{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T08:52:31Z","timestamp":1791535951021,"version":"4.3.4"},"reference-count":129,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    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 (\n                    <jats:italic>Pyrrhocorax pyrrhocorax<\/jats:italic>\n                    ,\n                    <jats:italic>n<\/jats:italic>\n                    \u00a0=\u00a065) and the alpine chough (\n                    <jats:italic>Pyrrhocorax graculus<\/jats:italic>\n                    ,\n                    <jats:italic>n<\/jats:italic>\n                    \u00a0=\u00a033), 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\n                    <jats:italic>Pyrrhocorax<\/jats:italic>\n                    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\n                    <jats:italic>P. graculus<\/jats:italic>\n                    , two main mitochondrial lineages were identified: a highly divergent Himalayan and European\u2013Moroccan lineages (around 94 kya). In contrast,\n                    <jats:italic>P. pyrrhocorax<\/jats:italic>\n                    exhibited pronounced phylogeographic complexity, with major east\u2013west differentiation and additional regional structuring across Europe, North Africa, Canary Islands, Ethiopia, and Central Asia, with divergence times ranging from \u00a00.75 Mya to 61\u201394 kya. Quantitative metrics (\n                    <jats:italic>\u03c0<\/jats:italic>\n                    and\n                    <jats:italic>Da<\/jats:italic>\n                    ) 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\n                    <jats:italic>Pyrrhocorax<\/jats:italic>\n                    . This phylogeographic framework provides essential guidance for conservation management, emphasizing the importance of preserving distinct evolutionary lineages in fragmented and declining populations.\n                  <\/jats:p>","DOI":"10.7717\/peerj.21799","type":"journal-article","created":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T08:36:21Z","timestamp":1791534981000},"page":"e21799","source":"Crossref","is-referenced-by-count":0,"title":["Comparative range-wide phylogeography and evolutionary history of the two\n                    <i>Pyrrhocorax<\/i>\n                    species (Passeriformes: Corvidae)"],"prefix":"10.7717","volume":"14","author":[{"given":"I\u00f1igo","family":"Palacios-Mart\u00ednez","sequence":"first","affiliation":[{"name":"Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales, CSIC, Consejo Superior de Investigaciones Cient\u00edficas, Madrid, Spain"},{"name":"Escuela de Doctorado UAM, Centro de Estudios de Posgrado, Universidad Aut\u00f3noma de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Morinha","sequence":"additional","affiliation":[{"name":"Laboratory of Biodiversity and Molecular Genetics, Morinha Lab, Vila Real, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Antonio","family":"D\u00e1vila","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n en Recursos Cineg\u00e9ticos, IREC (CSIC, UCLM, JCCM), Consejo Superior de Investigaciones Cient\u00edficas, Ciudad Real, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Tohidifar","sequence":"additional","affiliation":[{"name":"Iran Bird Records Committee, Tehran, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Stubbe","sequence":"additional","affiliation":[{"name":"Martin-Luther Universit\u00e4t Halle-Wittenberg, Halle-Wittenberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annegret","family":"Stubbe","sequence":"additional","affiliation":[{"name":"Martin-Luther Universit\u00e4t Halle-Wittenberg, Halle-Wittenberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Augusto","family":"De Sanctis","sequence":"additional","affiliation":[{"name":"Stazione Ornitologica Abruzzese, Pescara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stavros","family":"Xirouchakis","sequence":"additional","affiliation":[{"name":"School of Sciences and Engineering, Natural History Museum of Crete, University Campus (Knossos), University of Crete, Crete, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillermo","family":"Blanco","sequence":"additional","affiliation":[{"name":"Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales, CSIC, Consejo Superior de Investigaciones Cient\u00edficas, Madrid, 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