Metagenomic insights into the dietary diversity of the adaptive radiation of cichlid fishes in Lake Tanganyika

Diet specialization is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterize trophic specializations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specializations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids’ diet. Based on their dietary compositi..., , , # Metagenomic insights into the dietary diversity of the adaptive radiation of cichlid fishes in Lake Tanganyika

[https://doi.org/10.5061/dryad.cjsxksnh7](https://doi.org/10.5061/dryad.cjsxksnh7)

## Description of the data and file structure

This data is part of the publication \"Metagenomic insights into the dietary diversity of the adaptive radiation of cichlid fishes in Lake Tanganyika\" by Charlotte E.T. Huyghe, Antoine Fages, Fabrizia Ronco, Adrian Indermaur, Frederic D.B. Schedel, Ismael Kimirei, Lawrence Makasa, Patrick Tschopp & Walter Salzburger.

The data was collected from the digestive tract content of fresh wild-caught cichlid fish individuals, representing 58 species (56 from the adaptive radiation) from Lake Tanganyika. The sequences acquired through shotgun metagenomics were identified using a k-mer approach (Kraken2), only keeping Eukaryotic taxa. The bioinformatics scripts to construct the data matrices can be found on GitHub ([https://github.com/CETHuyghe/Dietary_m...,