Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan

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 <i>Phylloscopus ijimae</i> 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.