Loss of genetic variation and effective population size of Kirikuchi charr: implications for the management of small, isolated salmonid populations

Abstract Small, isolated populations may face extinction due to a combination of inbreeding depression and other threats. Effective population size (Ne) is one comprehensive measure that allows us to evaluate the genetic status of a population, and to make management decisions regarding genetic viability. We simulated loss of genetic variation and estimated Ne for two small, isolated populations of Kirikuchi charr Salvelinus leucomaenis japonicus, the endangered, southernmost local populations of the genus Salvelinus in the world, using VORTEX, an individual‐based stochastic PVA model. Approximately half of the genetic variation was lost over 200 years regardless of census population size and demographic parameters, and Ne estimates were roughly 50 in each of the two populations, suggesting the possibility of inbreeding depression. The target population size of Ne>500, by securing long‐term viability, is several times that of the present size of each of the populations studied, and no local habitats maintaining such a target number are considered to exist. The results strongly indicate a need for recovering natural connections and potential gene flow among local populations. However, the impending threat to these populations from non‐native charr widely distributed throughout the drainage has prevented the recovery of the connections. Given the small Ne of the two populations, it would be necessary to retain gene flow artificially within or across local populations. This will be true of many other salmonid populations that have been isolated or fragmented recently.