Huang Y , Feulner PGD , Eizaguirre C, Lenz TL, Bornberg-Bauer E , Milinski M, Reusch TBH, Chain FJJ
Genome-wide genotype-expression relationships reveal that copy number differentiation contributes to differential gene expression between stickleback ecotypes
Genome Biology and Evolution, 2018

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Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of single nucleotide polymorphisms (SNPs), copy number variants (CNVs), and gene expression across four pairs of lake and river populations of the three-spined stickleback fish (Gasterosteus aculeatus). We tested whether habitat-specific gene expression patterns emerged as a result of frequency differences of SNPs occurring in putative cis-regulatory regions and of CNVs that span entire genes. We found 135 genes that showed a significant positiveassociation between gene copy number and gene expression, suggesting that CNVs produce dosage effects that can fuel phenotypic variation and serve as substrates for habitat-associated selection. Furthermore, we report evidence that copy number differentiation between lake and river sticklebacks contributes to the habitat-specific expression of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In contrast, genes with habitat-specific expression did not show differentiation in their putative cis-regulatory regions. Our study highlights copy number variation as an important source of genetic variation with prevalent effects on the evolution of gene expression and its potential to facilitate repeated adaptation to novel environments.