Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency

Abstract

Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater-saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.

Fig. 1.

—(a) General map of Finland and of the two watersheds locations. (b) Koutajoki watershed. Three resident populations (R) and three migratory populations (M) were sampled in corresponding tributaries and main stems. (c) Oulujoki watershed. Three resident populations (R) and one migratory populations (M) were sampled in corresponding tributaries and lake.

Fig. 2.

—Overlap among outlier approaches (a) Koutajoki watershed: consistent outliers identified using multiple genome approaches are presented within white circles. UPGMA tree compiled based on 5,519 SNPs. Heatmap of the major allele frequencies of the seven most consistent outlier SNPs. (b) Oulujoki watershed: consistent outlier identified using multiple genome approaches is presented within white circle. UPGMA tree compiled based on 5,670 SNPs. Heatmap of the major allele frequencies of the most consistent outlier SNPs.

Fig. 3.

—Principal component analysis of River Koutajoki samples based on (a) 5519 SNPs and (b) 7 outlier SNPs. Resident populations (KR) are plotted in blue while migratory populations (KM) are plotted in green.