Abstract
Background: The Balkan Peninsula has served as an important migration corridor between Asia Minor and Europe throughout humankind's history and a refugium during the Last Glacial Maximum. Past migrations such as the Neolithic expansion, Bronze Age migrations, and the settlement of Slavic tribes in the Early Middle Ages, are well known for their impact on shaping the genetic pool of contemporary Balkan populations. They have contributed to the high genetic diversity of the region, especially in mitochondrial DNA (mtDNA) lineages. Serbia, located in the heart of the Balkans, reflects this complex history in a broad spectrum of mtDNA subhaplogroups. Methods: To explore genetic diversity in Serbia and the wider Balkan region, we analyzed rare mtDNA subclades-R0a, N1a, N1b, I5, W, and X2-using publicly available data. Our dataset included already published sequences from 3499 HVS-I/HVS-II and 1426 complete mitogenomes belonging to West Eurasian and African populations, containing both contemporary and archaeological samples. We assessed the parameters of genetic diversity found in different subclades across the studied regions and constructed detailed phylogeographic trees and haplotype networks to determine phylogenetic relationships. Results: Our analyses revealed the observable geographic structure and identified novel mtDNA subclades, some of which may have originated in the Balkan Peninsula (e.g., R0a1a5, I5a1, W1c2, W3b2, and X2n). Conclusions: The geographic distribution of rare subclades often reveals patterns of past population movements, routes, and gene flows. By tracing the origin and diversity of these subclades, our study provided new insights into the impact of historical migrations on the maternal gene pool of Serbia and the wider Balkan region, contributing to our understanding of the complex genetic history of this important European crossroads.