Genetic Structure and Population Affinities of Albanians: A Regional STR-Based Analysis Within the European Context

Abstract

Background/Objectives: Albania occupies a key geographic position in the Balkan Pen-insula, yet its fine scale population structure and genetic relationship with neighboring European populations, remain incompletely characterized. This study investigated the regional genetic structure of the Albanian population and its affinities within the broader European context using autosomal short tandem repeats (STR) markers. Methods: A total of 2000 unrelated individuals representing all 12 administrative regions of Albania were genotyped for 16 autosomal STR loci (D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, THO1, FGA, D10S1248, D22S1045, D2S441, D1S1656, D12S391 and SE33) together with the Amelogenin sex marker. Individuals were grouped into Northern, Central and Southern Albania. Population structure was evaluated using Principal Component Analysis (PCA), pairwise Weir-Cockerham F_ST estimates, Nei’s standard genetic distance, and phylogenetic reconstruction. Comparative analysis in-cluded reference populations from Greece, Italy, Montenegro, Bosnia and Herzegovina, Slovenia, Slovakia, Hungary, Germany and France, using published allele frequency data. Results: PCA demonstrated extensive overlap among individuals from all three Albanian regions, with no distinct regional clustering. The principal components explained only a small proportion of the total genetic variation (PC1 = 0.80%; PC2 = 0.77%), indicating minimal population substructure. F_ST estimates between Northern, Central and South Albania were consistently close to zero, with bootstrap – derived 95% confidence inter-vals overlapping zero for all comparisons, confirming the absence of statistically signif-icance regional differentiation. Nei’s genetic distances among the analyzed European populations varies from approximately 0.004 to 0.014, consistent with the low levels of differentiation typically observed among European STR datasets. Phylogenetic analysis identified three major clusters: Albania and Greece formed the closest genetic pair, with Montenegro and subsequently Italy joinig this southeastern cluster: France and Germany clustered together; whereas Bosnia nd Herzegovina, Slovenia, Slovakia and Hungary formed a distinct Central Balkan/Central European cluster. Conclusions: The Albanian population exhibits a high degree of genetic homogeneity across its geographic regions, reflecting extensive historical gene flow and limited inter-nal population stratification. Comparative analyses place Albanians in close genetic proximity to neighboring southeastern European populations, particularly Greece, while preserving the broader genetic structure expected across Europe.