Cryptic bird species in Japan.

The Japanese archipelago comprises the islands that form the country of Japan. It consists of 6,852 islands with at least 100 m circumference, 430 of those are inhabited. The four main islands, from north to south, are Hokkaido, Honshu, Shikoku, and Kyushu. Honshu is the largest and referred to as the Japanese mainland.

The archipelago has been recognized as a biodiversity hot spot and a new zoogeographic region based on the phylogenetic relationships of its birds and other vertebrates. 

The high degree of biodiversity in Japan is the result of a wide variety of climates and ecosystems, ranging from the humid subtropics in the Ryukyu and Ogasawara islands to the boreal zones in northern Japan, the alpine zone at over 3000 m above sea level, and all its islands and straits between them that have separated species extended periods of time.

The bird fauna of Japan consists of 633 described bird species, including birds that also occur on the eastern Eurasian continent. The Japanese Archipelago is home to 11 endemic resident bird species and six migratory species breeding only in that area. A total of about 250 species are known to breed in Japan. It has been repeatedly disputed whether some populations isolated on the many islands should be recognized as subspecies or as distinct species as many of those birds form morphologically well-defined groups. For a very limited number of species researchers had conducted molecular analyses and found that those groups are rather distinct lineages and a new study using DNA Barcoding adds more species to this list.

The researchers build a DNA Barcode library comprising 93.2% of the bird species breeding in Japan. They found 24 cryptic species candidates in their study. Patterns of these deep intraspecific sequence divergences were consistent with some of the biogeographical boundaries across the Japanese Archipelago such as the Tsugaru Strait, or the Ryukyu Islands. About 10% of the species the team looked at seem to contain some cryptic representatives and they have some explanations for this:

The fluctuating sea levels during the Quaternary would have led to repeated periods of connection, isolation and submergence of the islands of the Japanese Archipelago, which could have isolated bird populations for lengthy periods. Such populations would have retained geographical and temporal isolation without admixture of other populations and extinction for glacial and interglacial periods.These isolated populations may lead to the deep intraspecific genetic divergence observed in 11 Japanese bird species. The distinct intraspecific divergence observed between 23 trans-Palearctic species may reflect the history of isolation and gene flow of these bird populations with respect to the changes in the land-bridges over the straits between the Japanese Archipelago and the Eurasian continent.

This is an extraordinary amount of potentially new species of birds. Finding so many new species in a vertebrate group other than fishes is quite rare. Usually we hear about one or two but not two dozens.