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Objectives: The research objective of this study is to enlarge and deepen the Y chromosome research on the Croatian population and enable additional insights into the population diversity and historic events that shaped the current genetic landscape of Croatia and Southeastern Europe (SEE). Materials and Methods: A high-resolution phylogenetic and phylogeographic analysis of 66 biallelic (SNPs) and 17/19 microsatellite (STRs) markers of the Y chromosome was performed using 720 Croatian samples. The obtained results were placed in a wider European context by comparison with ~4450 samples from a number of other European populations. Results: A high diversity of haplogroups was observed in the overall Croatian sample, and all typical European Y chromosome haplogroups with corresponding clinal patterns were observed. Three distinct genetic signals were identifiable in the Croatian paternal gene pool - I2a1b-M423, R1a1a1b1a*-M558 and E1b1b1a1b1a- V13 haplogroups. Discussion: The analyses of the dominant and autochthonous I2a1b-M423 lineage (>30%) suggest that SEE had a significant role in the Upper Paleolithic, the R1a1a1b1a*-M558 lineage (19%) represents a signal from present day Slavic populations of Central Europe in the Croatian population, and the phylogeography of the E1b1b1a1b1a-V13 clade (around 9%) implies cultural diffusion of agriculture into Europe via the Balkan Peninsula.

Croatian islands are examples of genetic isolates, with low level of heterozygosity and high level of inbreeding due to endogamy, but also due to ethnohistory, biological characteristics, migrational patterns, and ecological and sociocultural environments. Such small communities can reflect large demographic processes that happened in human prehistory and history and give us insight into the ancient migratory routes and the formation of Croatian and Southeast European gene pool. The aim of this study was to evaluate the level of isolation of an insular population from the island of Lastovo in the Dubrovnik archipelago, based on the observed mitochondrial and Y chromosome haplogroup distribution. We analyzed 51 mtDNAs and 12 Y chromosomes to observe the differences and similarities in the maternal and paternal landscapes of the island. The observed haplogroups are considered to originate from Neolithic times, when the Island served as an important point on the sailing routes connecting the western and eastern coast of the Adriatic. Lastovo was in complete isolation for 500 years during the period of Dubrovnik Republic, when evolutionary forces and practice of consanguinity affected the demography of the island. Based on both mtDNA and Y chromosome markers, Lastovo showed elevated frequencies of certain subclades, most probably as a result of genetic drift, which makes the island a great outlier when compared to other Croatian populations.

Croatian Eastern Adriatic islands represent well-characterized genetic isolates, concerning their ethnohistory, biological traits, disease prevalence, migration patterns and environmental and sociocultural characteristics. Such small communities can reflect large demographic processes that happened in human prehistory and history and give us insight into the ancient migratory paths and forming of the Croatian and Southeast European gene pool. The aim of this study was to evaluate the level of isolation of insular populations based on the observed haplogroup distribution and frequencies of 720 samples from 12 Croatian subpopulations and to define the main processes that have shaped present Y chromosome variation of Eastern Adriatic islands and Croatia in general. A high level of haplogroup and haplotype diversity has been detected in the overall sample and the observed haplogroup frequency distributions correspond to an average European population, suggesting a dynamic gene flow in this region throughout history. The PCA plots show that the position of different Croatian subpopulations mostly corresponds to their actual geographic location. Also, it is noticeable that most of them are stretched along an axis, depending of the portion of I2a2-M423 and R1a-M458/M558 sublineages in their sample. Although the studied insular populations show an expected (mostly Paleolithic) paternal genetic structure corresponding to their geographic location, genetic structure of some islands exhibits interesting results due to the significant effect of evolutionary forces and specific historic episodes (like Lastovo, Cres and Dugi otok).

Island of Hvar is situated in the central Eastern Adriatic, and its relatively small rural population has been reproductively isolated throughout history. Therefore, founder effects, genetic drift and inbreeding have had a significant role in the shaping of the current genetic diversity of Hvar Islanders. Island isolates are among the most suitable populations for theoretical analyses of microevolutionary processes and population differentiation. In this context, mitochondrial DNA (mtDNA) an Y chromosome studies are used to reveal demographic history, migrations, population origins and genetic structure of a population. We analyzed SNP markers of 161 mtDNAs and of 412 Y chromosomes from the island of Hvar, including STRs of 20 male islanders. Results showed a much higher number of mtDNA haplogroups (34) than Y chromosome ones (15). Haplotype diversity analysis showed low gene diversity among both mtDNAs and Y chromosomes on the island, while haplogroup distribution points to a significant population differentiation between the eastern and western part of the island. This substructure effect stems from different representation of subhaplogroups, as well as from differences between haplotypes within the same subhaplogroups and is based on specific demographic processes which occurred on Hvar during its history. When put in a wider context, haplogroups of both uniparental markers placed Hvar in the context of South- Eastern Europe, but the frequencies and the distribution of certain haplogroups significantly deviate from other SEE populations.

