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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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Zupanič Pajnič I, Leskovar T, Črešnar M. Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology. Int J Legal Med 2023; 137:1629-1638. [PMID: 37284851 PMCID: PMC10421759 DOI: 10.1007/s00414-023-03032-y] [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: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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3
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Zupanič Pajnič I, Geršak ŽM, Leskovar T, Črešnar M. Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. Forensic Sci Int Genet 2023; 65:102886. [PMID: 37137206 DOI: 10.1016/j.fsigen.2023.102886] [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: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Živa Miriam Geršak
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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Mihajlovic M, Tanasic V, Markovic MK, Kecmanovic M, Keckarevic D. Distribution of Y-chromosome haplogroups in Serbian population groups originating from historically and geographically significant distinct parts of the Balkan Peninsula. Forensic Sci Int Genet 2022; 61:102767. [PMID: 36037736 DOI: 10.1016/j.fsigen.2022.102767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022]
Abstract
Our study enrolled 1200 Serbian males originating from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija. These samples were genotyped using the combination of 23 Y-chromosomal short tandem repeats (Y-STRs) loci and 17 Ychromosomal single nucleotide polymorphisms (Y-SNPs) loci for the haplotype and haplogroup analysis in order to characterize in detail Y chromosome flow in the recent history. Serbia's borders have changed through history, forcing Serbs constantly to migrate to different regions of Balkan Peninsula. The most significant migration waves in the recent history towards present-day Serbia occurred from the regions of Old- Herzegovina and Kosovo and Metohija that lie in the south-west/south. High haplotype diversity and discrimination capacity were observed in all three datasets, with the highest number of unique haplotypes (381) and discrimination capacity (0.97) detected in the samples originating from the present-day Serbia. Haplogroup composition didn't differ significantly among datasets, with three dominant haplogroups (I-M170, E-P170 and R-M198), and haplogroup I-M170 being the most frequent in all three datasets. Haplogroup E-P170 was the second most dominant in the dataset originating from geographical region of Kosovo and Metohija, whereas haplogroup R-M198 was the second most prevalent in the dataset from historical region of Old Herzegovina. Based on the phylogenetic three for haplogroup I constructed within this study, haplogroup I2a1-P37.2 was the most dominant within all three datasets, especially in the dataset from historical region of Old Herzegovina, where 182 out of 400 samples were derived for SNP P37.2. Genetic distances between three groups of samples, evaluated by the Fst and Rst statistical values, and further visualized through multidimensional scaling plot, showed great genetic similarity between datasets from Old Herzegovina and present-day Serbia. Genetic difference in the haplogroup distribution and frequency between datasets from historical region of Old Herzegovina and from geographical region of Kosovo and Metohija was confirmed with highest Fst and Rst vaules. In this study we have distinguished genetic structure, diversity and haplogroup frequencies within 1200 Serbian males from three datasets, relationships among them as well as with other Balkan and European populations, which is useful for studying recent demographic history.
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Affiliation(s)
- Milica Mihajlovic
- University of Belgrade, Faculty of Biology, Center for Forensic and Applied Molecular Genetics, Studentski trg 16, Belgrade 11000, Serbia
| | - Vanja Tanasic
- University of Belgrade, Faculty of Biology, Center for Forensic and Applied Molecular Genetics, Studentski trg 16, Belgrade 11000, Serbia
| | - Milica Keckarevic Markovic
- University of Belgrade, Faculty of Biology, Center for Forensic and Applied Molecular Genetics, Studentski trg 16, Belgrade 11000, Serbia
| | - Miljana Kecmanovic
- University of Belgrade, Faculty of Biology, Center for Forensic and Applied Molecular Genetics, Studentski trg 16, Belgrade 11000, Serbia.
| | - Dusan Keckarevic
- University of Belgrade, Faculty of Biology, Center for Forensic and Applied Molecular Genetics, Studentski trg 16, Belgrade 11000, Serbia
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Mutations in Collagen Genes in the Context of an Isolated Population. Genes (Basel) 2020; 11:genes11111377. [PMID: 33233744 PMCID: PMC7699876 DOI: 10.3390/genes11111377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/16/2023] Open
Abstract
Genetic studies of population isolates have great potential to provide a unique insight into genetic differentiation and phenotypic expressions. Galičnik village is a population isolate located in the northwest region of the Republic of North Macedonia, established around the 10th century. Alport syndrome-linked nephropathy with a complex inheritance pattern has been described historically among individuals in the village. In order to determine the genetic basis of the nephropathies and to characterize the genetic structure of the population, 23 samples were genotyped using a custom-made next generation sequencing panel and 111 samples using population genetic markers. We compared the newly obtained population data with fifteen European population data sets. NGS analysis revealed four different mutations in three different collagen genes in twelve individuals within the Galičnik population. The genetic isolation and small effective population size of Galičnik village have resulted in a high level of genomic homogeneity, with domination of R1a-M458 and R1b-U106* haplogroups. The study explains complex autosomal in cis digenic and X-linked inheritance patterns of nephropathy in the isolated population of Galičnik and describes the first case of Alport syndrome family with three different collagen gene mutations.
