Data from: Rapid and repeated evolution of the pigmentation patterns in reef fishes

Description of the data and file structure
Files and variables
File: Additional_file_1_Data.xlsx
This Excel file provides raw data about pigmentation pattern and biogeographic information.
Description: Each sheet provides the information for one fish family. You will find a total of six sheets : Acanthuridae, Chaetodontidae, Lutjanidae, Mullidae, Pomacanthidae and Pomacentridae. For every family, you will find the list of studied species (rows). Columns include geographic data (yellow) and motif data (orange). These two types of data are coded as presence (1)/absence (0).
Geographic data : presence/absence
CIP = Central Indo-PacificWI = Western Indian OceanCP = Central PacificA = AtlanticTEP = Tropical Eastern PacificMotif data : presence/absence. These motifs data were repeated for the three body regions : head (H), trunk (Tr) and tail (Ta).
Number of colours (one or more (+)).Colour separation (H-sep : H-sep - different background colors are separated following the body axis ; V-sep - different background colors are separated perpendicularly to the body axis ; O-sep - different background colors are separated with an orientation deviating from the body axis from around 20° to 70°).Stripe patterns (five possible types: H-stripes - horizontal stripe following the body axis ; V-stripe - vertical stripe oriented perpendicularly to the body axis ; O- stripes - oblique stripe deviating from the body axis from about 20° to 70° ; Marbling: irregular, elongated and connected patterns without a directional trend ; and Honeycomb: juxtaposed hexagonal patterns).Blotch patterns (two types : Regular blotches - large and irregular markings ; Saddle - blotch located on dorsal part ahead of the caudal peduncle).Type of colored structures (two structures: Mouth - mouth has a different color than head’s background color ; Scalpel - scalpel has a different color from body’s background color).Other patterns (four possible types: Dots - small and rounded area of color ; Reticulations - net-like pattern ; Eyespot - large dot surrounded by a ring of a different color ; Edging - structure is outlined with a color different from the structure’s background color).File: Description_file.txt
This file describes the inputs for running the analyses in R envrionment. See the associated R-code file. Here, we provide data from the surgeonfishes (Acanthuridae) as an exemple to run our R-code. The files are described below.
File: coord_Acanthuridae.txt
This file contains PC scores generated from PCoA analysis for the surgeonfishes.
File: coord_Acanthuridae_ar.txt
This file is a modified version of “coord_Acanthuridae.txt” where species species are duplicated when they live in multiple regions.
File: grouping_Acanthuridae.txt
This file contains the grouping factor to assign species to regions. This file is use to calculate functional indices in every regions.
File: tree_Acanthuridae.tree
This file is the consensus time-calibrated phylogeny produced by Sorenson et al. (2013). All information about the building of phylogenetic hypotheses and time calibration are provided in the following paper :
L. Sorenson, F. Santini, G. Carnevale, M. E. Alfaro, A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy. Mol. Phylogenet. Evol. 68, 150–160 (2013).
Code/software
The Excel file can be view in Excel, Numbers or in the R environment.
File: Color_patterns_evolution_Code.R
This R code allows the production of all analyses introduced in the paper.