Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

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Abstract

Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

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Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

David Bryant, Vincent Moulton (2004)

We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.

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Tracing European founder lineages in the Near Eastern mtDNA pool.

M. Richards, V. Macaulay, E. Hickey … (2000)

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

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Harvesting the fruit of the human mtDNA tree.

Antonio Torroni, Alessandro Achilli, Vincent Macaulay … (2006)

Human mitochondrial DNA (mtDNA) studies have entered a new phase since the blossoming of complete genome analyses. Sequencing complete mtDNAs is more expensive and more labour intensive than restriction analysis or simply sequencing the control region of the molecule. But the efforts are paying off, as the phylogenetic resolution of the mtDNA tree has been greatly improved, and, in turn, phylogeographic interpretations can be given correspondingly greater precision in terms of the timing and direction of human dispersals. Therefore, despite mtDNA being only a fraction of our total genome, the deciphering of its evolution is profoundly changing our perception about how modern humans spread across our planet. Here we illustrate the phylogeographic approach with two case studies: the initial dispersal out of Africa, and the colonization of Europe.

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Author and article information

Contributors

Peristera Paschou: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2014

Publication date (Electronic): 22 August 2014

Volume: 9

Issue: 8

Electronic Location Identifier: e105090

Affiliations

[1 ]Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Estonia

[2 ]Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina

[3 ]Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia

[4 ]Faculty of Pharmacy, University of Sarajevo; Bosnia and Herzegovina

[5 ]University Center of Forensic Science, Split, Croatia

[6 ]Genos doo, Zagreb, Croatia

[7 ]Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia

[8 ]Institute for forensic medicine, criminology and and medical deontology, Medical Faculty, University of St. Cyril and Methodius, Skopje, F.Y.R of Macedonia

[9 ]National forensic laboratory, Ministry of the Interior, Slovenia

[10 ]Forensic Center, Police Directorate, Danilovgrad, Montenegro

[11 ]Croatian Academy of Science and Art, Zagreb, Croatia

Democritus University of Thrace, Greece

Author notes

* E-mail: lejla_kova@ 123456yahoo.com

Competing Interests: The authors have the following interests. Dr. Vedrana Skaro's affiliation to Genos company does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

Conceived and designed the experiments: LK KT DM. Performed the experiments: LK KT HVT EM TB VS. Analyzed the data: LK KT AMI HVT EM AK BY AS. Contributed reagents/materials/analysis tools: PR SK KD DP ZJ AL VS. Wrote the paper: LK KT EM DM AMI. Revised the manuscript: TB DP VS AL ZJ KD HVT SK PR AK BY.

Article

Publisher ID: PONE-D-14-04156

DOI: 10.1371/journal.pone.0105090

PMC ID: 4141785

PubMed ID: 25148043

SO-VID: ef399cf6-4f5a-4f7f-9a11-ae229adadb1e

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 4 February 2014

Date accepted : 20 July 2014

Page count

Pages: 15

Funding

This work was supported by the European Union European Regional Development Fund through the Centre of Excellence in Genomics, by the Estonian Biocentre (EBC) and the University of Tartu, by the European Commission grant 205419 ECOGENE to the EBC, and by the Estonian Basic Research Grant SF 0270177s08. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

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Most cited references 21

Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

Tracing European founder lineages in the Near Eastern mtDNA pool.

Harvesting the fruit of the human mtDNA tree.

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