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Grochowalski Ł, Jarczak J, Urbanowicz M, Słomka M, Szargut M, Borówka P, Sobalska-Kwapis M, Marciniak B, Ossowski A, Lorkiewicz W, Strapagiel D. Y-Chromosome Genetic Analysis of Modern Polish Population. Front Genet 2020; 11:567309. [PMID: 33193657 PMCID: PMC7644898 DOI: 10.3389/fgene.2020.567309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
The study presents a full analysis of the Y-chromosome variability of the modern male Polish population. It is the first study of the Polish population to be conducted with such a large set of data (2,705 individuals), which includes genetic information from inhabitants of all voivodeships, i.e., the first administrative level, in the country and the vast majority of its counties, i.e., the second level. In addition, the available data were divided into clusters corresponding to more natural geographic regions. Genetic analysis included the estimation of FST distances, the visualization with the use of multidimensional scaling plots and analysis of molecular variance. Y-chromosome binary haplogroups were classified and visualized with the use of interpolation maps. Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level. The use of regional clustering as an alternative to counties and voivodeships provided a more detailed view of the genetic structure of the population. Those regional differences identified in the present study highlighted the need for additional division of the population by cultural and ethnic criteria in such studies rather than just by geographical or administrative regionalization.
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Affiliation(s)
- Łukasz Grochowalski
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Justyna Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Urbanowicz
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
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Kačar T, Stamenković G, Blagojević J, Krtinić J, Mijović D, Marjanović D. Y chromosome genetic data defined by 23 short tandem repeats in a Serbian population on the Balkan Peninsula. Ann Hum Biol 2019; 46:77-83. [PMID: 30829546 DOI: 10.1080/03014460.2019.1584242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Serbs mainly live in the territory of the recently re-established state of Serbia. However, the turbulent history in the Balkan Peninsula has led to settlement of Serbs not only within present day Serbia, but also in different parts of neighbouring countries. AIM To define polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci in a modern Serbian population from the central part of the Balkan Peninsula. SUBJECTS AND METHODS The reference sample consisted of 303 men declared as Serbs over three generations. Localities of the collected materials include the territories of Serbia, Bosnia and Herzegovina, Croatia and Montenegro. DNA samples were typed using the PowerPlex®Y23 amplification kit. RESULTS The highest locus diversity was observed for DYS385 and DYS481. In this study the most abundant haplogroups were I2a, E1b1b, R1a and I1. The largest genetic distances between the Serbs and other close Southern Slavs were for the Macedonians and Slovenians. CONCLUSION This study is the first one to define STR polymorphism of Serbian people not only from Serbia but also from other parts of the Balkan Peninsula. The presented genetic data may be useful in further examinations of the genesis and genetic structuring of the present-day Serbian gene pool.
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Affiliation(s)
- Tamara Kačar
- a DNA Laboratory , National Crime Technical Center, Ministry of the Interior , Belgrade , Serbia
| | - Gorana Stamenković
- b Department for Genetic Research , Institute for Biological Research 'Siniša Stanković', University of Belgrade , Belgrade , Serbia
| | - Jelena Blagojević
- b Department for Genetic Research , Institute for Biological Research 'Siniša Stanković', University of Belgrade , Belgrade , Serbia
| | - Jovica Krtinić
- c 'Milutin Bojić' Library , Belgrade , Serbia and Society of Serbian Genealogists - Origin
| | - Dragan Mijović
- d National Crime Technical Center, Ministry of the Interior , Belgrade , Serbia
| | - Damir Marjanović
- e Department of Genetics and Bioengineering , International Burch University, Francuske revolucije bb , Ilidža , Bosnia and Herzegovina.,f Institute for Anthropological Researches , Zagreb , Croatia
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Maisano Delser P, Ravnik-Glavač M, Gasparini P, Glavač D, Mezzavilla M. Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern. Front Genet 2018; 9:551. [PMID: 30510563 PMCID: PMC6252347 DOI: 10.3389/fgene.2018.00551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
