DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.

Morphological differentiation of island-dwelling organisms provides model systems for studying evolution. Computed tomography (CT) scanning is an entirely non-destructive technique that provides detailed three-dimensional (3D) images of physical structures. Geometric morphometrics has been increasingly used in avian morphology studies by analyzing 3D data obtained from CT scans. We used geometric morphometrics to evaluate the morphological details of the skulls of three, genetically distinct, island populations of the Ryukyu Scops Owl Otus elegans: O. e. elegans from the northern part of the Ryukyu Archipelago, O. e. elegans from the southern part of the Ryukyu Archipelago, and O. e. interpositus from Minami-daito Island. Skulls were scanned using an X-ray CT system and the digitized 3D coordinates of 16 landmarks for each skull were analyzed in order to describe geometric morphometric features. O. e. interpositus was found to have a significantly smaller skull than either population of O. e. elegans. From principle component analysis of shape variation, we also found that the skull shape of O. e. interpositus differed significantly from both the northern and southern groups of O. e. elegans. This difference was in terms of PC1, which mainly represented relative anteroposterior length, and angle of the orbit. We inferred that the small skull of O. e. interpositus is partly a consequence of the particular founders of the population, or evolutionary selection that has taken place on Minami-daito Island and that the distinctive shape of the skull of O. e. interpositus is partly a consequence of adaptations for foraging efficiency, or of morphological integration.

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Although cranial morphology of modern birds has been an important subject of evolutionary studies, detailed information on postnatal ontogeny of the avian skull remains very scarce. Herein, a wild population of the black-tailed gull (Larus crassirostris) breeding on Kabu Island was examined to explore relationships between their growth strategies and ontogenetic changes in the cranial shape. By examining growth series covering a major part of the postnatal ontogenetic period, it was clarified that the typical form of the adult larid skull was produced through dynamic proportional changes among cranial structures after hatching. Cranial structures related to the oral capacity and deglutition (e.g., some elements of hyoid bones) attained the adult sizes before fledging, whereas other structures apparently reached the adult sizes well after leaving the nest. The palatal width exhibited positively allometric growth against the skull volume in chicks in the early nestling stage, followed by a period of negative allometry in the later growth stage. A nestling gull has to acquire swallowing ability by the time of fledging at the latest because this ability is apparently essential for a food intake without parental aid. In addition, because nestlings mainly feed on foodstuffs supplied by their parents, previous studies suggested the possibility that siblings within a nest compete for food resources. Under this scenario, early acquisition of swallowing abilities, as indicated by the allometric patterns of relevant cranial structures, may be an adaptive trait that enhances survival of nestlings.