A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups

Emir Šehović 1 , Martin Zieger 3 , Lemana Spahić 1 , Damir Marjanović 1 , 2 , and Serkan Dogan 1
  • 1 International Burch University, Department of Genetics and Bioengineering, Sarajevo, Bosnia and Herzegovina
  • 2 Institute for Anthropological Research, , Zagreb, Croatia
  • 3 Institute of Forensic Medicine, Forensic Molecular Biology Dpt., University of Bern, 3007, Bern, Switzerland

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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  • Athey TW. 2006. Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. J Genet Geneal 2:34-39.

  • Babicki S, Arndt D, Marcu A, Liang Y, Grant JR, Maciejewski A, Wishart DS. 2016. Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. (epub ahead of print). doi:10.1093/nar/gkw419

  • Ballantyne K. N, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, et al. 2010. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. The American Journal of Human Genetics 87(3): 341-353.

  • Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, et al.2014. Toward Male Individualization with Rapidly Mutating Y -Chromosomal Short Tandem Repeats. Human mutation 35(8):1021-1032.

  • Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular biology and evolution 16(1):37-48.

  • Barbarii LE, Burkhard R, Dan Dermengiu D. Y-chromosomal STR haplotypes in a Romanian population sample. 2003. International journal of legal medicine 117(5):312-315.

  • Bar-Yosef Ofer, 2002. The Upper Palaeolithic Revolution. Annual Reviews Anthropology 31:1, 363-393

  • Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, Myres NM, et al. 2009. Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. European Journal of Human Genetics 17(6):820-830.

  • Belledi M, Poloni ES, Casalotti R, Conterio F, Mikerezi I, Tagliavini J, et al. 2000.Maternal and paternal lineages in Albania and the genetic structure of Indo-European populations. European journal of human genetics: EJHG 8(7):480.

  • Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, et al. 2012. Mapping the origins and expansion of the Indo-European language family. Science 337(6097):957-960.

  • Cullen J, 2008. World Haplogroup and Haplo-I Subclade Predictor. www.members.bex.net/jtcullen515/haplotest.htm. Accessed 27 May 2016.

  • Ćetković, Gentula M, Nevski A. 2015.Y-DNA haplogroup predictor – NevGen. www.nevgen.org/. Accessed 27 May 2016.

  • Davidović S, Malyarchuk B, Aleksic J. M, Derenko M, Topalovic V, et al. 2015. Mitochondrial DNA perspective of Serbian genetic diversity. American journal of physical anthropology 156(3), 449-465.

  • Doğan S, Ašić A, Doğan G, Besic L, Marjanović D. 2016. Y-Chromosome Haplogroups in the Bosnian-Herzegovinian Population Based on 23 Y-STR Loci. Human biology 88(3):201-9.

  • Doğan S, Babic N, Gurkan C, Goksu A, Marjanović D, Hadziavdic V. 2016. Y-chromosomal haplogroup distribution in the Tuzla Canton of Bosnia and Herzegovina: A concordance study using four different in silico assignment algorithms based on Y-STR data. HOMO-Journal of Comparative Human Biology 1;67(6):471-83.

  • Doğan S, Gurkan C, Dogan M, Balkaya HE, Tunc R, Demirdov DK, Ameen NA, Marjanović D. 2017. A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis. PloS one 3;12(11):e0187408.

  • Emmerova B, Ehlera E, Comasd D, Votrubovaa J, Vanek D. 2017. Comparison of Y-chromosomal haplogroup predictors. Forensic Science International 6:145-147.

  • Ferri G, Tofanelli S, Alu M, Taglioli L, Radheshi E, Corradini B, et al. 2010. Y-STR variation in Albanian populations: implications on the match probabilities and the genetic legacy of the minority claiming an Egyptian descent. International journal of legal medicine 124(5):363-370.

  • Grugni V, Battaglia V, Kashani BH, Parolo S, Al-Zahery N, Achilli et al. 2012. Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PloS one 7(7): e41252.

  • Gurkan C, Sevay H, Demirdov DK, Hossoz S, Ceker D, Teralı K, Erol AS. 2017. Turkish Cypriot paternal lineages bear an autochthonous character and closest resemblance to those from neighbouring Near Eastern populations. Annals of human biology 17;44(2):164-74.

  • Gusmao L, Sanchez-Diz P, Calafell F, Martin P, Alonso CA, Alvarez-Fernandez F, et al. 2005. Mutation rates at Y chromosome specific microsatellites. Human Mutation 26(6):520-528.

  • Hammer, Ø, Harper D.A.T, Ryan P.D. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4(1):9.

  • Heraclides A, Bashiardes E, Fernández-Domínguez E, Bertoncini S, Chimonas M, Christofi V, King J, Budowle B, Manoli P, Cariolou MA. 2017. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots. PloS one 16;12(6):e0179474.

  • Kayser M, Lao O, Anslinger K, Augustin C, Bargel G. Edelmann J, et al. 2005. Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromo-some analysis. Human Genetics 117(5): 428-443.

  • Kushniarevich A, Utevska O, Chuhryaeva M, Agdzhoyan A, Dibirova K, Uktveryte I, et al. 2015. Genetic heritage of the Balto-Slavic speaking populations: a synthesis of autosomal, mitochondrial and Y-chromosomal data. PLoS One 10(9):e0135820.

