Species that exhibit intraspecific variation in migratory behavior provide a valuable opportunity to study the evolution of avian migration. The Northern Boobook (Ninox japonica) has two subspecies in East Asia, one sedentary (N. j. totogo) and one migratory (N. j. japonica). The validity and residential status of the two subspecies has never been examined through genetic analysis. Their coexistence in Taiwan provides an excellent opportunity to explore their genetic differentiation and migratory behavior. Analyzing the mitochondrial cytochrome b gene of 77 samples including ascertained breeders, ascertained migrants, and topotypes of the sedentary N. j. totogo from Lanyu, we found a coexistence of two clades with a 1.72 % sequence divergence, and both clades were highly supported in phylogenetic analyses. The clade containing ascertained breeders occurs year round in Taiwan and is the only resident population during the breeding season. The other clade containing ascertained migrants appears only in non-breeding seasons and coexists with the former during these months. Topotypes of N. j. totogo from Lanyu were clustered with N. j. japonica, which undermines its classification as a subspecies. We suggest treating N. j. totogo as an invalid taxon and treating the sedentary population in Taiwan as a unique cryptic lineage until further information is available. The discovery of this lineage will improve our understanding of the owls in terms of animal conservation, genetic biodiversity, and the evolution of their migratory behavior. ? 2013 Dt. Ornithologen-Gesellschaft e.V.
