Abstract
BackgroundUnderstanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genus Paramormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in these features.ResultsPatterns of gene expression among Paramormyrops are highly correlated, and 3274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 145–183 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied.ConclusionsIn this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.
Highlights
Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits
We explored the data with a heatmap of pairwise correlations of gene expression for 24,960 genes across all 11 samples (Fig. 2), and carried out all possible pairwise differential gene expression (DGE) comparisons of Operational taxonomic unit (OTU) (n = 10, Table 2)
For the phenotypes of waveform duration, we identified a combined total of 309 Differentially expressed gene (DEG) and 43 enriched Gene Ontology (GO) terms, for waveform polarity we found 169 DEG and 14 enriched GO terms, and for waveform complexity the totals were 413 DEG and 38 enriched GO terms
Summary
Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. Adaptive radiations and explosive diversification of species [2] are frequently characterized by interspecific phenotypic differences in divergence of few, hypervariable phenotypic traits [3,4,5,6]. Such systems offer exceptional advantages to study the genomic bases of phenotypic diversity: they can provide replication under a controlled phylogenetic framework [7], and couple ample phenotypic differentiation with relatively “clean” genomic signals between recently diverged species [8]. While these studies do not investigate mutational causes, analysis of differential gene expression (DGE) can be a useful approach in examining the genomic basis of divergent phenotypes
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