Transitions between colour mechanisms affect speciation dynamics and range distributions of birds
Data files
Jun 11, 2024 version files 7.59 MB
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dataset1.csv
18.46 KB
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dataset10.csv
28.61 KB
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dataset2.csv
335.09 KB
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dataset3.csv
2.92 MB
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dataset4.csv
2.81 MB
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dataset5.csv
177.52 KB
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dataset6.csv
207.47 KB
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dataset7.csv
245.25 KB
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dataset8.csv
394.36 KB
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dataset9.csv
329.88 KB
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dbase_for_analysis.RDS
119.30 KB
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README.md
5.03 KB
Jun 17, 2024 version files 7.59 MB
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dataset1.csv
18.46 KB
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dataset10.csv
28.61 KB
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dataset2.csv
335.09 KB
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dataset3.csv
2.92 MB
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dataset4.csv
2.81 MB
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dataset5.csv
177.52 KB
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dataset6.csv
207.47 KB
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dataset7.csv
245.25 KB
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dataset8.csv
394.36 KB
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dataset9.csv
329.88 KB
-
dbase_for_analysis.RDS
119.30 KB
-
README.md
5.06 KB
Abstract
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.
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/