Croatian Genetic Heritage: Renewed Y Chromosome Story Two Decades Later

Abstract

Aim: To analyze an additional set of Y-Chromosome genetic markers to acquire a more detailed insight into the diversity of the Croatian population. Methods: The total number of 518 Yfiler™ Plus profiles were genotyped. Allele, haplotype frequencies, and haplotype diversity were calculated using the STRAF software package v2.0.4. Genetic distances were quantified by Rst using AMOVA online tool from the YHRD. The evolutionary history was inferred using the neighbor-joining method of phylogenetic tree construction in MEGAX software. Whit Athey's Haplogroup Predictor v5 was used for additional comparison with available regional and other European populations. Results: The total of 507 haplotypes were used for genetic STR analysis. The interpopulation study on 17 Y-STR markers shows the lowest genetic diversity between the Croatian and Bosnian-Herzegovinian populations and the highest between the Croatian and Irish populations. Additional interpopulation comparison with the original 27 Y-STR markers (for the population with available data) was also performed. A total of 518 haplotypes were used in the determination of haplogroup diversity. Haplogroup I with its sublineage I2a expressed the highest prevalence. Haplogroup R, with its major sublineage R1a, is the second most abundant in the studied Croatian population, except for the subpopulation of Hvar, where E1b1b is the second most abundant haplogroup. Rare haplogroups also confirmed in this study are L, T, and Q. G1 is detected for the very first time in the Croatian population. Conclusion: New insight into differences between examined subpopulations of Croatia and their possible (dis)similarities with neighboring abroad populations was notified. bioRxiv preprint doi: https://doi.org/10.1101/2022.03.21.485134; this version posted May 2, 2022. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. The Y chromosome (∼ 60 Mb) is relatively small and inherited from father to son unchanged (except for occasional mutations). Except for the small pseudoautosomal regions (PAR), there is no recombination between the X and Y chromosome (1-3). This event is the reason why haplotype inheritance through the male lineage can be tracked and analyzed (2, 4-6). The Y chromosome mostly consists of repetitive sequences (around 50%), which are singlebase substitutions, Alu elements, and Long Interspersed Nuclear Elements (LINEs). Short tandem repeats (STRs), as repetitive elements are the base of population genetic studies. Their average mutational frequency is ∼0.2% per generation (7, 8). Y haplogroup can be defined as a part of the Y chromosome family related by ancestry and determined by a specific set of Y chromosomal single nucleotide polymorphisms (Y-SNPs). It is of great importance to better understand of the demographic processes that shaped modern populations (8, 9). The low mutation rate makes Y-SNP markers suitable for the conventional method of Y haplogroup defining. Y chromosome haplogroups can also be successfully predicted from Y-STR markers (Y-STR haplotype) using Y-STR haplogroup predicting tools. Lately, this method has gained much attention due to its labor-, time-, and cost-effectiveness (10). The haplotype helps analyze the influence of genes on disease-related alleles and represents the set of alleles on the same chromosome. On the other hand, major haplogroups (branches of Y-chromosome phylogeny), labeled A-T, define the establishment and expansion of major population groups and can indicate the time scale and the route of major migration events (11). The main aim of this research is to update information about Croatian Y chromosome diversity by using additional Y STR loci to compare new results with the previously published results generated using Y-STR and Y-SNP markers (12-20). Another goal was to analyze the genetic structure of five regional subpopulations (with the local centers in Osijek, Pula, Varaždin, Split, and Hvar Island) by identifying the most common haplogroups in these regions. The analysis also included genetic differences between these five subpopulations and their potential (dis)similarity with neighboring countries.