Assessing thermal adaptation using family‐based association and F ST outlier tests in a threatened trout species

Abstract

Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance ( p p F ST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests ( p

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