Exploration of Neutral and Functional Genetic Variation in a Highly Diverse Inland Trout through Paired-End RAD Sequencing

The Lahontan cutthroat trout (LCT) represents one of the deepest lineages of cutthroat trout.  LCT have persisted through dramatic Pleistocene climate fluctuations, and currently occupy a broad landscape characterized by contrasting alpine/desert stream and lake environments.  Accordingly, LCT have diversified into several major geographic units (possibly even sub-species), likely experiencing different selective pressures across diverse temperature and hydrologic environments (e.g., small mountain streams, large terminal desert lakes).  We used ~5000 SNPs discovered from paired-end RAD sequencing to characterize population genetic structure and to explore potential signals of selection across the genome using wild populations and family contrasts.  Samples included hatchery broodstock families developed for recovery of the western lake form of LCT, derived from an out-of-basin population transplanted from the now-extirpated Pyramid Lake.  LCT from Pyramid Lake historically attained world-record body sizes and are thought to have been adapted to the warm, prey-rich, alkaline and saline environment of this desert terminal lake.  We discuss results from various contrasts using both an F_ST outlier test in the presence of high levels of genetic drift, and an association test (qfam) correlating genetic variation among known, individual family members from the broodstock to their individual phenotypes of temperature tolerance and body condition.