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

• Published in: Molecular ecology 2019-05, Vol.28 (10), p.2573-2593
• Main Authors: Amish, Stephen J., Ali, Omar, Peacock, Mary, Miller, Michael, Robinson, Morgan, Smith, Seth, Luikart, Gordon, Neville, Helen
• Format: Article
• Language: English
• Subjects: Adaptation; Basins; Biological evolution; body condition; Conservation; conservation hatchery adaptation; Demographics; Desert environments; Deserts; Divergence; full‐sibling families; Genetic markers; Genomes; genome‐wide association studies; High temperature; Historical account; Homeostasis; Immunity; Lahontan cutthroat trout; lake life history; Lakes; Loci; Markers; Metabolism; Nucleotides; Oncorhynchus clarkii henshawi; Outliers (statistics); Populations; Principal components analysis; Salmon; Single-nucleotide polymorphism; Temperature tolerance; Thermal stress; thermal tolerance; Threatened species; Trout; Wildlife conservation
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.15100

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