Conclusion
Many studies have focused on understanding digestion and assimilation within a variety of vertebrates and invertebrates, but there is limited information about the cooperative process between the host intestine cells and gut microbiota, and their role in eco-evolutionary dynamics during rapid species diversification (German et al. 2015; Terra et al. 2019; Baldo et al. 2017). We found evidence for a genetically-based adaptive shift in the scale-eater microbiome, even when hosts were reared in identical environments on identical non-scale diets. However, it is still unknown to what extent this microbiome shift will improve digestion of the collagen found in scales, for example, as demonstrated for the gut fauna in the scale-eating khavalchor catfish (Gosavi et al. 2018). Despite unique and highly specialized pupfish dietary adaptations within shared hypersaline lake habitats, overall gut microbial diversity did not follow the expected pattern of rapid diversification and divergence as observed in their hosts, calling into question how eco-evolutionary dynamics between host and symbiont proceed during adaptive radiation.