unidentified cases of limb girdle muscular dystrophy R1 calpain 3-related in Eastern and Central Europe.
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Affiliation(s)
- Magdalena Mroczek
- Department of Neurology and Neurophysiology, Balgrist University Hospital, University of Zurich, Zürich, Switzerland
| | | | | | | | - Andrey Khrunin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ieva Micule
- Biomedical Research and Study Center, Riga, Latvia
| | - Victorija Kenina
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Rare Disease Center, Riga East Clinical University Hospital, Riga, Latvia
| | | | - Jana Zídková
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Svetlana Limborska
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Anneke J van der Kooi
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lea Leonardis
- Department of Neurology, University Medical Centre Ljubljana, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sanna Puusepp
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Paula Dobosz
- MNM Diagnostics Sp. z o.o., Poznań, Poland.,Department of Hematology, Transplantation and Internal Medicine, University Clinical Center of the Medical University of Warsaw, Warsaw, Poland.,Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | | | - Birute Burnyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Baiba Lace
- Biomedical Research and Study Center, Riga, Latvia.,Medical Genetics Clinic, Children's Clinical University Hospital, Riga, Latvia
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16
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Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank. Proc Natl Acad Sci U S A 2022; 119:e2119281119. [PMID: 35696575 PMCID: PMC9233301 DOI: 10.1073/pnas.2119281119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Haplotype-based analyses have recently been leveraged to interrogate the fine-scale structure in specific geographic regions, notably in Europe, although an equivalent haplotype-based understanding across the whole of Europe with these tools is lacking. Furthermore, study of identity-by-descent (IBD) sharing in a large sample of haplotypes across Europe would allow a direct comparison between different demographic histories of different regions. The UK Biobank (UKBB) is a population-scale dataset of genotype and phenotype data collected from the United Kingdom, with established sampling of worldwide ancestries. The exact content of these non-UK ancestries is largely uncharacterized, where study could highlight valuable intracontinental ancestry references with deep phenotyping within the UKBB. In this context, we sought to investigate the sample of European ancestry captured in the UKBB. We studied the haplotypes of 5,500 UKBB individuals with a European birthplace; investigated the population structure and demographic history in Europe, showing in parallel the variety of footprints of demographic history in different genetic regions around Europe; and expand knowledge of the genetic landscape of the east and southeast of Europe. Providing an updated map of European genetics, we leverage IBD-segment sharing to explore the extent of population isolation and size across the continent. In addition to building and expanding upon previous knowledge in Europe, our results show the UKBB as a source of diverse ancestries beyond Britain. These worldwide ancestries sampled in the UKBB may complement and inform researchers interested in specific communities or regions not limited to Britain.
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17
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Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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18
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Balanovska EV, Gorin IO, Ponomarev GY, Pylev VY, Petrushenko VS, Markina NV, Mamaeva AD, Larin AK, Agdzhoyan AT. Footprints of interaction among Finniс-speaking, Slavic, and Turkic-speaking populations in modern gene pool and their reflection in pharmacogenetics. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic contribution of pre-Slavic populations to gene pools of modern Russia is increasingly relevant, along with genetic footprints of the Golden Horde invasion. The novel genome-wide approaches enable advanced solutions in this field. The study aimed at searching for the footprints of genetic interaction among Finnicspeaking, Slavic and Turkic-speaking populations of Central Russia and Volga Region and their reflection in pharmacogenetic landscape. Modeling ancestral components by ADMIXTURE software and their mapping involved genome-wide genotyping data for 248 individual genomes representing 47 populations of 9 ethnic groups. Of specific ancestral components identified in each of the Finnic-speaking peoples, only Mordovian ancestral components are common for all populations within the studied geographic area, regardless of their linguistic affiliation. Gene pools of Russian populations include 80% of intrinsic component, 19% contribution from Finnic-speaking peoples, and 1% of Central Asian influence. The Tatar gene pool combines all identified ancestral components, including 81% contribution from Finnic-speaking peoples and only 12% of Central Asian influence, which prevents using it as a reference for the assessment of Golden Horde footprints in Russian gene pools. A map of genetic distances from Ryazan Russians based on a panel of 42 pharmacogenetic markers reveals a landscape strikingly independent from the selectively neutral ancestral genomic patterns. For instance, populations of Mordovia, Kaluga, Smolensk, and Kostroma regions are the closest to Ryazan Russians in pharmacogenetic status, whereas populations of Ryazan and Nizhny Novgorod regions have strikingly divergent pharmacogenetic status despite the similarity of the selectively neutral ancestral genomic patterns. These findings confirm the relevance of targeted pharmacogenetic characterization for gene pools of Russia.
