Comparative range-wide phylogeography and evolutionary history of the two Pyrrhocorax species (Passeriformes:...

Phylogeographic analyses provide key insights into how historical climate change, geographic barriers, and species-specific ecological traits shape evolutionary divergence. We investigated the phylogeography and evolutionary history of the two extant chough species, the red-billed chough (Pyrrhocorax pyrrhocorax, n = 65) and the alpine chough (Pyrrhocorax graculus, n = 33), across most of their Palearctic range. Using concatenated mitochondrial DNA sequences, complemented by nuclear intron markers, we reconstructed and test lineage divergence and historical dispersal patterns. Haplotype networks revealed long branches separating geographically isolated populations, indicating prolonged historical isolation. Phylogenetic analyses confirmed the monophyly of Pyrrhocorax and revealed a deep split between the two species at approximately 2.5 million years ago. Formal Ancestral Range Analysis (ARA) indicates that Himalayan regions served as the ancestral hub for both species. Within P. graculus, two main mitochondrial lineages were identified: a highly divergent Himalayan and European-Moroccan lineages (around 94 kya). In contrast, P. pyrrhocorax exhibited pronounced phylogeographic complexity, with major east-west differentiation and additional regional structuring across Europe, North Africa, Canary Islands, Ethiopia, and Central Asia, with divergence times ranging from  0.75 Mya to 61-94 kya. Quantitative metrics (π and Da) revealed significant interspecific divergence and distinct population-level structuring. Our results highlight the combined roles of historical isolation, Pleistocene climate dynamics, altitudinal gradients, and ecological constraints in shaping divergence in Pyrrhocorax. This phylogeographic framework provides essential guidance for conservation management, emphasizing the importance of preserving distinct evolutionary lineages in fragmented and declining populations.