High Mitochondrial Haplotype Diversity and Western Palearctic Genetic Connectivity in White Stork (Ciconia ciconia) Populations of the South Caucasus

Understanding how historical climatic oscillations and contemporary dispersal interact to shape genetic diversity is central to interpreting population structure in long-distance migratory birds. The White Stork (Ciconia ciconia) has a broad trans-Eurasian distribution, yet populations from the Caucasus region remain underrepresented in population genetic studies. Here, we investigate mitochondrial and nuclear genetic variation in breeding populations from Armenia, a region located at the junction of Europe and Southwest Asia. We analyzed sequence variation in the mitochondrial control region and COI gene together with a nuclear intron (SPIN) from 102 individuals sampled across northern, central, and southern Armenia and integrated these data with publicly available Eurasian sequences. Genetic diversity indices, haplotype networks, mismatch distributions, and hierarchical analyses of molecular variance were used to evaluate spatial genetic structure and demographic history. Armenian populations exhibited high mitochondrial haplotype diversity but heterogeneous nucleotide diversity, consistent with complex demographic histories. AMOVA revealed no significant genetic differentiation among Armenian populations (FST = 0.019, p = 0.226) or between Armenia and Europe (FCT = −0.021, p = 0.754), indicating that Armenian breeding populations form part of a single, well-connected Western Palearctic mitochondrial gene pool. Mismatch distributions revealed a consistent secondary peak across all three populations, suggesting demographic complexity that may reflect the retention of older mitochondrial lineage diversity, though this interpretation remains tentative given the limited discriminatory power of mismatch analyses alone and requires confirmation through expanded sampling and complete mitogenome sequencing. These results indicate that Armenian White Stork populations are genetically diverse and well-connected to the broader Western Palearctic population, while also carrying signatures of a complex demographic history potentially shaped by Pleistocene lineage divergence and post-glacial admixture. Our findings provide a regional genetic baseline for an understudied part of the species’ range and highlight the South Caucasus as a candidate area for future genomic studies integrating complete mitogenomes and genome-wide nuclear markers.