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With a broad sampling across five Hawaiian Islands, we deciphered the evolutionary history of <jats:italic>P. pellucidum<\/jats:italic>, identified nonhybrid lineages and intraspecific hybrids, and inferred the relative influence of geography and ecology on their distributions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p><jats:italic>Polypodium pellucidum<\/jats:italic> is monophyletic, dispersing to the Hawaiian archipelago 11.53\u20137.77\u2009Ma and diversifying into extant clades between 5.66 and 4.73\u2009Ma. We identified four nonhybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidated several intraspecific hybrid combinations and evidence for undiscovered or extinct \u201cghost\u201d lineages contributing to extant hybrid populations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We provide a foundation for revising the taxonomy of <jats:italic>P. pellucidum<\/jats:italic> to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific, divergent clades within <jats:italic>P. pellucidum.<\/jats:italic> Intraspecific hybrids have likely arisen due to ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawai'i's diverse fern flora and illuminated cryptic taxa to allow better\u2010informed conservation efforts.<\/jats:p><\/jats:sec>","DOI":"10.1002\/ajb2.16379","type":"journal-article","created":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T01:57:30Z","timestamp":1722391050000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern <i>Polypodium pellucidum<\/i>"],"prefix":"10.1002","volume":"111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3282-2175","authenticated-orcid":false,"given":"Jonas I.","family":"Mendez\u2010Reneau","sequence":"first","affiliation":[{"name":"Department of Biology University of Louisiana at Lafayette 410 East St. Mary Boulevard, Billeaud Hall Lafayette 70504 LA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph L.","family":"Richards","sequence":"additional","affiliation":[{"name":"Department of Biology University of Louisiana at Lafayette 410 East St. Mary Boulevard, Billeaud Hall Lafayette 70504 LA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2342-4346","authenticated-orcid":false,"given":"Julia","family":"Hobbie","sequence":"additional","affiliation":[{"name":"Department of Biology Utah State University BNR 117, 5305 Old Main Hill Logan 84322 UT USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Bollich","sequence":"additional","affiliation":[{"name":"Department of Biology University of Louisiana at Lafayette 410 East St. Mary Boulevard, Billeaud Hall Lafayette 70504 LA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3398-7377","authenticated-orcid":false,"given":"Nicholas J.","family":"Kooyers","sequence":"additional","affiliation":[{"name":"Department of Biology University of Louisiana at Lafayette 410 East St. Mary Boulevard, Billeaud Hall Lafayette 70504 LA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8656-7726","authenticated-orcid":false,"given":"Erin M.","family":"Sigel","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of New Hampshire 105 Main St. Durham 03824 NH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,7,30]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1420-9101.2012.02599.x"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1139\/b04-105"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.2307\/3237219"},{"key":"e_1_2_9_6_1","first-page":"1840","volume-title":"Molecular evolution and adaptive radiation","author":"Baldwin B.G.","year":"1997"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.2307\/2845635"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.3732\/ajb.1200199"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11406"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_2_9_12_1","first-page":"3","article-title":"Revised list of Hawaiian pteridophyta","volume":"25","author":"Christensen C.","year":"1925","journal-title":"Bernice P. 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