Assessing thermal adaptation using family‐based association andF_SToutlier 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 < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST 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 < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.

Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

“…These methodologies can enable the discovery of putative associations between SNPs and environmental factors that likely impact genetic structure of the studied species [18,19]. Additionally, there are now increased possibilities for the identification of the function of the candidate genes (see [20]).…”

Seascape Genomics of the Sugar Kelp Saccharina latissima Along the North Eastern Atlantic Latitudinal Gradient

“…For example, utilisation of a large number of SNP loci enables the detection, amongst these markers, of outlier loci that are potentially under selection and also facilitates searches for associations between SNPs and environmental factors that are likely to impact genetic structure [15,16]. Additionally, there are now increased possibilities for the identification of candidate genes with known functions (see [17]).…”

Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

“…Moreover, variations in temperature and precipitation affect phenomena such as changes in dispersal and reproduction timing, age at maturity, growth, fecundity, and survival (Crozier & Hutchings, 2014; Hecht et al, 2015). The very low overlap of outliers observed by the different approaches used in this study is expected when using different methods, since their algorithms and prior assumptions differ considerably (Ahrens et al 2018; Dalongeville et al 2018; Amish et al 2019).…”

“…precipitation of the driest month and temperature of the warmest quarter), suggest that these environmental variables may act as selective factors in O. chrysogaster . The influence of temperature and precipitation on adaptive genetic variation has also been suggested for steelhead trout from the Inner Columbia River Basin and for cutthroat trout from the Great Basin Desert both in U.S.A. (Hand et al 2016; Amish et al 2019). Temperature has been defined as a potential driver of adaptive processes in salmonids mainly because ectothermic body temperature is closely associated with the environment (Hecht et al 2015; Hand et al 2016).…”

“…However, most of the already published riverscape genetics studies used only a small number of neutral molecular markers. Lately, some studies started to include large Next Generation Sequencing (NGS) datasets to assess gene-environment interactions (Bourret et al 2013; Hecht et al 2015; Brauer et al 2016, 2018; Hand et al 2016; Amish et al 2019). The use of NGS datasets might be helpful for the genetic monitoring of endangered populations, as they provide information of local adaptation processes that is valuable for recovery programmes which could be apply in riverine environments (Faulks et al 2017; Kleinman-Ruiz et al 2017; Hunter et al 2018; Fan et al 2018).…”