Using a genetic approach to identify undetermined fish to species, with an example from Central Arizona

Authors: Matthew Mayer, Scott Bonar, Melanie Culver, Kaitlyn Gahl

Year: 2022

Abstract

Identification of small fish can be difficult if not impossible in the field. Genetic Identification can provide a solution; however, there are techniques that need to be followed to identify the organism. We used mitochondrial genetics to confirm the species identification of small cyprinids found in remote wilderness streams in the Coconino National Forest in Central Arizona. As part of a project to help protect and develop the in-stream water rights for these streams; we identified the fishes in these creeks and their habitat use. We found a few sites in the upper portions of the two streams and one of their tributaries that were occupied by juvenile cyprinids that we could not identify based off appearance and morphology. We were aware that assuming their identity would be risky and planning a return trip would be difficult, so we collected fish from each stream for a total of 27 specimens all of which we stored in alcohol. We returned them to the University of Arizona and isolated the DNA of the fish using a Qiagen kit and identified them to species using a portion of the Mitochondrial Cytochrome B gene. To do that we Sanger sequenced all the individual fish’s portions of the Cytochrome B gene after running a Polymerase Chain Reaction to amplify the sequences. Then after sequencing we cleaned the sequences and used the National Library of Medicines, National Institute of Biotechnology Resources, Nucleotide Blast Query option to determine the specific identity of the fish. By going through this process, we learned that genetic identification is straightforward and can be done easily by people with no prior experience in genetics. Using this process, we were able to identify fish that otherwise would not have been Identifiable and provide this knowledge to the managers of these streams to improve future decisions and conservation efforts.