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| Phylloscopus tokaraensis Saitoh, Shipilina, Xia, Zhang, Seki, Olsson & Alström, 2026 Tokara Leaf Warbler || DOI: doi.org/10.1093/pnasnexus/pgag037 |
Abstract
Despite the escalating biodiversity crisis, many species remain unknown to science and may even disappear unnoticed. This is particularly true for many island populations. We illustrate the problem of detecting overlooked species and its consequences by exploring a rare and geographically restricted migratory songbird. We find that this consists of two—hence even rarer—species: the Japanese endemic Ijima's Leaf Warbler Phylloscopus ijimae from the Izu Islands and the Tokara Leaf Warbler from the Tokara Islands. We describe the latter as a new cryptic species, ie one that is morphologically highly similar to, but genetically distinct from, a known species. The genetic divergence is revealed by analyses of nuclear genome-wide and mitochondrial DNA and supported by differences in vocalizations, while the morphological differences are minimal. We evaluate key conservation genomic indicators, showing that both species show low levels of genetic diversity and signs of a decrease of effective population size. Our genome-wide analysis revealed short runs of homozygosity and a low estimated deleterious load, suggesting limited recent inbreeding and possible purging of harmful alleles—indicators of genetic recovery after past demographic fluctuations. Ijima's Leaf Warbler is already classified as Vulnerable as well as a “Natural Monument” in Japan, and we propose that the Tokara Leaf Warbler should retain this status, with continued focused monitoring. Our study not only highlights the importance of integrating genomics with taxonomy for uncovering cryptic avian diversity but also provides a critical foundation for future conservation efforts.
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| Tokara Leaf Warbler Nakanoshima Phylloscopus tokaraensis (the same individual as in photo labeled A singing male Tokara Leaf Warbler). photo: Per Alström, Uppsala University |
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| Tokara Leaf Warbler Nakanoshima 11June2017-1 Per Alstrom. A singing male Tokara Leaf Warbler Phylloscopus tokaraensis on Nakanoshima, Tokara Islands, in June 2017. P. photo: Per Alström, Uppsala University |
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| One of the Tokara Leaf Warblers Phylloscopus tokaraensis caught on Nakanoshima, Tokara Islands, in June 2017. |
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| Cryptic populations of P. ijimae are geographically separated by more than 1,000 km and have distinct songs. A) Global distribution of P. ijimae. Insets provide detailed maps of the Tokara Islands and northern Izu Islands (map source: Japan Aerospace Exploration Agency (2021). ALOS World 3D-30m DEM, V3.2, January 2021. Distributed by OpenTopography, doi.org/10.5069/G94M92HB. Accessed 2025 March 12). Island names in gray indicate locations where P. ijimae was not observed, while those in black indicate presence. B, C) Adult male, holotype of Phylloscopus tokaraensis new species, Tokara Leaf Warbler (Yamashina Institute for Ornithology number YIO-76774), Nakanoshima, Tokara Islands, 2017 June 10 (photo: Per Alström; for additional photographs, see Table S18). |
Phylloscopus tokaraensis, sp. nov.
Tokara Leaf Warbler
Diagnosis: Phylloscopus tokaraensis and P. ijimae are characterized by the uniformly greyish crown, lacking darker or paler stripes; mainly whitish underparts with contrastingly pale yellow undertail-coverts; narrow pale tips to the greater coverts, forming a thin, sometimes very indistinct, pale wing-bar; and pale orange lower mandible. Easily distinguishable from P. coronatus by the uniformly coloured crown; from P. borealis, P. examinandus and P. xanthodryas by the less distinct pale supercilium and narrower and less contrasting dark stripe on the ear-coverts behind the eye, whiter underparts with contrastingly pale yellow undertailcoverts, and pale orange lower mandible (usually prominent dark tip in P. borealis, P. examinandus and P. xanthodryas but rarely entirely orange); and from P. borealoides and P. tenellipes by the greener upperparts, paler crown which does not ...
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| Cryptic populations of P. ijimae are geographically separated by more than 1,000 km and have distinct songs. A) Global distribution of P. ijimae. Insets provide detailed maps of the Tokara Islands and northern Izu Islands (map source: Japan Aerospace Exploration Agency (2021). ALOS World 3D-30m DEM, V3.2, January 2021. Distributed by OpenTopography, doi.org/10.5069/G94M92HB. Accessed 2025 March 12). Island names in gray indicate locations where P. ijimae was not observed, while those in black indicate presence. B, C) Adult male, holotype of new species, Tokara Leaf Warbler (Yamashina Institute for Ornithology number YIO-76774), Nakanoshima, Tokara Islands, 2017 June 10 (photo: Per Alström; for additional photographs, see Table S18). Examples of single song strophes of type I songs from Tokara (D–G) and Izu (I–L), with a plot of the two PCs from a PCA based on 12 variables (H). Examples of single strophes of type II songs from Tokara (M and N) and Izu (O and P) (recordings: D: ML647192043; E: ML647191975; F: ML647192039; G: ML 647191951; M: 647192011; N: 647191965; all by P.A.; I: by T. Kabaya; J: ML647192103, by T.S.; K: XC749104; L: XC749102; O: XC749102), K, L, O by Geoff Carey; P: ML647356514, by Haruo Kuroda. |
Takema Saitoh, Daria Shipilina, Canwei Xia, Lijun Zhang, Shin-Ichi Seki, Urban Olsson and Per Alström. 2026. Discovering and Protecting Cryptic Biodiversity: A Case Study of A previously Undescribed, Vulnerable Bird Species in Japan. PNAS Nexus. 5(3); pgag037. DOI: doi.org/10.1093/pnasnexus/pgag037 [17 March 2026]