The Slovenian territory played a crucial role in the past serving as gateway for several human migrations. Previous studies used Slovenians as a source population to interpret different demographic events happened in Europe but not much is known about the genetic background and the demographic history of this population. Here, we analyzed genome-wide data from 96 individuals to shed light on the genetic role and history of the Slovenian population. Y chromosome diversity splits into two major haplogroups R1b and R1a with the latter suggesting a genetic contribution from the steppe. Slovenian individuals are more closely related to Northern and Eastern European populations than Southern European populations even though they are geographically closer. This pattern is confirmed by an admixture and clustering analysis. We also identified a single stream of admixture events between the Slovenians with Sardinians and Russians around ∼2630 BCE (2149-3112). Using ancient samples, we found a significant admixture in Slovenians using Yamnaya and the early Neolithic Hungarians as sources, dated around ∼1762 BCE (1099-2426) suggesting a strong contribution from the steppe to the foundation of the observed modern genetic diversity. Finally, we looked for signals of selection in candidate variants and we found significant hits in HERC2 and FADS responsible for blue eye color and synthesis of long-chain unsaturated fatty acids, respectively, when Slovenians were compared to Southern Europeans. While the comparison was done with Eastern Europeans, we identified significant signals in PKD2L1 and IL6R which are genes associated with taste and coronary artery disease, respectively.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
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Nadalin S, Buretić-Tomljanović A, Lavtar P, Starčević Čizmarević N, Hodžić A, Sepčić J, Kapović M, Peterlin B, Ristić S. The lack of association between angiotensin-converting enzyme gene insertion/deletion polymorphism and nicotine dependence in multiple sclerosis. Brain Behav 2017; 7:e00600. [PMID: 28127518 PMCID: PMC5256183 DOI: 10.1002/brb3.600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/14/2016] [Accepted: 10/03/2016] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Blood-borne angiotensin II is generated from angiotensinogen via cleavage by renin and angiotensin-converting enzyme (ACE), an enzymatic cascade known as the renin-angiotensin system (RAS). Several lines of evidence indicate that ACE, beyond its classical role of mediating blood pressure regulation, might contribute to the etiology of substance addictions by influencing dopaminergic signaling. A functional insertion/deletion (I/D) polymorphism of the ACE gene was associated with risk for being a smoker among individuals with depression and with smoking severity in studies comprising patients with depression and healthy controls. Several reports have described significantly increased ACE activity in cerebrospinal fluid and serum among MS patients. Furthermore, in our previous work with MS patients from Croatian and Slovenian populations, we demonstrated that the ACE-I/D polymorphism contributes to an elevated MS risk among male patients. Here we investigated whether the ACE-I/D polymorphism might influence smoking behavior among patients with MS. PATIENTS AND METHODS Genotyping was performed in 521 patients (males/females: 139/382) using polymerase chain reaction. RESULTS We revealed no significant differences in ACE genotype and allele frequencies between smokers and nonsmokers and no significant association between the ACE-I/D polymorphism and either pack-year smoking history or number of cigarettes smoked daily (p > .05, respectively). CONCLUSION The ACE-I/D polymorphism does not contribute either to risk for nicotine dependence or to smoking severity among MS patients. In the context of reports on the ACE-I/D polymorphism and nicotine dependence among healthy controls and patients with depression, we may speculate that the mechanism by which this polymorphism influences nicotine dependence risk differs in MS compared to depression, although not compared to a healthy population. In addition to angiotensin II, other potential ACE substrates, such as substance P and neurotensin, which also influence dopaminergic neurotransmission (and are proposed to be associated with MS), may deserve study in future.
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Affiliation(s)
- Sergej Nadalin
- Department of Biology and Medical Genetics School of Medicine University of Rijeka Rijeka Croatia
| | | | - Polona Lavtar
- Clinical Institute of Medical Genetics University Medical Centre Ljubljana Slovenia
| | | | - Alenka Hodžić
- Clinical Institute of Medical Genetics University Medical Centre Ljubljana Slovenia
| | - Juraj Sepčić
- Postgraduate Studies School of Medicine University of Rijeka Rijeka Croatia
| | - Miljenko Kapović
- Department of Biology and Medical Genetics School of Medicine University of Rijeka Rijeka Croatia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics University Medical Centre Ljubljana Slovenia
| | - Smiljana Ristić
- Department of Biology and Medical Genetics School of Medicine University of Rijeka Rijeka Croatia
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10
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Babić N, Dogan S, Čakar J, Pilav A, Marjanović D, Hadžiavdić V. Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina. Ann Hum Biol 2016; 44:419-426. [PMID: 27826995 DOI: 10.1080/03014460.2016.1259430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations. SUBJECTS AND METHODS The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses. RESULTS The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations. CONCLUSION These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.
