The prevalence of copy number increase at multiallelic CNVs associated with cave colonization

Abstract

Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surface and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy-number increases in cave fish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications, and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life. Significance StatementDuplications and deletions of genomic sequences occur frequently within a population. Such inter-individual difference in the amount of genetic material is known as copy number variation and is associated with differences in phenotypic traits. Despite its pervasiveness, the evolutionary impact of copy number variation in complex organisms is difficult to discern, primarily due to the infeasibility of setting up evolutionary experiments in the laboratory. Instances of multiple populations that evolved the same traits in similar environments represent naturally occurring evolutionary experiments and valuable opportunities to study the molecular basis of adaptation. Mexican tetra represents such a system and we use the genomes of surface and cave-dwelling populations to study the role of copy number variation in the recurrent cave adaptation.