Assessing genetic diversity among lineages of Gila Trout based on neutral and adaptive single nucleotide polymorphic loci

Authors: David Camak, Megan Osborne, David Propst, Thomas Turner

Year: 2019

Abstract

Gila Trout, Oncorhynchus gilae, is a federally protected species that inhabits headwater streams of the Gila and San Francisco rivers in New Mexico and Arizona. Gila Trout occupy habitats that test the limits of their physiological tolerances. Severe droughts, floods, and wildfires present risks of local extirpation. Gila Trout is actively managed and past focus has been on preserving ‘purity’ of individual lineages. Now, genetic rescue and restoration of metapopulation dynamics are planned. Therefore, it is imperative to understand sources of genetic variation available to effectively conserve genetic diversity and existing population structure within Gila Trout. Using a dataset of 961 high-quality single nucleotide polymorphisms (SNPs), we characterized genetic diversity among all known lineages of Gila Trout. Gila Trout lineages are highly structured. Individual lineages contain low, yet unique, genetic diversity and low effective population sizes. Spruce Creek lineage had the lowest diversity with an expected heterozygosity estimate of 0.02 and 75% of loci monomorphic. Iron Creek lineage had the highest observed heterozygosity (0.30). All lineages were significantly differentiated from one another, but Iron Creek, Main Diamond Creek, and South Diamond Creek lineages showed the least differentiation relative to other lineages. A set of SNPs associated with genes related to immunity, ion homeostasis, growth, and thermal tolerances were also characterized and analyzed. Our data indicate evidence for local adaptation despite low genetically effective population sizes. The data suggest a management strategy focused on increasing genetic diversity while retaining the unique diversity within each lineage.