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Affiliation(s)
- Naida Babić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
| | - Serkan Dogan
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina
| | - Jasmina Čakar
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Amela Pilav
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Damir Marjanović
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina.,d Institute for Anthropological Researches , Zagreb , Croatia
| | - Vesna Hadžiavdić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
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Schregel J, Eiken HG, Grøndahl FA, Hailer F, Aspi J, Kojola I, Tirronen K, Danilov P, Rykov A, Poroshin E, Janke A, Swenson JE, Hagen SB. Y chromosome haplotype distribution of brown bears (Ursus arctos
) in Northern Europe provides insight into population history and recovery. Mol Ecol 2015; 24:6041-60. [DOI: 10.1111/mec.13448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/17/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
| | | | - Frank Hailer
- School of Biosciences; Cardiff University; Cardiff CF10 3AX Wales UK
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Jouni Aspi
- Department of Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Ilpo Kojola
- Natural Resources Institute; P.O. Box 16 96301 Rovaniemi Finland
| | - Konstantin Tirronen
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Piotr Danilov
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Alexander Rykov
- Pinezhsky Strict Nature Reserve; Pervomayskaja 123a 164610 Pinega Russian Federation
| | - Eugene Poroshin
- Institute of Biology; Komi Research Centre of the Russian Academy of Science; 016761 Syktvkar Russian Federation
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
- Goethe University Frankfurt; Institute for Ecology; Evolution & Diversity; 60438 Frankfurt am Main Germany
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
- Norwegian Institute for Nature Research; 7485 Trondheim Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
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12
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Zupan A, Hauptman N, Glavač D. The maternal perspective for five Slovenian regions: The importance of regional sampling. Ann Hum Biol 2015; 43:57-66. [PMID: 26065896 DOI: 10.3109/03014460.2015.1006678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events. AIM The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations. SUBJECTS AND METHODS A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA. RESULTS Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region. CONCLUSION The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.
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Affiliation(s)
- Andrej Zupan
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Nina Hauptman
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Glavač
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
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13
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Juhász Z, Fehér T, Bárány G, Zalán A, Németh E, Pádár Z, Pamjav H. New clustering methods for population comparison on paternal lineages. Mol Genet Genomics 2014; 290:767-84. [PMID: 25388803 DOI: 10.1007/s00438-014-0949-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
Abstract
The goal of this study is to show two new clustering and visualising techniques developed to find the most typical clusters of 18-dimensional Y chromosomal haplogroup frequency distributions of 90 Western Eurasian populations. The first technique called "self-organizing cloud (SOC)" is a vector-based self-learning method derived from the Self Organising Map and non-metric Multidimensional Scaling algorithms. The second technique is a new probabilistic method called the "maximal relation probability" (MRP) algorithm, based on a probability function having its local maximal values just in the condensation centres of the input data. This function is calculated immediately from the distance matrix of the data and can be interpreted as the probability that a given element of the database has a real genetic relation with at least one of the remaining elements. We tested these two new methods by comparing their results to both each other and the k-medoids algorithm. By means of these new algorithms, we determined 10 clusters of populations based on the similarity of haplogroup composition. The results obtained represented a genetically, geographically and historically well-interpretable picture of 10 genetic clusters of populations mirroring the early spread of populations from the Fertile Crescent to the Caucasus, Central Asia, Arabia and Southeast Europe. The results show that a parallel clustering of populations using SOC and MRP methods can be an efficient tool for studying the demographic history of populations sharing common genetic footprints.
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Affiliation(s)
- Z Juhász
- Department of Complex Systems, Research Centre for Natural Sciences of the HAS, Budapest, Hungary
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Nováčková J, Dreslerová D, Černý V, Poloni ES. The place of Slovakian paternal diversity in the clinal European landscape. Ann Hum Biol 2014; 42:511-22. [PMID: 25374405 DOI: 10.3109/03014460.2014.974668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration. AIM The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape. SUBJECTS AND METHODS This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities. RESULTS It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation. CONCLUSION The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.
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Affiliation(s)
- Jana Nováčková
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| | - Dagmar Dreslerová
- b Department of the Archaeology of Landscape and Archaeobiology , Institute of Archaeology of the Academy of Sciences of the Czech Republic , Czech Republic
| | - Viktor Černý
- c Archaeogenetics Laboratory, Department of the Archaeology of Landscape and Archaeobiology, Institute of Archaeology of the Academy of Sciences of the Czech Republic , Czech Republic , and
| | - Estella S Poloni
- d Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution , University of Geneva , Geneva , Switzerland
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Haplotype data and mutation rates for the 23 Y-STR loci of PowerPlex® Y 23 System in a Northeast Italian population sample. Int J Legal Med 2014; 129:725-8. [DOI: 10.1007/s00414-014-1053-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
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