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Affiliation(s)
- EV Balanovska
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - IO Gorin
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - GYu Ponomarev
- Vavilov Institute of General Genetics, Moscow, Russia
| | - VYu Pylev
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - VS Petrushenko
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - NV Markina
- Vavilov Institute of General Genetics, Moscow, Russia
| | - AD Mamaeva
- Vavilov Institute of General Genetics, Moscow, Russia
| | - AK Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - AT Agdzhoyan
- Vavilov Institute of General Genetics, Moscow, Russia
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19
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Balanovsky O, Petrushenko V, Mirzaev K, Abdullaev S, Gorin I, Chernevskiy D, Agdzhoyan A, Balanovska E, Kryukov A, Temirbulatov I, Sychev D. Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:1391-1402. [PMID: 34764675 PMCID: PMC8575442 DOI: 10.2147/pgpm.s320609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/04/2021] [Indexed: 01/10/2023]
Abstract
Background Information about the distribution of clinically significant genetic markers in different populations may be helpful in elaborating personalized approaches to the clinical management of COVID-19 in the absence of consensus guidelines. Aim Analyze frequencies and distribution patterns of two markers associated with severe COVID-19 (rs11385942 and rs657152) and look for potential correlations between these markers and deaths from COVID-19 among populations in Russia and across the world. Methods We genotyped 1883 samples from 91 ethnic groups pooled into 28 populations representing Russia and its neighbor states. We also compiled a dataset on 32 populations from other regions using genotypes extracted or imputed from the available databases. Geographic maps showing the frequency distribution of the analyzed markers were constructed using the obtained data. Results The cartographic analysis revealed that rs11385942 distribution follows the West Eurasian pattern: the marker is frequent among the populations of Europe, West Asia and South Asia but rare or absent in all other parts of the globe. Notably, the transition from high to low rs11385942 frequencies across Eurasia is not abrupt but follows the clinal variation pattern instead. The distribution of rs657152 is more homogeneous. The analysis of correlations between the frequencies of the studied markers and the epidemiological characteristics of COVID-19 in a population revealed that higher frequencies of both risk alleles correlated positively with mortality from this disease. For rs657152, the correlation was especially strong (r = 0.59, p = 0.02). These reasonable correlations were observed for the "Russian" dataset only: no such correlations were established for the "world" dataset. This could be attributed to the differences in methodology used to collect COVID-19 statistics in different countries. Conclusion Our findings suggest that genetic differences between populations make a small yet tangible contribution to the heterogeneity of the pandemic worldwide.
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Affiliation(s)
- Oleg Balanovsky
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Valeria Petrushenko
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Department of Bioinformatics Moscow Institute of Physics and Technology, Moscow, Russia
| | - Karin Mirzaev
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Sherzod Abdullaev
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Igor Gorin
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Department of Bioinformatics Moscow Institute of Physics and Technology, Moscow, Russia
| | - Denis Chernevskiy
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Anastasiya Agdzhoyan
- Laboratory of Genome Geography, Vavilov Institute of General Genetics, Moscow, Russia.,Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Elena Balanovska
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Alexander Kryukov
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Ilyas Temirbulatov
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, Moscow, Russia.,Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Dmitriy Sychev
- Department of Clinical Pharmacology and Therapeutics, Russian Medical Academy of Continuous Professional Education, Moscow, Russia
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20
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Urnikyte A, Molyte A, Kučinskas V. Genome-Wide Landscape of North-Eastern European Populations: A View from Lithuania. Genes (Basel) 2021; 12:genes12111730. [PMID: 34828336 PMCID: PMC8623362 DOI: 10.3390/genes12111730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 01/15/2023] Open
Abstract
There are still several unanswered questions regarding about ancient events in the Lithuanian population. The Lithuanians, as the subject of this study, are of great interest as they represent a partially isolated population maintaining an ancient genetic composition and show genetic uniqueness in European comparisons. To elucidate the genetic relationships between the Lithuania and North-Eastern European and West Siberian populations, we analyzed the population structure, effective population size, and recent positive selection from genome-wide single nucleotide polymorphism (SNP) data. We identified the close genetic proximity of Lithuanians to neighboring populations (Latvians, Estonians, Belarusians) and in part with West and South Slavs (Poles, Slovaks, and Slovenians), however, with particular genetic distinctiveness. The estimated long-term Ne values ranged from ~5900 in the Estonian population to ~2400 in the South Russian population. The divergence times between the Lithuanian and study populations ranged from 240 to 12,871 YBP. We also found evidence of selection in 24 regions, 21 of which have not been discovered in previous analyses of selection. Undoubtedly, the genetic diversity analysis of geographically specific regions may provide new insights into microevolutionary processes affecting local human populations.
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Affiliation(s)
- Alina Urnikyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
- Correspondence: ; Tel.: +370-698-55292
| | - Alma Molyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
- Department of Information Systems, Faculty of Fundamentals Sciences, Vilnius Gediminas Technical University, Saulėtekio Al. 11, LT-10223 Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
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21
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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes. Eur J Hum Genet 2021; 29:1510-1519. [PMID: 33958743 PMCID: PMC8484622 DOI: 10.1038/s41431-021-00897-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.