  • Lemmen C, Gronenborn, D, & Wirtz, K. W. 2011. A simulation of the Neolithic transition in Western Eurasia. Journal of Archaeological Science 38(12), 3459-3470.

  • Marjanović D, Fornarino S, Montagna S, Primorac D, Hadziselimovic R, Vidovic S, et al. 2005. The peopling of modern Bosnia -Herzegovina: Y -chromosome haplogroups in the three main ethnic groups. Annals of Human Genetics 69(6): 757-763.

  • Mirabal S, Varljen T, Gayden T, Regueiro M, Vujović S, Popović D, et al. 2010. Human Y -chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan Peninsula. American journal of physical anthropology 142(3):380-390.

  • Özdoğan M. 2011. Archaeological evidence on the westward expansion of farming communities from eastern Anatolia to the Aegean and the Balkans. Current Anthropology 52(S4), S415-S430.

  • Pala M, Olivieri A, Achilli A, Accetturo M, Metspalu E, et al. 2012. Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. The American journal of human genetics 90(5), 915-924.

  • Peričić M, Barać Lauc L, Martinović Klarić I, Janićijević B, Behluli I, Rudan P. 2004. Y chromosome haplotypes in Albanian population from Kosovo. Forensic science international 146(1):61-64.

  • Peričić M, Barać Lauc L, Martinović Klarić I, Rootsi S, Janićević B, et al. 2005. High-Resolution Phylogenetic Analysis of Southeastern Europe Traces Major Episodes of Paternal Gene Flow Among Slavic Populations. Molecular Biology and Evolution 22(10):1964-1975

  • Petrejčíková E, Čarnogurská J, Hronská D, Bernasovská J, Boroňová I, Gabriková D, et al. 2014. Y-SNP analysis versus Y-haplogroup predictor in the Slovak population. Anthropologischer Anzeiger 71(3):275-285.

  • Posada D, Crandall KA. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends in ecology & evolution 16(1):37-45.

  • Primorac D, Marjanović D, Rudan P, Villems R, Underhill P. A. 2011. Croatian genetic heritage: Y-chromosome story. Croatian medical journal 52(3): 225-234.

  • Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, et al. 2014. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Science International. Genetics 12: 12-23.

  • Regueiro M, Rivera L, Damnjanovic T, Lukovic L, Milasin J, Herrera RJ. 2012. High levels of Paleolithic Y-chromosome lineages characterize Serbia. Gene 498(1):59-67.

  • Roostalu U, Kutuev I, Loogväli E. L, Metspalu E, Tambets K, et al. 2006. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Molecular biology and evolution 24(2), 436-448.

  • Rootsi S, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, et al. 2004. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. The American Journal of Human Genetics 75(1):128-137

  • Semino O, Passarino G, Oefner P J., Lin Alice A., Arbuzova S, et al. 2000. The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective. Science 290 (5494):1155-1159.

  • Semino O, Passarino G, Brega A, Fellous M, Santachiara-Benerecetti AS. 1996. A view of the neolithicdemic diffusion in Europe through two Y chromosome-specific markers. American journal of human genetics 59(4):964.

  • Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, et al. 2005.Y-chromosome evidence of southern origin of the East Asian–specific haplogroup O3-M122. The American Journal of Human Genetics 77(3):408-419.

  • Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139(1), 457-462.

  • Stevanović M, Dobricić V, Keckarević D, Perović A, Savić-Pavićević D, Keckarević-Marković M, et al. Human Y-specific STR haplotypes in population of Serbia and Montenegro. 2007. Forensic science international 171(2):216-221.

  • Šarac J, Auguštin D. H, Metspalu E, Novokmet N, Missoni S, Rudan P. 2018. Maternal Genetic Profile of Serbian And Montenegrin Populations from Southeastern Europe. Genetics & Applications 1(2), 14-22.

  • Šarac J, Šarić T, Auguštin D. H, Novokmet N, Vekarić N, Mustać M, et al. 2016. Genetic heritage of Croatians in the Southeastern European gene pool—Y chromosome analysis of the Croatian continental and Island population. American Journal of Human Biology 28(6): 837-845.

  • Urasin V. 2013.Y Predictor by VadimUrasin v1.5.0. http://predictor.ydna.ru/. [Accessed 27 May 2016].

  • Veldhuis D, Underdown S.J. (2017) Human biology of migration, Annals of Human Biology 44:5, 393-396

  • Wang CC, Jin L, Li H. 2014. Natural selection on human Y chromosomes. J. Genet. Genomics 41:47-52.

  • Wang CC, Yan S, Li H. 2010. Surnames and the Y chromosomes. Commun. Contemp. Anthropol 4:26-33.

  • Willuweit S, Roewer L. 2015. The new Y chromosome haplotype reference database. Forensic Science International: Genetics 15:43-48.

  • Zaharova B, Andonova S, Gilissen A, Cassiman JJ, Decorte R, Kremensky I. 2001. Y-chromosomal STR haplotypes in three major population groups in Bulgaria. Forensic science international 124(2):182-186.

  • Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, et al. 2003. The genetic legacy of the Mongols. The American Journal of Human Genetics 72(3):717-721.

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