Genomic tests of divergent trophic adaptation along ecological gradients in Lake Victoria cichlid fish.

The Lake Victoria cichlid fish species flock presents a text book example of adaptive radiation and spectacular diversity in terms of morphology, ecology and behaviour. However, this lake which is a home to hundreds of haplochromine species has been subjected to strong loss of diversity during the end of the previous century due to various anthropogenic activities. Combining these two facts, Lake Victoria is an ideal model ecosystem for the study of adaptive radiation, and interactions between environmental heterogeneity, species diversity and biodiversity dynamics in an evolutionary and conservation biology frame work. To this end, this study uses a comparative genome scan to evaluate the impact of ecological gradients on genomic differentiation between replicate pairs of divergent rock dwelling Neochromis spp. from 3 islands in the southern region of Lake Victoria.We tested how genomic differentiation varies with steepness of ecological gradient using population of Neochromis spp.that live along environmental gradients created by water depth and associated light condition. We hypothesized that 1. Variation in gradient steepness induced by variation in shore slope, water clarity and rock size explains variation between islands in the extent of trophic adaptation and genetic differentiation 2) shallower environmental gradients are more prone to induce genetic differentiation and speciation than steeper environmental gradients. From our analysis based on 574 polymorphic loci, we observed low to moderate genetic diversity within population. A mean gene diversity (Hex) of 0.11±0.01 and a mean proportion of polymorphic loci varying from 20 to 32% were observed. We found very low genetic differentiation between trophic morphs (FST= 0.4%) at the island with very steep ecological gradients and high genetic differentiation (FST 4̃%) at the island with an ecological gradient of intermediate steepness. Furthermore, we found the strongest adaptive differentiation (revealed by highest number of outliers, highest BayeScan over all FST value and Phenotype divergence) in the sympatric trophic morph at the shallow ecological gradients as predicted by theory. In conclusion we found genomic signature of divergent selection between trophic morphs at Igombe and Makobe revealed by high FST value and strong association of markers to adaptive phenotypic traits. But we did found no evidence of selection at Bihiru Island, with very steep ecological gradients. Thus, our findings support the hypothesis that variation in steepness of resource gradients determines the extent of trophic adaptation and its genomic signature and suggests that shallow resources gradients induce stronger adaptive genetic differentiation compared to steeper resource gradients