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22
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Warshauer EM, Brown A, Fuentes I, Shortt J, Gignoux C, Montinaro F, Metspalu M, Youssefian L, Vahidnezhad H, Jacków J, Christiano AM, Uitto J, Fajardo-Ramírez ÓR, Salas-Alanis JC, McGrath JA, Consuegra L, Rivera C, Maier PA, Runfeldt G, Behar DM, Skorecki K, Sprecher E, Palisson F, Norris DA, Bruckner AL, Kogut I, Bilousova G, Roop DR. Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry. Am J Med Genet A 2021; 185:3390-3400. [PMID: 34435747 DOI: 10.1002/ajmg.a.62456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 11/11/2022]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare genodermatosis caused by mutations in the gene coding for type VII collagen (COL7A1). More than 800 different pathogenic mutations in COL7A1 have been described to date; however, the ancestral origins of many of these mutations have not been precisely identified. In this study, 32 RDEB patient samples from the Southwestern United States, Mexico, Chile, and Colombia carrying common mutations in the COL7A1 gene were investigated to determine the origins of these mutations and the extent to which shared ancestry contributes to disease prevalence. The results demonstrate both shared European and American origins of RDEB mutations in distinct populations in the Americas and suggest the influence of Sephardic ancestry in at least some RDEB mutations of European origins. Knowledge of ancestry and relatedness among RDEB patient populations will be crucial for the development of future clinical trials and the advancement of novel therapeutics.
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Affiliation(s)
- Emily Mira Warshauer
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Adam Brown
- Avotaynu Research Partnership LLC, Englewood, New Jersey, USA
| | - Ignacia Fuentes
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.,Fundación DEBRA Chile, Santiago, Chile
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology and Genetics, University of Bari, Bari, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joanna Jacków
- Department of Dermatology, Columbia University, New York, New York, USA.,St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | - Angela M Christiano
- Department of Dermatology, Columbia University, New York, New York, USA.,Department of Genetics and Development, Columbia University, New York, New York, USA
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Óscar R Fajardo-Ramírez
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Julio C Salas-Alanis
- DEBRA Mexico, Azteca Guadalupe, Mexico.,Instituto Dermatologico de Jalisco, Zapopan, Mexico
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London, UK
| | | | - Carolina Rivera
- Fundación DEBRA Colombia, Bogotá, Colombia.,Department of Medical Genetics, Pediatric Hospital, Fundacion Cardioinfantil-Universidad del Rosario, Bogotá, Colombia
| | - Paul A Maier
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Goran Runfeldt
- Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Gene by Gene, Genomic Research Center, Houston, Texas, USA
| | - Karl Skorecki
- Azrieli Faculty of Medicine of the Galilee, Bar-Ilan University, Safed, Israel
| | - Eli Sprecher
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Francis Palisson
- Fundación DEBRA Chile, Santiago, Chile.,Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David A Norris
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anna L Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Igor Kogut
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dennis R Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA.,Charles C. Gates Center for Regenerative Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
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23
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Mermeklieva E, Kamenarova K, Mihova K, Shakola F, Kaneva R. A rare case of RGR/CDHR1 haplotype identified in Bulgarian patient with cone-rod dystrophy. Ophthalmic Genet 2021; 42:747-752. [PMID: 34229535 DOI: 10.1080/13816810.2021.1946700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AIM To present a rare clinical case of CDHR1-related retinopathy with cone and rod involvementconfirmed clinically, electrophysiologically and genetically as a cone-rod dystrophy. MATERIAL AND METHODS A 26-year-old woman underwent detailed ophthalmic examinationincluding fundus photography, full-field and multifocal electroretinography, visual field testing, optical coherence tomography and fluorescein angiography, which established the clinical diagnosis. Next-generation sequencing of a custom panel including 140 of the most common genes for inherited retinal degenerations was used for mutation screening. RESULTS The symptoms onset was two years ago included gradual loss of vision and photophobia. The clinical findings were reduced visual acuity, central and peripheral scotomas, sporadic pigmentary cells localized mainly in the peripheral retina, a thinner retina in the macula and peripherally, moderate retinal vessels attenuation and reduced cone and rod ERG responses. The genetic analysisfound that the patient was homozygous for two already reported mutations: RGR-c.196A>C (p.Ser66Arg) variant and a co-segregating frame-shift deletion in CDHR1-c.2522_2528delTCTCTGA (p.Ile841Serfs119*). Segregation analysis showed that the two mutations were transmitted by the asymptomatic heterozygous parents. CONCLUSION The rare haplotype of RGR mutation co-segregating incis- with CDHR1 mutation in our patient has been previously described in Albanian patients with recessive retinal dystrophy. Our findings add further support to the hypothesis of a common ancestral haplotype spread in the Balkan population. The comprehensive clinical, electrophysiological and genetic testing of patients with rare hereditary retinal dystrophies is essential for the correct diagnosis and the choice of potential novel therapies.
