RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs

Abstract Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic paral...

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Published in:G3 : genes - genomes - genetics 2015-07, Vol.5 (7), p.1481-1491
Main Authors: Laporte, Martin, Rogers, Sean M, Dion-Côté, Anne-Marie, Normandeau, Eric, Gagnaire, Pierre-Alexandre, Dalziel, Anne C, Chebib, Jobran, Bernatchez, Louis
Format: Article
Language:English
Subjects:
Animals
Biodiversity and Ecology
Biological Evolution
Chromosome Mapping
Environmental Sciences
Female
Genetic Markers
Genetic Variation
Genetics
Genome
Genotype
Investigations
Life Sciences
Male
Phenotype
Polymorphism, Single Nucleotide
Populations and Evolution
Quantitative Trait Loci
Salmonidae - anatomy & histology
Salmonidae - genetics
Sequence Analysis, DNA
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Summary:Abstract Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site−associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
ISSN:2160-1836
2160-1836
DOI:10.1534/g3.115.019067