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Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes
- Publication Year :
- 2018
-
Abstract
- Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene-environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
- Subjects :
- 0301 basic medicine
Atlantic salmon
POSITIVE SELECTION
Genotype
microgeographic adaptation
ta1172
Population
Salmo salar
ecotype
Polymorphism, Single Nucleotide
sockeye salmon
03 medical and health sciences
EVOLUTIONARY ECOLOGY
Genetics
Animals
Homeostasis
14. Life underwater
Sexual Maturation
Salmo
Allele
Selection, Genetic
education
Gene
Ecology, Evolution, Behavior and Systematics
Local adaptation
CLASS-II COMBINATIONS
education.field_of_study
Genome
biology
ta1184
STRUCTURED POPULATIONS
Haplotype
local selection
ONCORHYNCHUS-TSHAWYTSCHA
Genomics
biology.organism_classification
MAJOR HISTOCOMPATIBILITY COMPLEX
MHC CLASS-I
030104 developmental biology
Genetics, Population
Evolutionary biology
HOMEODOMAIN PROTEIN SIX6
SOCKEYE-SALMON
1181 Ecology, evolutionary biology
ta1181
Oncorhynchus
WILD POPULATIONS
Adaptation
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....61c2a7ef75fec661f4c783c977ee6819