Data from: Intra- and interspecific niche variation as reconstructed from stable isotopes in two ecologically different Ethiopian Rift Valley lakes

1. The concept of species niches has enhanced our understanding of community assembly and food web structure in a variety of ecosystem types. Niche-based species sorting profoundly determines community composition along strong environmental gradients, while interspecific interactions tend to be more important within habitats at local spatial scales. The role of intraspecific niche variation in community assembly and ecosystem functioning has only recently been highlighted. 2. The present study undertakes a quantitative comparison of the trophic structure of fish communities in two iconic Ethiopian Rift Valley lakes, Lake Abaya and Lake Chamo, which are biodiversity hotspots with high societal importance. The lakes differ strongly in ecology: whereas Lake Abaya is turbid due to a very high sediment loading, Lake Chamo is a clear-water lake, which in recent years is, however, rapidly becoming more turbid. Using stable isotopes, we compare the structure of the food web in both lakes, and investigate the degree to which differences in trophic structure between the two lakes are mediated by changes in species composition with fixed within-species niches or rather by flexibility in food acquisition within species. 3. Different food web compartments, including fish and the main basal sources, were sampled in both lakes. We used Bayesian stable isotope mixing models and Bayesian community-wide metrics for a quantitative comparison of the food web structure between the two lakes. 4. We demonstrate that the isotopic niche of the fish community in Lake Abaya is larger and more diversified compared to that in Lake Chamo. Sediment organic material seems to be a major energy source for fish in Abaya, while zooplankton is a dominant source for fish in Chamo. This is consistent with the different ecology of the two lakes, where high turbidity impedes primary and secondary production in Abaya. Differences in trophic structure between the two lakes resulted from intraspecific isotopic niche variation rather than from compositional variation between fish communities. 5. Our results point to the importance of intraspecific variation in feeding ecology of fish communities inhabiting two large Ethiopian Rift Valley Lakes with distinct environmental conditions. We anticipate that the approach we used has strong potential to explore large-scale patterns in food web organization in relation to niche variation across different types of ecosystems