DOI: 10.5061/dryad.02v6wwqc0
title: Transitions between colour mechanisms affect speciation dynamics and range distributions of birds

description: Several ecogeographical "rules" have been proposed to explain
 colour variation at broad spatial and phylogenetic scales, but these
 rarely consider whether colours are based on pigments or structural
 colours. However, mechanism can have profound effects on the function and
 evolution of colours. Here, we combine geographic information, climate
 data, and colour mechanism at broad phylogenetic (9409 species) and
 spatial scales (global) to determine how transitions between pigmentary
 and structural colours influence speciation dynamics and range
 distributions in birds. Among structurally coloured species, we find that
 rapid dispersal into tropical regions drove the accumulation of iridescent
 species, whereas the build-up of non-iridescent species in the tropics was
 driven by a combination of dispersal and faster in situ evolution in the
 tropics. These results could be explained by pleiotropic links between
 colouration and dispersal behaviour, or ecological factors influencing
 colonisation success. These data elucidate geographic patterns of
 colouration at a global scale and provide testable hypotheses for future
 work on birds and other animals with structural colours.
description: # **Transitions between colour mechanisms affect speciation dynamics and
 range distributions of birds** Authors: Chad M. Eliason, Michaël P.J.
 Nicolaï, Cynthia Bom, Eline Blom, Liliana D’Alba, Matthew D. Shawkey
 Description: Data sets and R code for analysis of structural colour
 evolution in birds. #### Data ``` dataset1.csv - Confirmed structural
 color mechanisms from literature Species - Scientific name Type - Type of
 structural color: iridescent structural color (irid) or non-iridescent
 structural color (nonirid) Structure - Nanostructure type (see Durrer
 1977, Prum 2006 for details) dataset2.csv - Final colour database used in
 phylogenetic analyses Species - Scientific name matched to GBIF bird
 species ISC - Presence (1) or absence (0) of iridescent structural colour
 NISC - Presence (1) or absence (0) of non-iridescent structural colour
 PhyJetz - Whether a species is present (1) or absent (0) from the Jetz et
 al. 2012 tree PhyBurl - Whether a species is present (1) or absent (0)
 from the Burleigh et al. 2015 tree Map1Deg - Whether a species is present
 (1) or absent (0) from the 1-degree map data set Map2Deg - Whether a
 species is present (1) or absent (0) from the 2-degree map data set
 dataset3.csv - Mean WorldClim bioclimatic variables using a 1-degree grid
 cell resolution of bird maps (raw data downloaded from
 https://datazone.birdlife.org/) Species - Scientific name Map ID - Map
 number landprop - Proportion of range over land trop - Proportion of
 species' range between -23.4 and 23.4 degrees upper - Proportion of
 species' range above 23.4 degrees lower - Proportion of species'
 range below -23.4 degrees centroidX - Mean longitude centroidY - Mean
 latitude bio1-19 - BioClim variables dataset4.csv - Mean WorldClim
 bioclimatic variables using a 2-degree grid cell resolution of bird maps
 (raw data downloaded from https://datazone.birdlife.org/) Species -
 Scientific name Map ID - Map number landprop - Proportion of range over
 land trop - Proportion of species' range between -23.4 and 23.4
 degrees upper - Proportion of species' range above 23.4 degrees lower
 - Proportion of species' range below -23.4 degrees centroidX - Mean
 longitude centroidY - Mean latitude bio1-19 - BioClim variables
 dataset5.csv - Evolutionary transitions inferred using a 2-degree
 resolution and the Jetz et al. (2012) phylogeny Transition - Evolutionary
 transition between states (1: temperate PBC, 2: tropical PBC, 3:
 widespread PBC, 4: temperate ISC, 5: tropical ISC, 6: widespread ISC, 7:
 temperate NISC, 8: tropical NISC, 9: widespread NISC) Node - Node in Jetz
 et al. (2012) phylogeny at which shift occurs Families - list of families
 included in transition dataset6.csv - Colour scores assessed by CME using
 Handbook of the Birds of the World (HBW) Species - Scientific name NISC -
 Non-iridescent structural colour presence (1) or absence (0) ISC -
 Iridescent structural colour presence (1) or absence (0) dataset7.csv -
 Colour scores assessed by MPJN using HBW Species - Scientific name NISC -
 Non-iridescent structural colour presence (1) or absence (0) ISC -
 Iridescent structural colour presence (1) or absence (0) dataset8.csv -
 Colour scores assessed by LDA using HBW and museum specimens Species -
 Scientific name NISC - Non-iridescent structural colour presence (1) or
 absence (0) verif - Whether NISC was verified using specimens (1) or not
 (0) method - Method of verifying NISC color - Structural colour observed
 mus_id - Museum ID number NISC_dimorph - Whether males, females, or both
 have NISC dataset9.csv - Colour scores assessed by MPJN using museum
 specimens Species - Scientific name ISC - Iridescent structural colour
 presence (1) or absence (0) Sex - Sex of specimen used in ISC assessment
 Age - Specimen age Institution - Institution of specimen used for ISC
 assessment Cat_num - Catalog number of specimen used for ISC assessment
 dataset10.csv - Manual fixes used to produce final colour database Species
 - Scientific name ISC - Iridescent structural colour presence (1) or
 absence (0) NISC - Non-iridescent structural colour presence (1) or
 absence (0) Group - Data type to replace or ammend in the final database
 ``` # Programs ``` analysis.Rmd - main R script for analyses and producing
 figures in manuscript utility.R - Utility R functions used in comparative
 and statistical analyses prep.R - R script used to assemble the structural
 color database rasterize-2deg.R - R script for rasterizing and calculating
 bioclim variables from 2-degree resolution range maps rasterize-1deg.R - R
 script for rasterizing and calculating bioclim variables from 1-degree
 resolution range maps ``` # Other data sets ``` dbase_for_analysis.RDS -
 Data file for analyses easily loaded into R using readRDS ``` # Other
 Published Data ``` Kingfisher data downloaded from
 https://doi.org/10.5061/dryad.3680n0c Burleigh tree downloaded from
 https://datadryad.org/stash/dataset/doi:10.5061/dryad.qv871g8 Jetz tree
 downloaded from https://birdtree.org/ ```