Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

Replicated ecological gradients are prime systems to study processes of molecularevolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fishby sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelismfrom SNPs to molecular pathways. Coalescence analyses showed that the divergenceoccurred in the face of substantial bidirectional gene flow. Population divergenceinvolved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelicstate changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution ofJcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genestherein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545,indicating increasing parallelism with increasing level of biological integration. Themajority of pathways contained positively selected genes in both sulphide populations.Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportionof de novo mutations driving the divergence. Our findings favour Gould’s view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.