This study aimed to clarify the effect that evolutionary forces and historical events have had on the population structure of Mljet, an Eastern Adriatic island, through the analyses of mtDNA and Y chromosome variability and comparison between the two markers. As previously reported, island of Mljet has the lowest mtDNA diversity among the Eastern Adriatic islands. We used 39 Y chromosome samples and previously published 68 mtDNA. For comparison, we also used 179 Y chromosome samples from the mainland city of Dubrovnik together with previously reported 181 mtDNAs. Results of both maternal and paternal haplogroup lineages on the island fit within the south-east European context. But, analysis of the mtDNA haplogroup variability showed very low diversity, which was not expected considering the relative closeness of the mainland city of Dubrovnik, as reported in previous research. After Y chromosome analysis, the variation of paternal lineages showed average diversity as usually expected, but it is not in concordance with the low mtDNA diversity. Both mtDNA and Y chromosome results could tell their own separate stories about the shaping of Mljet’s genetic landscape, but combined, they are both an outcome of numerous past demographic and migration processes. Considering very turbulent and unlucky historical events that occurred on the island, severe living environment, the practice of consanguinity and the presence of autochthonous diseases, the island of Mljet serves as an excellent example for studying the interplay of microevolutionary forces and demographic actions that shape the population structure of genetic isolates.

Slovenia is a European country situated at the crossroads of main European cultural and trade routes. It is geographically more linked to Central Europe, but history draws it closer together to its ex-Yugoslavian, Southeast European (SEE) neighbors. Slovenian maternal heritage has not been analyzed since 2003 and our aim was to analyze SNP markers of 97 Slovenian mtDNAs in high resolution to see where this population fits according to its maternal genetic variation. We compared the Slovenian sample with the neighboring SEE populations, as well as with other published European population datasets. Also, we compared the obtained mtDNA variation results with the available Slovenian Y chromosome data to see how these two uniparental marker systems correspond to each other. In the PC plot based on mtDNA haplogroups frequencies, Slovenian population has an outlying position mostly due to the increased prevalence of J (14.4%) and T (15.4%) clade and especially because of the abundance and diversity of J1c samples in Slovenia, represented with 8 haplotypes and in a percentage of >11%. Although in an outlying position, Slovenian mtDNA variation still shows a certain degree of affinity to SEE. On the contrary, Slovenia’s paternal genetic heritage yielded results that correspond to the population's geographic location and groups Slovenian population considerably closer to Central European countries, based on increased prevalence of Northern/Central European R1a-M198 and decreased frequency of Balkan-specific I2a2- M423. Such differences in maternal and paternal marker systems could indicate that Slovenian genetic variation was influenced by sex-biased demographic events.

The Island of Hvar is situated in the central eastern Adriatic, and its relatively small rural population has been reproductively isolated thought history. Therefore, founder effects, genetic drift and inbreeding have had significant role in the shaping of current genetic diversity of Hvar Islanders. We analyzed Y-chromosome SNP markers of 412 Hvar islanders in high resolution, with the aim to investigate the current paternal genetic diversity. We found a relatively high frequency (6.1%) of unrelated male samples belonging to the Q*-M424 haplogroup, which is unusual for European populations. Interestingly, a previous study showed 9 individuals from Hvar with mitochondrial haplogroup F, which is almost absent in Europe. Both findings could indicate a certain connection with Asian populations, where these haplogroups are most common. This might be a result of several migratory events in the history, one of which could be linked to the ancient Silk Road, the other a consequence of the arrival of the Slavs, following the Avars, to the eastern Adriatic in the 6th century or due to the expansion of the Ottoman Empire in 16th to 18th century. The presence of these rare mitochondrial and Y-chromosome lineages are an example of founder effect and random genetic drift which, in this small island with a high degree of isolation and endogamy, had a strong impact on shaping the genetic diversity of the population.