DOI: 10.5061/dryad.cjsxksnh7
title: Data from: Metagenomic insights into the dietary diversity of the adaptive radiation of cichlid fishes in Lake Tanganyika

description: 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
 compositions, the Tanganyikan cichlids can be grouped into herbivores,
 invertivores, piscivores, and mixed-feeders. Further, we showed that
 trophic disparity in the radiation is shaped by rapid divergence and
 documented cases of dietary niche convergence. Diet composition correlated
 with carbon and nitrogen stable isotope values, gut length, and body
 morphology. Differences in diet – such as the consumption of diatoms,
 streptophytes, and chlorophytes versus fish and arthropods – were
 associated with changes in body, upper oral jaw and lower pharyngeal jaw
 shape. Collectively, this study presents a comprehensive and detailed diet
 classification of the Tanganyikan cichlids, highlighting the power of
 metagenomic approaches in delineating dietary adaptations.
description: # 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_metagenomics_LT_cichlids](https://github.com/CETHuyghe/Dietary_metagenomics_LT_cichlids)). These data matrices were filtered and further analysed in R. These RScripts can be found on the GitHub repository as well. Supplementary tables (Table S1, S2, S3, S5, S6) of the publication can be found here as well and are uploaded to Zenodo. ### Files and variables #### File: CichlidLT\_Diet\_Cichlidae\_DataMatrix\_SampleNames\_CETH.txt **Description:** The sample names of the cichlidae data matrix, used in the R script 01_Cichlid_Prepare_Dataset.R #### File: CichlidLT\_Diet\_Focus\_DataMatrix\_SampleNames\_CETH.txt **Description:** The sample names of the focus data matrix, used in the R script 01_Focus_Prepare_Dataset.R #### File: CichlidLT\_Diet\_Focus\_DataMatrix\_CETH.txt **Description:** The data matrix constructed from using Kraken2 and the custom focus database, used in the R script 01_Focus_Prepare_Dataset.R #### File: CichlidLT\_Diet\_RefSeq\_DataMatrix\_SampleNames\_CETH.txt **Description:** The sample names of the main RefSeq data matrix, used in the R script 01_Prepare_Dataset.R #### File: CichlidLT\_Diet\_MetaData\_CETH.txt **Description:** The data matrix containing the metadata of the gut content samples, used in the R scripts 01_Prepare_Dataset.R, 01_Focus_Prepare_Dataset.R and 01_Cichlid_Prepare_Dataset.R ##### Variables * TissueTubeID: The sample ID * SpeciesID: The cichlid species ID * SpecimenID: The specimen ID * TissueID: The tissue type ID, with the gut content of the posterior (ContentFG) and anterior (ContentHG) gut  * Sex: The sex of the specimen, female (F), male (M) or undetermined (NA) * Location: Location name, see Table S1 for coordinates * Date: Date of collection (dd.mm.yyyy) * SL: Standard length specimen in centimetre (cm) * TL: Total length specimen in centimetre (cm) * Weight: Weight of specimen in gram (g) * GL: Total gut length (excluding stomach) in centimetre (cm) * Sampling: Country of collection * Tribe: Cichlid taxonomic tribe * BreedingType: Type of breeding species * BreedingMode: Mode of breeding species * d15N_mean: Mean nitrogen isotope value of species, extracted from Ronco et al., 2021 (‰) * d13C_mean: Mean carbon isotope value of species, extracted from Ronco et al., 2021 (‰) * d15N_std_dev: Standard deviation nitrogen isotope value of species, extracted from Ronco et al., 2021 (‰) * d13C_std_dev: Standard deviation carbon isotope value of species, extracted from Ronco et al., 2021 (‰) * FoodCat: Trophic category based on previous assessments * Habitat: Habitat category based on previous assessments #### File: CichlidLT\_Diet\_Cichlidae\_DataMatrix\_CETH.txt **Description:** The data matrix constructed from using Kraken2 and the custom cichlidae database, used in the R script 01_Cichlid_Prepare_Dataset.R #### File: CichlidLT\_Diet\_RefSeq\_DataMatrix\_CETH.txt **Description:** The main data matrix constructed from using Kraken2 and the RefSeq v205 database, used in the R script 01_Prepare_Dataset.R