Application of a method for estimating effective population size and admixture using diagnostic single nucleotide polymorphisms (SNPs): implications for conservation of threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris) in Silver King Creek, California

The threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris, PCT) is endemic to Silver King Creek, California, USA, which was stocked with non-native trout beginning in 1930. Single nucleotide polymorphism (SNP) and microsatellite data reveal that the trout population in Silver King Creek is weakly structured and composed of introgressed California golden trout (Oncorhynchus mykiss aguabonita, CAGT), hatchery rainbow trout (Oncorhynchus mykiss, RT), and some native PCT. Two SNP groups were analyzed: (i) one mitochondrial and five autosomal SNPs, diagnostic between Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) or PCT and CAGT or RT and (ii) one mitochondrial and five autosomal SNPs nearly diagnostic between CAGT and RT. The five autosomal cutthroat-rainbow SNPs were used to jointly estimate the cutthroat trout mixing proportion in Silver King Creek and effective population size (N(e)) of the admixed population, using a coalescent-based maximum likelihood method. Given the stocking history of Silver King Creek, there are two different scenarios that bound the range of expected point estimates for N(e). We obtain point estimates of N(e) = 150 and N(e) = 750 for Silver King Creek under these two scenarios. This method will be useful in cases with differentiated taxa and in prioritizing conservation and restoration programs where the populations of concern are introgressed.