3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia.

Communities with increased shared ancestry represent invaluable tools for genetic studies of complex traits. "1001 Dalmatians" research program collects biomedical information for genetic epidemiological research from multiple small isolated populations ('metapopulation') in the islands of Dalmatia, Croatia. Random samples of 100 individuals from 10 small island settlements (n<2000 inhabitants) were collected in 2002 and 2003. These island communities were carefully chosen to represent a wide range of distinct and well-documented demographic histories. Here, we analysed their genetic make-up using 26 short tandem repeat (STR) markers, at least 5 cM apart. We found a very high level of differentiation between most of these island communities based on Wright's fixation indexes, even within the same island. The model-based clustering algorithm, implemented in STRUCTURE, defined six clusters with very distinct genetic signatures, four of which corresponded to single villages. The extent of background LD, assessed with eight linked markers on Xq13-21, paralleled the extent of differentiation and was also very high in most of the populations under study. For each population, demographic history was characterised and 12 "demographic history" variables were tentatively defined. Following stepwise regression, the demographic history variable that most significantly predicted the extent of LD was the proportion of locally born grandparents. Strong isolation and endogamy are likely to be the main forces maintaining this highly structured overall population.

The population history of the Croatian linguistic minority of Molise (southern Italy): a maternal view.

This study examines the mitochondrial DNA (mtDNA) diversity of the Croatian-speaking minority of Molise and evaluates its potential genetic relatedness to the neighbouring Italian groups and the Croatian parental population. Intermatch, genetic distance, and admixture analyses highlighted the genetic similarity between the Croatians of Molise and the neighbouring Italian populations and demonstrated that the Croatian-Italian ethnic minority presents features lying between Croatians and Italians. This finding was confirmed by a phylogeographic approach, which revealed both the prevalence of Croatian and the penetrance of Italian maternal lineages in the Croatian community of Molise. These results suggest that there was no reproductive isolation between the two geographically proximate, yet culturally distinct populations living in Italy. The gene flow between the Croatian-Italians and the surrounding Italian populations indicate, therefore, that ethnic consciousness has not created reproductive barriers and that the Croatian-speaking minority of Molise does not represent a reproductively isolated entity.

Y chromosomal heritage of Croatian population and its island isolates.

Y chromosome variation in 457 Croatian samples was studied using 16 SNPs/indel and eight STR loci. High frequency of haplogroup I in Croatian populations and the phylogeographic pattern in its background STR diversity over Europe make Adriatic coast one likely source of the recolonization of Europe following the Last Glacial Maximum. The higher frequency of I in the southern island populations is contrasted with higher frequency of group R1a chromosomes in the northern island of Krk and in the mainland. R1a frequency, while low in Greeks and Albanians, is highest in Polish, Ukrainian and Russian populations and could be a sign of the Slavic impact in the Balkan region. Haplogroups J, G and E that can be related to the spread of farming characterize the minor part (12.5%) of the Croatian paternal lineages. In one of the southern island (Hvar) populations, we found a relatively high frequency (14%) of lineages belonging to P*(xM173) cluster, which is unusual for European populations. Interestingly, the same population also harbored mitochondrial haplogroup F that is virtually absent in European populations--indicating a connection with Central Asian populations, possibly the Avars.

Y chromosome STRs in Croatians.

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) were analyzed in the sample of 457 unrelated Croatian men. A general STR allelic frequency pattern in Croatians corresponds to other European populations with the exception of the loci DYS19 and DYS389II. The most frequent DYS19 allele was 16, while at the DYS389II the most frequent were alleles 30 and 31. The most frequent Y chromosome haplotype (16-13-13-31-24-11-11-13) was found in 33 individuals (7.22%). One hundred and seventy-four haplotypes (38.07%) were observed in single copies.

Inbreeding and susceptibility to osteoporosis in Croatian island isolates.

The aim of this study was to investigate a recessive genetic component in susceptibility to osteoporosis (OP) by comparing its prevalence in isolated villages of three Croatian islands: Brac, Hvar and Korcula with different levels of inbreeding. A random sample of 20-30% adults from 14 villages was obtained, including a total of 1,389 examinees. The average inbreeding coefficient (F) of examinees from each village population was estimated using Wright's path method (based on genealogical information). The morphometry of the metacarpal bones was performed on hand-wrist radiographs of both hands in all examinees. OP was defined as values of cortical index smaller than 2 standard deviations based on distribution of values in examinees of the same sex under 45 years of age. Mean values of cortical index (CI) and prevalence of OP (both standardized by age and weighted for the sample size) in each village were correlated to the mean inbreeding coefficient (F). The coefficient of correlation (r) between F values and CI was -0.28 in males (p = 0.08) and -0.42 in females (p = 0.005), and between F and OP prevalence 0.32 in males (p < 0.001) and 0.43 in females (p < 0.001). These results indicate a trend of increased susceptibility to osteoporosis with increasing level of inbreeding in isolated communities of Croatian islands.

Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits.

The dramatic changes in human population structure over the last 200 years have resulted in significant levels of outbreeding, which, in turn, is predicted to lead to increased levels of individual genetic diversity (genome-wide heterozygosity, h). To investigate possible effects of these large demographic changes on global health, we studied the effect of h, measured as relative heterozygosity, h(R), on 15 disease-related traits in four groups of individuals with widely differing ancestral histories (ranging from outbred to inbred) from the Dalmatian islands in Croatia. Higher levels of h(R), estimated using 1184 STR/indel markers, were found in the outbred group (P < 0.0001) and were associated with lower blood pressure (BP) and total/LDL cholesterol (P = 0.01 and 0.01, respectively) after controlling for other factors, with BP showing a strong sex effect (males P > 0.5 and females P = 0.002). These findings, if replicated, suggest that h(R) be considered as a genetic risk factor in genetic epidemiological studies on common disease traits. They are consistent with the well-known effects of heterosis (hybrid vigour) described when outcrossing animals and plants. Outbreeding resulting from urbanization and migration from traditional population subgroups may be leading to increasing h(R) and may have beneficial effects on a range of traits associated with human health and disease. Other traits, such as age at menarche, IQ and lifespan, which have been changing during the decades of urbanization, may also have been influenced by demographic factors.

Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe.

To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.

The western and eastern roots of the Saami--the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes.

The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the "Saami motif" variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the "Saami motif," was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.

Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia.

It has been often stated that the overall pattern of human maternal lineages in Europe is largely uniform. Yet this uniformity may also result from an insufficient depth and width of the phylogenetic analysis, in particular of the predominant western Eurasian haplogroup (Hg) H that comprises nearly a half of the European mitochondrial DNA (mtDNA) pool. Making use of the coding sequence information from 267 mtDNA Hg H sequences, we have analyzed 830 mtDNA genomes, from 11 European, Near and Middle Eastern, Central Asian, and Altaian populations. In addition to the seven previously specified subhaplogroups, we define fifteen novel subclades of Hg H present in the extant human populations of western Eurasia. The refinement of the phylogenetic resolution has allowed us to resolve a large number of homoplasies in phylogenetic trees of Hg H based on the first hypervariable segment (HVS-I) of mtDNA. As many as 50 out of 125 polymorphic positions in HVS-I were found to be mutated in more than one subcluster of Hg H. The phylogeographic analysis revealed that sub-Hgs H1*, H1b, H1f, H2a, H3, H6a, H6b, and H8 demonstrate distinct phylogeographic patterns. The monophyletic subhaplogroups of Hg H provide means for further progress in the understanding of the (pre)historic movements of women in Eurasia and for the understanding of the present-day genetic diversity of western Eurasians in general.