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Affiliation(s)
- Elena Mermeklieva
- Clinic of Оphthalmology, "Lozenetz" University Hospital, Medical Faculty, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Felitsiya Shakola
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
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24
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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Babić Jordamović N, Kojović T, Dogan S, Bešić L, Salihefendić L, Konjhodžić R, Škaro V, Projić P, Hadžiavdić V, Ašić A, Marjanović D. Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina. Front Genet 2021; 12:671467. [PMID: 34178033 PMCID: PMC8226213 DOI: 10.3389/fgene.2021.671467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
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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Affiliation(s)
- Naida Babić Jordamović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Tamara Kojović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Serkan Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Lana Salihefendić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Vedrana Škaro
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Petar Projić
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Vesna Hadžiavdić
- Department of Biology, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
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Parfenchyk MS, Kotava SA. The Theoretical Framework for the Panels of DNA Markers Formation in the Forensic Determination of an Individual Ancestral Origin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Balanovska EV, Petrushenko VS, Koshel SM, Pocheshkhova EA, Chernevskiy DK, Mirzaev KB, Abdullaev S, Balanovsky OP. Cartographic atlas of frequency variation for 45 pharmacogenetic markers in populations of Russia and its neighbor states. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lack of information about the frequency of pharmacogenetic markers in Russia impedes the adoption of personalized treatment algorithms originally developed for West European populations. The aim of this paper was to study the distribution of some clinically significant pharmacogenetic markers across Russia. A total of 45 pharmacogenetic markers were selected from a few population genetic datasets, including ADME, drug target and hemostasis-controlling genes. The total number of donors genotyped for these markers was 2,197. The frequencies of these markers were determined for 50 different populations, comprised of 137 ethnic and subethnic groups. A comprehensive pharmacogenetic atlas was created, i.e. a systematic collection of gene geographic maps of frequency variation for 45 pharmacogenetic DNA markers in Russia and its neighbor states. The maps revealed 3 patterns of geographic variation. Clinal variation (a gradient change in frequency along the East-West axis) is observed in the pharmacogenetic markers that follow the main pattern of variation for North Eurasia (13% of the maps). Uniform distribution singles out a group of markers that occur at average frequency in most Russian regions (27% of the maps). Focal variation is observed in the markers that are specific to a certain group of populations and are absent in other regions (60% of the maps). The atlas reveals that the average frequency of the marker and its frequency in individual populations do not indicate the type of its distribution in Russia: a gene geographic map is needed to uncover the pattern of its variation.
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Affiliation(s)
- EV Balanovska
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia
| | - VS Petrushenko
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
| | - SM Koshel
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - EA Pocheshkhova
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Kuban State Medical Institute, Krasnodar, Russia
| | - DK Chernevskiy
- Bochkov Research Center for Medical Genetics, Moscow, Russia
| | - KB Mirzaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - ShP Abdullaev
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - OP Balanovsky
- Bochkov Research Center for Medical Genetics, Moscow, Russia; Biobank of North Eurasia, Moscow, Russia; Vavilov Institute of General Genetics, Moscow, Russia
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28
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Ádám V, Bánfai Z, Maász A, Sümegi K, Miseta A, Melegh B. Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania. J Hum Genet 2020; 65:1093-1103. [PMID: 32653894 DOI: 10.1038/s10038-020-0799-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/09/2022]
Abstract
Csango people are an East-Central European ethnographic group living mostly in the historical region of Moldavia, Romania. Their traditional language, the Csango is an old Hungarian dialect, which is a severely endangered language due to language shift. Their origin is still disputed among experts and there are many hypotheses since the 19th century. Previous genetic studies found connection with ethnic groups living in Hungary and provided evidence which might support their Hungarian origin. Another study found Inner Asian Altaic ancestry in their genetic makeup. The goal of this study was to analyze the genetic characteristics of the Csango people by comparing their genetic characteristics to contemporary Eurasian populations based on genome-wide autosomal marker data. Our findings suggest that genetic affinity of Csangos to Hungarians is more significant than to Romanians. They also have a detectable connection with Central-Asian and Siberian Turkic ethnic groups. Besides the presumable Middle Eastern/Central-Asian Turkic ancestry, Csangos show ~4% Turkic ancestry from Central Asia/Siberia, which makes them unique in comparison to all other East-Central European populations investigated in this study. The admixture that resulted in this Turkic ancestry could have occurred 30-40 generations ago, which date interval corresponds to Hungarian historical events regarding their migration and the conquest of the Carpathian basin.
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Affiliation(s)
- Valerián Ádám
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Zsolt Bánfai
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary. .,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
| | - Anita Maász
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Katalin Sümegi
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Miseta
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary. .,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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29
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Recent effective population size in Eastern European plain Russians correlates with the key historical events. Sci Rep 2020; 10:9729. [PMID: 32546820 PMCID: PMC7298007 DOI: 10.1038/s41598-020-66734-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15–20 generations ago, i.e. in the 16–18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.
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30
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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31
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Mallory J, Dybo A, Balanovsky O. The Impact of Genetics Research on Archaeology and Linguistics in Eurasia. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Ongaro L, Scliar MO, Flores R, Raveane A, Marnetto D, Sarno S, Gnecchi-Ruscone GA, Alarcón-Riquelme ME, Patin E, Wangkumhang P, Hellenthal G, Gonzalez-Santos M, King RJ, Kouvatsi A, Balanovsky O, Balanovska E, Atramentova L, Turdikulova S, Mastana S, Marjanovic D, Mulahasanovic L, Leskovac A, Lima-Costa MF, Pereira AC, Barreto ML, Horta BL, Mabunda N, May CA, Moreno-Estrada A, Achilli A, Olivieri A, Semino O, Tambets K, Kivisild T, Luiselli D, Torroni A, Capelli C, Tarazona-Santos E, Metspalu M, Pagani L, Montinaro F. The Genomic Impact of European Colonization of the Americas. Curr Biol 2019; 29:3974-3986.e4. [PMID: 31735679 DOI: 10.1016/j.cub.2019.09.076] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/06/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022]
Abstract
The human genetic diversity of the Americas has been affected by several events of gene flow that have continued since the colonial era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored. Here, we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected (1) the genetic structure, (2) the admixture profile, (3) the demographic history, and (4) sex-biased gene-flow dynamics of the Americas. We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East, and to specific regions of Africa.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, Tartu 51010, Estonia.
