{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T10:52:25Z","timestamp":1774349545932,"version":"3.50.1"},"reference-count":71,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PAPIIT\/DGAPA"},{"DOI":"10.13039\/501100005739","name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","doi-asserted-by":"crossref","award":["IN214523"],"award-info":[{"award-number":["IN214523"]}],"id":[{"id":"10.13039\/501100005739","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003141","name":"CONAHCYT","doi-asserted-by":"crossref","award":["CF-2023-G188"],"award-info":[{"award-number":["CF-2023-G188"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"crossref"}]},{"name":"PAPIIT\/DGAPA UNAM","award":["IN220620"],"award-info":[{"award-number":["IN220620"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    The evolutionary drivers of genetic and phenotypic diversity in widespread Neotropical birds remain poorly understood, particularly in species with high dispersal capabilities. In this study, we examine the population genetic structure, demographic history, and phenotypic variation of\n                    <jats:italic>Euphonia hirundinacea<\/jats:italic>\n                    across its Mesoamerican range using NextRad genomic data, as well as geographic and phenotypic variables. A maximum-likelihood phylogeny confirmed the monophyly of\n                    <jats:italic>E. hirundinacea<\/jats:italic>\n                    , with two well-supported clades corresponding to geographically segregated populations that align with the subspecies\n                    <jats:italic>E. h. hirundinacea<\/jats:italic>\n                    and\n                    <jats:italic>E. h. gnatho<\/jats:italic>\n                    . Our findings indicate moderate genetic differentiation partially shaped by isolation by distance (IBD), with the Nicaragua Depression acting as a semi-permeable barrier that allows limited gene flow. Most phenotypic traits did not correlate with genetic divergence, geographic distance, or environmental variables. However, in females, wing chord and throat coloration were significantly associated with both genetic and geographic distances. Demographic analyses support a scenario of divergence initiated during Pleistocene climatic fluctuations (\u223c2,668,739.13 years ago), followed by population expansion during Holocene (\u223c20,000 years ago) and secondary contact, supported by ecological niche models. The species\u2019 ecological flexibility and high vagility likely mitigated long-term isolation and facilitated rapid post-glacial recolonization. Overall, our findings highlight the roles of isolation by distance, Pleistocene climatic dynamics, geographic barriers, and sex-specific traits in shaping diversification in a highly mobile Neotropical bird.\n                  <\/jats:p>","DOI":"10.7717\/peerj.20916","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T08:25:27Z","timestamp":1774340727000},"page":"e20916","source":"Crossref","is-referenced-by-count":0,"title":["Genomic structure, phenotypic variation and drivers of diversification in\n                    <i>Euphonia hirundinacea<\/i>\n                    (Aves: Fringilidae)"],"prefix":"10.7717","volume":"14","author":[{"given":"Melisa","family":"V\u00e1zquez-L\u00f3pez","sequence":"first","affiliation":[{"name":"Posgrado en Ciencias Biol\u00f3gicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"},{"name":"Museo de Zoolog\u00eda, Departamento de Biolog\u00eda Evolutiva, Facultad de Ciencias, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luz E.","family":"Zamudio-Beltr\u00e1n","sequence":"additional","affiliation":[{"name":"Museo de Zoolog\u00eda, Departamento de Biolog\u00eda Evolutiva, Facultad de Ciencias, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra M.","family":"Ram\u00edrez-Barrera","sequence":"additional","affiliation":[{"name":"Instituto de Ciencias de la Atm\u00f3sfera y Cambio Clim\u00e1tico, Universidad Nacional Aut\u00f3noma de M\u00e9xico,  Mexico City, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patricia","family":"Escalante-Pliego","sequence":"additional","affiliation":[{"name":"Instituto de Biolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Blanca E.","family":"Hern\u00e1ndez-Ba\u00f1os","sequence":"additional","affiliation":[{"name":"Museo de Zoolog\u00eda, Departamento de Biolog\u00eda Evolutiva, Facultad de Ciencias, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2026,3,24]]},"reference":[{"issue":"1694","key":"10.7717\/peerj.20916\/ref-1","doi-asserted-by":"publisher","first-page":"2675","DOI":"10.1098\/rspb.2010.0343","article-title":"Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna","volume":"277","author":"Barber","year":"2010","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"3","key":"10.7717\/peerj.20916\/ref-2","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1016\/j.ympev.2011.11.020","article-title":"Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae)","volume":"62","author":"Barrera-Guzm\u00e1n","year":"2012","journal-title":"Molecular Phylogenetics and Evolution"},{"issue":"2","key":"10.7717\/peerj.20916\/ref-3","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1038\/s41437-023-00662-1","article-title":"Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil","volume":"132","author":"Batalha-Filho","year":"2024","journal-title":"Heredity (Edinb)"},{"key":"10.7717\/peerj.20916\/ref-4","doi-asserted-by":"publisher","first-page":"iii\u2013418","DOI":"10.2307\/40167673","article-title":"A distributional survey of the birds of the Mexican state of Oaxaca","volume":"43","author":"Binford","year":"1989","journal-title":"Ornithological Monographs"},{"issue":"5","key":"10.7717\/peerj.20916\/ref-5","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1111\/cobi.13486","article-title":"Generation lengths of the world\u2019s birds and their implications for extinction risk","volume":"34","author":"Bird","year":"2020","journal-title":"Conservation Biology"},{"key":"10.7717\/peerj.20916\/ref-6","doi-asserted-by":"publisher","DOI":"10.2305\/IUCN.UK.2020-3.RLTS.T22722727A139236054.en","article-title":"Euphonia hirundinacea. 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