Evidence for Long-Term Persistence and Local Diversification of the White-Tailed Sea-Eagle Haliaeetus albicilla in the Lower Danube Region: Insights from Mitochondrial DNA Phylogeography

Background/Objectives: The White-tailed Sea-eagle, Haliaeetus albicilla, experienced severe population declines throughout Europe during the nineteenth and twentieth centuries, followed by a remarkable recovery in recent decades. Although the genetic structure of northern and central European populations has been extensively investigated, the phylogeographic history and contribution of the lower Danube population to the mitochondrial genetic diversity of the species remain poorly understood. Methods: We analyzed mitochondrial control region (MT-CR HVR1) sequences from White-tailed Sea-eagles breeding in the Danube Delta Biosphere Reserve (DDBR) and integrated these data with previously published sequences covering the species’ distribution across Europe and Asia; a total of 480 samples were examined. Results: The analysis revealed 47 haplotypes, including 11 haplotypes unique to the DDBR population. Phylogeographic analyses support the Scandinavian Peninsula as the ancestral source area of the species, followed by an early colonization of Central Europe and subsequent expansion into the Balkan Peninsula through the Danube corridor. The Romanian population exhibited the highest haplotype diversity among the investigated regions (Hd = 0.9367) and was characterized by numerous private haplotypes and a predominance of haplogroup C (approximately 76% of individuals), which was rare or absent in most northern and central European populations. Demographic analyses revealed significant evidence of recent population expansion following historical bottlenecks (Fu’s Fs = −5.736, p = 0.006), whereas gene-flow estimates indicated only moderate connectivity with neighbouring Balkan and Central European populations. Conclusions: The high frequency of private haplotypes, the absence of significant isolation-by-distance patterns, and the distinct distribution of mitochondrial haplogroups, characterized by the predominance of haplogroup C, suggest that the current DDBR population may have originated primarily through local demographic recovery rather than recent large-scale recolonization. Our results indicate that the lower Danube region represents an important reservoir of genetic diversity and support the hypothesis that the Danube Delta may have acted as a potential secondary refugium and center of diversification for H. a. in southeastern Europe.