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo, São Paulo, SP 05508-090, Brazil; Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40100, Italy
| | - Guido A Gnecchi-Ruscone
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40100, Italy; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Marta E Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Pasteur Institute, UMR2000, CNRS, Paris 75015, France
| | - Pongsakorn Wangkumhang
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305-5101, USA
| | - Anastasia Kouvatsi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow 117971, Russia; Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow 115478, Russia; Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow 115201, Russia
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow 117971, Russia; Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow 115478, Russia; Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow 115201, Russia
| | - Lubov Atramentova
- Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| | - Shahlo Turdikulova
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Academy of Sciences Republic of Uzbekistan, Tashkent 100047, Uzbekistan
| | - Sarabjit Mastana
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough LE11 3TU, UK
| | - Damir Marjanovic
- Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo 71000, Bosnia and Herzegovina; Institute for Anthropological Researches, Zagreb, Croatia
| | | | - Andreja Leskovac
- Vinca Institute of Nuclear Sciences, University of Belgrade, M. Petrovica Alasa 12-14, Belgrade 11001, Serbia
| | - Maria F Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG 30190-002, Brazil
| | - Alexandre C Pereira
- Instituto do Coração, Universidade de São Paulo, São Paulo, SP 05403-900, Brazil
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA 0110-040, Brazil; Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, BA 41745-715, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, 464, Pelotas, RS 96001-970, Brazil
| | - Nédio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N 1, Província de Maputo, Maputo 1120, Mozambique
| | - Celia A May
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Herestraat 49 - box 602, Leuven 3000, Belgium
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna Campus, Ravenna 48100, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Biology, University of Padua, Via Ugo Bassi 58B, Padua 35100, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.
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33
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Tamm E, Di Cristofaro J, Mazières S, Pennarun E, Kushniarevich A, Raveane A, Semino O, Chiaroni J, Pereira L, Metspalu M, Montinaro F. Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. Sci Rep 2019; 9:13581. [PMID: 31537848 PMCID: PMC6753063 DOI: 10.1038/s41598-019-49901-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/31/2019] [Indexed: 01/13/2023] Open
Abstract
Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.
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Affiliation(s)
- Erika Tamm
- Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | | | - Erwan Pennarun
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Belarus
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-135, Porto, Portugal
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia. .,Department of Zoology, University of Oxford, Oxford, UK.
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Jankova R, Seidel M, Videtič Paska A, Willuweit S, Roewer L. Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia. Forensic Sci Int Genet 2019; 42:165-170. [PMID: 31351212 DOI: 10.1016/j.fsigen.2019.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. SCIENCE ADVANCES 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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Järve M, Saag L, Scheib CL, Pathak AK, Montinaro F, Pagani L, Flores R, Guellil M, Saag L, Tambets K, Kushniarevich A, Solnik A, Varul L, Zadnikov S, Petrauskas O, Avramenko M, Magomedov B, Didenko S, Toshev G, Bruyako I, Grechko D, Okatenko V, Gorbenko K, Smyrnov O, Heiko A, Reida R, Sapiehin S, Sirotin S, Tairov A, Beisenov A, Starodubtsev M, Vasilev V, Nechvaloda A, Atabiev B, Litvinov S, Ekomasova N, Dzhaubermezov M, Voroniatov S, Utevska O, Shramko I, Khusnutdinova E, Metspalu M, Savelev N, Kriiska A, Kivisild T, Villems R. Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance. Curr Biol 2019; 29:2430-2441.e10. [PMID: 31303491 DOI: 10.1016/j.cub.2019.06.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/03/2019] [Accepted: 06/07/2019] [Indexed: 01/08/2023]
Abstract
The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.
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Affiliation(s)
- Mari Järve
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia.
