Data from: Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

Background: Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts' biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of extremely young adaptive radiations of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus) from two crater lakes to test the hypothesis that parallel divergence in trophic ecology is associated with parallel changes of the gut microbiota.

Results: Bacterial communities of the water and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology.

Conclusions: Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.