Refining Phylogenetic Relationships Among Cutthroat Trout

The modern recognition of the diversity within Oncorhynchus clarkii was based on a combination of morphological traits and geographical distribution.  This was quickly followed by the application of molecular tools to help refine the understanding of interrelationships among the cutthroat trout.  Our lab began with allozyme work, then shifted to Southern blots of ribosomal DNA and mitochondrial genomes, digested with restriction enzymes.  With the development of the PCR we began to use restriction enzyme digests of individual mtDNA genes, ultimately moving to gene sequencing.  While we developed some diagnostic nuclear markers we mainly focused our efforts on mtDNA because of the difficulty in developing primers for nuclear genes.  More recently we have used next-generation DNA sequencing to investigate single nucleotide polymorphisms (SNPs).  We are currently generating transcriptome sesquences for marker development.  Each advance in technique has added to our perspective and understanding of the evolution of cutthroat trout.  Based on mtDNA it appears that three major lineages of cutthroat trout exist, the Coastal, the Lahontan and Westslope, and the Yellowstone complex of Behnke - the Yellowstone, Bonneville, Colorado, Rio Grande, and Greenback.  Within these groups, further subdivisions are becoming more obvious.