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Ajai K Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi 58/B, Padova 35121, Italy
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Liivi Varul
- School of Humanities, Tallinn University, 29 Narva Street, Tallinn 10120, Estonia
| | - Stanislav Zadnikov
- Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Oleg Petrauskas
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Maryana Avramenko
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Boris Magomedov
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Serghii Didenko
- National Museum of History of Ukraine, 2 Volodymyrs'ka Street, Kyiv 02000, Ukraine
| | - Gennadi Toshev
- Zaporizhzhya National University, 33A Dniprovska Street, Zaporizhzhya 69061, Ukraine
| | - Igor Bruyako
- Odessa Archaeological Museum, 4 Lanzheronivs'ka Street, Odessa 65000, Ukraine
| | - Denys Grechko
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Vitalii Okatenko
- SC SRC "Protective Archeological Service of Ukraine," Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Kyrylo Gorbenko
- Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine
| | - Oleksandr Smyrnov
- Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine
| | - Anatolii Heiko
- National Museum of Ukrainian Pottery in Opishne, 102 Partyzanska Street, Opishne 38164, Ukraine
| | - Roman Reida
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Serheii Sapiehin
- Anton Makarenko Museum, Poltava Regional Makarenko Scientific Lyceum, 1-2 Makarenko Lane, Kovalivka 38701, Ukraine
| | - Sergey Sirotin
- Institute of Archaeology, Russian Academy of Sciences, 19 Dmitri Ulyanov Street, Moscow 117292, Russia
| | - Aleksandr Tairov
- South Ural State University, 76 Lenin Avenue, Chelyabinsk 454080, Russia
| | - Arman Beisenov
- A. Kh. Margulan Institute of Archaeology, 44 Dostyk Avenue, Almaty 480100, Kazakhstan
| | - Maksim Starodubtsev
- Sterlitamak Museum of Local History, 100 Karl Marx Street, Sterlitamak 453124, Russia
| | - Vitali Vasilev
- LoCom Medien Akademie Europäisches Bildungsinstitut, Bachstraße 4, Bonn 53115, Germany
| | - Alexei Nechvaloda
- Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Biyaslan Atabiev
- Institute for Caucasus Archaeology, 30 Katkhanova Street, Nalchik 361401, Russia
| | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Natalia Ekomasova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Murat Dzhaubermezov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Sergey Voroniatov
- Department of Archaeology of Eastern Europe and Siberia, State Hermitage Museum, 34 Dvortsovaya Embankment, St. Petersburg 190000, Russia
| | - Olga Utevska
- Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Irina Shramko
- Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Nikita Savelev
- Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, 2 Jakobi Street, Tartu 51014, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, O&N IV Herestraat 49, Leuven 3000, Belgium
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
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Malyarchuk BA, Litvinov AN, Derenko MV. Structure and Forming of Mitochondrial Gene Pool of Russian Population of Eastern Europe. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia. Sci Rep 2019; 9:7786. [PMID: 31127140 PMCID: PMC6534673 DOI: 10.1038/s41598-019-44272-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
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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Saag L, Laneman M, Varul L, Malve M, Valk H, Razzak MA, Shirobokov IG, Khartanovich VI, Mikhaylova ER, Kushniarevich A, Scheib CL, Solnik A, Reisberg T, Parik J, Saag L, Metspalu E, Rootsi S, Montinaro F, Remm M, Mägi R, D'Atanasio E, Crema ER, Díez-Del-Molino D, Thomas MG, Kriiska A, Kivisild T, Villems R, Lang V, Metspalu M, Tambets K. The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East. Curr Biol 2019; 29:1701-1711.e16. [PMID: 31080083 PMCID: PMC6544527 DOI: 10.1016/j.cub.2019.04.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/18/2019] [Accepted: 04/09/2019] [Indexed: 01/08/2023]
Abstract
In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.
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Affiliation(s)
- Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia.
| | - Margot Laneman
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Liivi Varul
- School of Humanities, Tallinn University, Tallinn 10120, Estonia
| | - Martin Malve
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Heiki Valk
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Maria A Razzak
- Department of Slavic and Finnic Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia
| | - Ivan G Shirobokov
- Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Valeri I Khartanovich
- Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | | | | | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 104 05, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Stockholm 106 91, Sweden
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia
| | - Valter Lang
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
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Reconstructing recent population history while mapping rare variants using haplotypes. Sci Rep 2019; 9:5849. [PMID: 30971755 PMCID: PMC6458133 DOI: 10.1038/s41598-019-42385-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
Haplotype-based methods are a cost-effective alternative to characterize unobserved rare variants and map disease-associated alleles. Moreover, they can be used to reconstruct recent population history, which shaped distribution of rare variants and thus can be used to guide gene mapping studies. In this study, we analysed Illumina 650 k genotyped dataset on three underrepresented populations from Eastern Europe, where ancestors of Russians came into contact with two indigenous ethnic groups, Bashkirs and Tatars. Using the IBD mapping approach, we identified two rare IBD haplotypes strongly enriched in asthma patients of distinct ethnic background. We reconstructed recent population history using haplotype-based methods to reconcile this contradictory finding. Our ChromoPainter analysis showed that these haplotypes each descend from a single ancestor coming from one of the ethnic groups studied. Next, we used DoRIS approach and showed that source populations for patients exchanged recent (<60 generations) asymmetric gene flow, which supported the ChromoPainter-based scenario that patients share haplotypes through inter-ethnic admixture. Finally, we show that these IBD haplotypes overlap with asthma-associated genomic regions ascertained in European population. This finding is consistent with the fact that the two donor populations for the rare IBD haplotypes: Russians and Tatars have European ancestry.
