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.