Background/Question/Methods Hybridization and genetic introgression between native endangered species and introduced species has been dramatically increasing worldwide, and lead to many population level as well as species level extinctions. One example of this is the introduction of rainbow trout, Oncorhynchus mykiss, into native Westslope cutthroat trout, Oncorhynchus clarki lewisi, and Yellowstone cutthroat trout, Oncorhynchus clarki bouvieri, habitats. Genetically “pure” Westslope cutthroat trout have been reduced to roughly 2% of their historic levels, and geneomic extinctions in both Westslope and Yellowstone cutthroat populations have been attributed to hybridization with introduced rainbow trout through the formation of hybrid swarms. Genomic extinctions occur when linked genes that contribute to local adaptations are broken up by the introgression of genes from another species. 
The WSUV Salmonid Genetics Lab is developing a suite of species specific markers to be able to quantitatively determine levels of hybridization and introgression between populations of Westslope and Yellowstone cutthroat trout with introduced rainbow trout. To accomplish this, 12 genes of interest have been examined for single nucleotide polymorphisms (SNPS), that are specific to only one species. A bacterial artificial chromosome (BAC) library, developed from a homozygous clonal line of rainbow trout, was screened for genes of interest. Identified clones were end sequenced to aid in the development of linked haplotype markers. Linked markers reduce the probability of point mutations giving false positive hybrid confirmations. TaqMan assays are being developed to easily score markers at various state and federal Fish and Wildlife labs as well as interested private labs. Management policies can then be devised for regions where hybridized and non-hybridized populations are confirmed. 
 Results/Conclusions Protein coding genes were targeted for species specific markers. Diagnostic SNPS have been identified in P-53, Met-B, CBR1, HSP70b, HSP90, Tnsf, TryIII, PrLc2, and Cal genes. BAC clones containing these genes have been end sequenced and linked markers are being developed from this data. 454 sequencing of entire BACs containing P-53, Met B, CBR1, HSP70b, and HSP90 is also being performed. Diverse populations are being screened using these genes to confirm markers prior to development of Taqman assays; to be completed by the summer of 2009.
This work is supported by a grant from the USFWS/Abernathy Fish Technology Center.