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Yurchenko AA, Yudin NS, Voevoda MI. Exome-wide survey of the Siberian Caucasian population. BMC MEDICAL GENETICS 2019; 20:51. [PMID: 30967127 PMCID: PMC6454596 DOI: 10.1186/s12881-019-0772-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Population structure is an important factor in the genetic association studies but often remains underexplored for many human populations. We identified exome variants in 39 Siberian Caucasian individuals from Novosibirsk, Russia and compared their genetic allele frequencies with European populations from 1000 Genomes Project. METHODS The study participants were from Novosibirsk and represented people with monogenic diabetes, healthy individuals and a cohort from the tick-borne encephalitis study. Isolated DNA was enriched using Agilent SureSelect V5 kit and sequenced on Illumina HiSeq 4000 and genetic variants were identified using GATK pipeline. To estimate the patterns of the population structure we used PCA and ADMIXTURE analysis. Pharmocogenetically and medically important variants were annotated based on PharmGKB and ClinVar databases. RESULTS The analysis identified low, but highly significant population differentiation attributed to numerous loci between the Siberian Caucasian population and other European population samples as well as a higher proportion of the Finnish genetic component in the studied sample. The medical and pharmacogenetic annotation of highly significantly differentiated variants between the Novosibirsk and the combined European populations revealed a number of important genetic polymorphisms located in such genes as FCGR3B, TYR, OCA2, FABP1, CHEK2 and SLC4A1. CONCLUSIONS The study reports for the first time an exome-wide comparison of a population from Russia with European samples and emphasizes the importance of population studies with medical annotation of variants.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Lavrentieva 10 St, Novosibirsk, Russia, 630090.
| | - Nikolai S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Lavrentieva 10 St, Novosibirsk, Russia, 630090.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Mikhail I Voevoda
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Lavrentieva 10 St, Novosibirsk, Russia, 630090.,Novosibirsk State University, Novosibirsk, 630090, Russia.,Institute of Internal and Preventive Medicine-branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 175/1, B. Bogatkov Street, 630089, Novosibirsk, Russia
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Modi A, Nesheva D, Sarno S, Vai S, Karachanak-Yankova S, Luiselli D, Pilli E, Lari M, Vergata C, Yordanov Y, Dimitrova D, Kalcev P, Staneva R, Antonova O, Hadjidekova S, Galabov A, Toncheva D, Caramelli D. Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians. Sci Rep 2019; 9:5412. [PMID: 30931994 PMCID: PMC6443937 DOI: 10.1038/s41598-019-41945-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/20/2019] [Indexed: 11/17/2022] Open
Abstract
One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | | | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Elena Pilli
- Department of Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Vergata
- Department of Biology, University of Florence, Florence, Italy
| | - Yordan Yordanov
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Petar Kalcev
- The Regional Historical Museum of Stara Zagora, Stara Zagora, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Angel Galabov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria.
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
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Zhernakova DV, Brukhin V, Malov S, Oleksyk TK, Koepfli KP, Zhuk A, Dobrynin P, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Gorbunova A, Chernyaeva E, Shevchenko A, Kolchanova S, Komissarov A, Simonov S, Antonik A, Logachev A, Polev DE, Pavlova OA, Glotov AS, Ulantsev V, Noskova E, Davydova TK, Sivtseva TM, Limborska S, Balanovsky O, Osakovsky V, Novozhilov A, Puzyrev V, O'Brien SJ. Genome-wide sequence analyses of ethnic populations across Russia. Genomics 2019; 112:442-458. [PMID: 30902755 DOI: 10.1016/j.ygeno.2019.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/15/2019] [Indexed: 12/22/2022]
Abstract
The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country.
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Affiliation(s)
- Daria V Zhernakova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sergey Malov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Department of Mathematics, St. Petersburg Electrotechnical University, St. Petersburg, Russian Federation
| | - Taras K Oleksyk
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico; Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Klaus Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Anna Zhuk
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russian Federation
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Nikolay Cherkasov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail Rotkevich
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Igor Evsyukov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sviatoslav Sidorov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anna Gorbunova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russian Federation
| | - Ekaterina Chernyaeva
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Andrey Shevchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sofia Kolchanova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Alexei Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Serguei Simonov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Alexey Antonik
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anton Logachev
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Dmitrii E Polev
- Centre Biobank, Research Park, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Olga A Pavlova
- Centre Biobank, Research Park, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Andrey S Glotov
- Laboratory of biobanking and genomic medicine of Institute of translation biomedicine, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Vladimir Ulantsev
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russian Federation
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russian Federation; JetBrains Research, St. Petersburg, Russian Federation
| | - Tatyana K Davydova
- Federal State Budgetary Scietific Institution, "Yakut science center of complex medical problems", Yakutsk, Russian Federation
| | - Tatyana M Sivtseva
- Institute of Health, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Svetlana Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation; Research Centre for Medical Genetics, Moscow, Russian Federation; Biobank of North Eurasia, Moscow, Russian Federation
| | - Vladimir Osakovsky
- Institute of Health, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Alexey Novozhilov
- Department of Ethnography and Anthropology, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Valery Puzyrev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russian Federation
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, Florida 33004, USA.
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Mohammed Ismail W, Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P. The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS One 2018; 13:e0208901. [PMID: 30566479 PMCID: PMC6300249 DOI: 10.1371/journal.pone.0208901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.
