Using New Technology to Answer an Old Question: Estimating Effective Population Size of an Isolated Endemic Sculpin

Estimating effective population size (N_e) is critical for understanding the vulnerability of species, especially species with restricted distributions. The Shoshone sculpin (Cottus greenei) is endemic to Idaho and restricted to spring habitats in the Hagerman Valley of the Snake River drainage. It is recognized as a species of special concern by Idaho Department of Fish and Game and US Fish and Wildlife Service. A previous survey of Shoshone sculpin using seven microsatellite DNA markers, developed in other Cottus species, succeeded in describing diversity and structure within and among populations of Shoshone sculpin, but failed to provide precision in N_e estimation. In this study, we developed a panel of 419 single nucleotide polymorphism (SNP) markers based on a restriction site associated DNA (RAD) library using 192 individuals from 11 populations. Using this suite of SNP markers, we re-evaluate the ability to estimate N_e for this species. We also assess the utility of these SNP markers for assessing population structure and diversity across the species range.