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An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago


The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.

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All DNA sequences generated for this project are archived on GenBank (MH379402-MH379451, MH384612-MH384765). Detailed sampling table (Online Appendix 1), Nexus-formatted alignments (Online Appendix 2), detailed phylogenetic trees (Online Appendix 3), and bGMYC output plots (Online Appendix 4), for each focal lineage are archived on Peter Hosner’s FigShare page at


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We would like to thank field collectors who contributed genetic samples and specimens to this project. Several museums supplied tissue grants: The American Museum of Natural History (Paul Sweet), Cincinnati Museum of Natural History (Herman Mays), Field Museum of Natural History (Dave Willard), Louisiana State Museum of Natural Science (Donna Dittman and Steve Cardiff) and the University of Kansas Biodiversity Institute (Mark Robbins). The National Science Foundation (DEB-0743491 and DEB-1241181), American Ornithologists’ Union, American Museum of Natural History Chapman Fund, and the University of Kansas Panorama Fund supported fieldwork, The National Science Foundation (DEB-1110619) and the University of Kansas Graduate Student Research Fund supported lab work. Consejo Nacional de Ciencia y Tecnología (CONACyT) funded a postdoctoral fellowship (Expediente 93730) to LASG at the University of Kansas. We are grateful to the Department of Environment and Natural Resources and the Protected Areas and Wildlife Bureau of the Philippines for facilitating collecting and export permits. Joe Manthey, Hannah Owens, and Town Peterson gave helpful comments that improved the manuscript.

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Correspondence to Peter A. Hosner.

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Hosner, P.A., Campillo, L.C., Andersen, M.J. et al. An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago. Conserv Genet 19, 1153–1168 (2018).

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