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Affiliation(s)
- Wazim Mohammed Ismail
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Kymberleigh A. Pagel
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Vikas Pejaver
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Simo V. Zhang
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Matthew W. Hahn
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Predrag Radivojac
- College of Computer and Information Science, Northeastern University, Boston, Massachusetts, United States of America
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45
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Pathak AK, Kadian A, Kushniarevich A, Montinaro F, Mondal M, Ongaro L, Singh M, Kumar P, Rai N, Parik J, Metspalu E, Rootsi S, Pagani L, Kivisild T, Metspalu M, Chaubey G, Villems R. The Genetic Ancestry of Modern Indus Valley Populations from Northwest India. Am J Hum Genet 2018; 103:918-929. [PMID: 30526867 DOI: 10.1016/j.ajhg.2018.10.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/25/2018] [Indexed: 11/26/2022] Open
Abstract
The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years.
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A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups. ANTHROPOLOGICAL REVIEW 2018. [DOI: 10.2478/anre-2018-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study is to provide an insight into Balkan populations’ genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), Croatia, Macedonia, Slovenia, Greece, Romany (Hungary), Hungary, Serbia, Montenegro, Albania, Kosovo, Romania and Bulgaria. The overall dataset contains a total of 2179 samples with 1878 different haplotypes.
I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively.
The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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48
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Shadrina A, Tsepilov Y, Smetanina M, Voronina E, Seliverstov E, Ilyukhin E, Kirienko A, Zolotukhin I, Filipenko M. Polymorphisms of genes involved in inflammation and blood vessel development influence the risk of varicose veins. Clin Genet 2018; 94:191-199. [PMID: 29660117 DOI: 10.1111/cge.13362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Heredity plays an important role in the etiology of varicose veins (VVs). However, the genetic basis underlying this condition remains poorly understood. Our aim was to replicate top association signals from genome-wide association studies (GWASs) for VVs of lower extremities using 2 independent datasets-our sample of ethnic Russian individuals (709 cases and 278 controls) and a large cohort of British residents from UK Biobank (10 861 cases and 397 594 controls). Associations of polymorphisms rs11121615, rs6712038, rs507666, rs966562, rs7111987, rs6062618, and rs6905288 were validated in the UK Biobank individuals at a Bonferroni-corrected significance level. In Russian cohort, only rs11121615 reached a nominal significance level of P < .05. Results of original GWAS and replication studies were combined by a meta-analysis, and polymorphisms listed above as well as rs111434909 and rs4463578 passed a genome-wide significant threshold. Notably, the majority of these polymorphisms were located within or near genes involved in vascular development and remodeling, and regulation of inflammatory response. Our results confirm the role of these polymorphisms in genetic susceptibility to VVs and indicate the revealed genomic regions as good candidates for further fine-mapping studies and functional analysis. Moreover, our findings implicate inflammation and abnormal vascular architecture in VVs pathogenesis.
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Affiliation(s)
- A Shadrina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - Y Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - M Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Fundamental Medicine, Novosibirsk State University, Novosibirsk, Russia
| | - E Voronina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Moscow, Russia
| | - E Seliverstov
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Ilyukhin
- Private Surgery Center "Medalp", Saint Petersburg, Russia
| | - A Kirienko
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Zolotukhin
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - M Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Moscow, Russia
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49
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Triska P, Chekanov N, Stepanov V, Khusnutdinova EK, Kumar GPA, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva EE, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet 2017; 18:110. [PMID: 29297395 PMCID: PMC5751809 DOI: 10.1186/s12863-017-0578-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. RESULTS We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. CONCLUSIONS Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.
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MESH Headings
- Algorithms
- Asia
- DNA
- Datasets as Topic
- Emigration and Immigration/history
- Ethnicity/genetics
- Europe
- Female
- Genetic Variation
- Genetics, Population
- Genotyping Techniques
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Male
- Russia
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Affiliation(s)
- Petr Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nikolay Chekanov
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- "Genoanalytica" CJSC, Moscow, Russia
| | - Vadim Stepanov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Konstantin Babalyan
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | | | - Vladimir Kharkov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | - Irina Khitrinskaya
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Ekaterina E Khrameeva
- "Genoanalytica" CJSC, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Andrey Marusin
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Alexandr M Mazur
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
| | - Valery Puzyrev
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Dinara Ivanoshchuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maria Spiridonova
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Anton Teslyuk
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Svetlana Tsygankova
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Martin Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Edward Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Ancha Baranova
- Research Centre for Medical Genetics, Moscow, Russia
- School of Systems Biology, George Mason University, Fairfax, VA, USA
- Atlas Biomed Group, Moscow, Russia
| | - Konstantin Skryabin
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- Russian Scientific Centre "Kurchatov Institute", Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Tatarinova
- Vavilov Institute of General Genetics, Moscow, Russia.
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Atlas Biomed Group, Moscow, Russia.
- Department of Biology, University of La Verne, La Verne, CA, USA.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Egor Prokhortchouk
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
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50
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Balanovska EV, Agdzhoyan AT, Skhalyakho RA, Balaganskaya OA, Freydin GS, Chernevskii KG, Chernevskii DK, Stepanov GD, Kagazezheva ZA, Zaporozhchenko VV, Markina NV, Palipana D, Koshel SM, Kozlov SA, Balanovsky OP. Gene pool of the Novgorod population: Between the north and the south. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417110023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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