Data from: Deep evolutionary roots of diet in seagrass bed fishes

Provided here are the datasets and R code for the study entitled "Deep evolutionary roots of diet in seagrass bed fishes". 

Summary of the study: Diet is a fundamental ecological trait of species that defines their roles in food webs and in regulating the functions of natural ecosystems. How diet has been shaped over deep evolution remains poorly understood, especially for marine species. Using a series of phylogenetic comparative analyses, we investigated conservatism and divergences in the diet evolution of fishes associated with seagrass beds globally. We find strong conservatism in fish trophic level, with closely related fishes being more trophically similar. However, rare, but profound diet divergences took place following seagrass recolonization of the ocean and diverfication around 70-100 mya. Furthermore, phylogeny explains >60% of the variation in diet composition, even when morphological, ecological, and geographical covariates are accounted for. These results highlight the importance of evolutionary history in shaping diet and provide a conciliation for diet divergence versus conservatism from a group of globally distributed and ecologically and economically important species.

#####Files ordered by file name######

# all_covariates.xlsxThis file contains the data of ecological, geographical, and morphological covariates.

# diet.xlsx This file contains the data of fish diet compositions extracted from FishBase.

#final.R This file contains the R code (version 1) to conduct all the analyses in our study.

#final_tree.nexThis file contains the time-calibrated phylogeny we produced using BEAST.

#o_finaltree.phyThis file contains the reduced tree of the final_tree.nex for fish species that were reported in FishBase to be associated only with seagrass beds.

#regimes.xlsxThis file contains the assumed regimes to reconstruct a MOU model.

#seq_id.xslxThis file contains the sequence ID for the genetic sequences used to construct the phylogeny.

#species_list.xlsxThis file contains the scientific names and their taxonomy.

#tree_mr.csvThis file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools.

#trophic_level.xlsxThis file contains the trophic level data of fish species estimated using dietr.

The metadata for interpreting the data in the Excel files are included in the Metadata sheet.