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.

Summary1. In many studies on cooperative breeding, helping by auxiliary individuals is considered to enhance the reproductive success of breeders. However, confounding factors other than helping could cause the differences. 2. The endemic Madagascan rufous vanga Schetba rufa (Vangidae) is known as a cooperatively breeding species. In order to evaluate the effect of helping in this species, we compared the reproductive success of breeding pairs helped by auxiliary birds, and pairs breeding alone, based on a 6-year study of an individually colour-banded population in the Ampijoroa Forest Station, western Madagascar. 3. This species is single-brooded. Brood reduction was rare and most cases of nesting failure were due to total loss of clutches and broods, probably as a result of predation. 4. Monogamous pairs with one to four auxiliary birds comprised 24 -43% of all breeding groups. Most auxiliary birds were male offspring remaining in their natal territory. Auxiliary males provided a considerable contribution towards antipredator defence, territory defence and to the provisioning of nestlings. In about one-third of the groups, however, the auxiliary males did not help at all. Male offspring may remain in their natal territory in order to avoid harassment by other territorial individuals, and to increase the probability of territory acquisition and of copulation with unrelated breeding females. 5. The probability of breeding successfully was higher, and the number of fledglings produced was larger among pairs with auxiliary birds than among those breeding alone. However, provisioning by auxiliaries neither enhanced the growth rate of nestlings, nor reduced the number of days they required to fledge. 6. A pair-match comparison of the same pairs between years with and without auxiliaries showed no effect of group size on their reproductive success. Even provisioning by auxiliaries did not affect the reproductive success. 7. Pairs accompanied by auxiliary birds for more than 1 year enjoyed higher reproductive success even in those years when they were without auxiliaries than did pairs always breeding alone. 8. Neither the simple presence of auxiliaries nor their helping behaviour enhanced the reproductive success of breeding pairs. The quality of the breeding pair and /or their territory may have affected their reproductive success and, as a result, increased the number of auxiliaries.

The Japanese subspecies of Hodgson's Hawk-eagle, Spizaetus nipalensis orientalis, is considered threatened and has been designated as Endangered by the Japanese government. We determined the complete mitochondrial DNA (mtDNA) sequence of this species and designed a primer set to amplify a highly variable region of mtDNA, part of the control region (CR), based on this complete sequence. Using the primers, we amplified the CR and then determined the haplotypes of 178 samples collected at different sites in Japan. A nested cladistic analysis indicated that gene flow within some clades was restricted. The inference key implied that isolation by distance had caused the restriction of gene flow. Moreover, the ranges of the clades in which restricted gene flow was detected overlapped with the ranges of other clades. These results suggest that there is no fragmental population of Hodgson's Hawk-eagle in Japan and that this species has dispersed within short distances, at least in some lineages. Genetic diversity was high in comparison with other species. Therefore, at least in terms of genetic diversity, the Japanese population of Hodgson's Hawk-eagle is probably not in a critical situation.

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