Intraspecific ecological and morphological polymorphism can promote ecological speciation and the build-up of reproductive isolation. Here, we evaluate correlations among morphology, trophic ecology, and genetic differentiation between two divergent morphs (elongate and deep-body) of the fish genus Astyanax in the San Juan River basin in Central America, to infer the putative evolutionary mechanism shaping this system. We collected the two morphs from three water bodies and analyzed: 1) the correlation between body shape and the shape of the premaxilla, a relevant trophic morphological structure, 2) the trophic level and niche width of each morph, 3) the correspondence between trophic level and body and premaxillary shape, and 4) the genetic differentiation between morphs using mitochondrial and nuclear markers. We found a strong correlation between the body and premaxillary shape of the morphs. The elongate-body morph had a streamlined body, a premaxilla with acuter angles and a narrower ascending process, and a higher trophic level, characteristic of species with predatorial habits. By contrast, the deep-body morph had a higher body depth, a premaxilla with less acute angles, and a broader trophic niche, suggesting generalist habits. Despite the strong correlation between morphological and ecological divergence, the morphs showed limited genetic differentiation, supporting the idea that morphs may be undergoing incipient ecological speciation, although alternative scenarios such as stable polymorphism or plasticity should also be considered. This study provides support for the role of ecological factors promoting diversification in lake and stream-dwelling freshwater fish.

The readme file contains an explanation of each of the variables in the datasets. Information on sampling number in each dataset can be found in the associated manuscript referenced above. 

The geometric morphometric and stable isotopes datasets were collected from two morphs of Astyanax (elongate and deep-body) from ten sampling sites across three water bodies in the San Juan River basin: the two Nicaraguan lakes, Managua and Nicaragua, and the Sarapiquí River. Fish were collected using either gill or cast nets during sampling campaigns that took place between November 2011 and January 2017. The subsample of fish used in the isotopic analyses were collected during the dry season between December 2016 and January 2017.