Hybridization, Isolation, and Low Genetic Diversity of Kirikuchi Char, the Southernmost Populations of the Genus Salvelinus

The Kirikuchi char Salvelinus leucomaenis japonicus, which is endemic to the Kii Peninsula, central Honshu, Japan, is a relict nonanadromous char adapted to the southernmost habitats of the genus Salvelinus. As a result of anthropogenic disturbance, the distribution of the Kirikuchi char is now limited to the two upper drainages of the Totsu River system in the Kii Peninsula and this subspecies is now threatened with extinction. The present study determined the genetic population structure of the Kirikuchi char by using partial sequences of the mitochondrial cytochrome b gene, seven microsatellites, and a major histocompatibility complex (MHC) gene (exon 2 of MHC class II beta). The results indicated that native Kirikuchi char populations in both drainages have hybridized extensively with stocked S. leucomaenis pluvius or S. leucomaenis leucomaenis that were originally distributed in eastern Honshu. Native populations were restricted to isolated headwaters above natural falls or sediment control dams and showed very low genetic diversity: one mitochondrial DNA haplotype and average heterozygosity of 0.00-0.12 in microsatellites and 0.00-0.50 in the MHC gene. The distinct genetic differences between the Kirikuchi char populations in the two drainages suggest that these populations should be managed as separate conservation units. A high risk of hybridization with stocked nonnative subspecies widely distributed throughout the drainages has prevented the recovery of natural connections that permit gene flow between local populations of Kirikuchi char. Given the extremely low genetic diversity of the remaining Kirikuchi char populations, it is necessary to take proactive management measures, such as the promotion of artificial gene flow across local populations within each drainage and genetic restoration using the data presented here.