Journal of Undergraduate Research


sequencing complete genome, Cutthroat Trout subspecies, classification


Life Sciences




Since the 1800s, biologists have studied cutthroat trout native to Western North America. Their early work and classification were based on the standards of the day: meristics, the observation and counting of physical features, and morphology. Further improvements came through later studies that added geographic distribution to their phylogenetic classification. Without the foresight of DNA genotyping methods, “traditional taxonomic assessments often failed to accurately capture phylogenetic diversity.” Many discrepancies have since arisen as genetic methods shed new light on cutthroat trout subspecies phylogenies. Current mtDNA work has identified errors in historical classifications of several of these subspecies in the Colorado, Utah, Wyoming, and Idaho regions. Our new knowledge of misclassification has subsequently identified problems in protecting the right endangered subspecies. Genetic diversity progresses as trout populations change due to “habitat fragmentation, overharvest, introduction of nonnative species”, and other factors like sport stocking. DNA genotyping is crucial to protect these species from possible endangerment. Until recently genetic methods for classification have been limited to mtDNA, which utilizes a single locus, so developing a more comprehensive understanding of the nuclear genome is of great importance. The collaboration of the Kauwe lab and the Shiozawa lab at BYU, along with labs at the University of San Francisco, have almost completed sequencing the entire genome of one subspecies of cutthroat trout. Though an important accomplishment, more distantly related cutthroat trout are known to have a different number of chromosomes, so in order to maximize the usefulness of this newly defined genome, we need at least one additional completed genome from a related subspecies. Having completed genome scaffolds from two related subspecies will facilitate accelerated analysis and assessment of all the genetic relationships of cutthroat trout. We further believe that this approach can be adopted to the study of other species to more effectively protect them from endangerment and extinction. Our studies focused on how to develop the protocols and procedures needed to sequence the genome.

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