Data from: Evolution of multiple colour mechanisms enhances opportunities for diversification in sunbirds (Nectariniidae)
Cite this dataset
Nicolaï, Michaël (2023). Data from: Evolution of multiple colour mechanisms enhances opportunities for diversification in sunbirds (Nectariniidae) [Dataset]. Dryad. https://doi.org/10.5061/dryad.7h44j0zxp
Abstract
How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colours may enable more precise and/or easier species recognition, and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of colouration on diversification is well-studied, the influence of the mechanisms that produce those colours (e.g. pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined colour data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel colour mechanisms increases diversification in sunbirds, one of the most colourful bird clades. Results suggest that (1) the evolution of novel colour mechanisms expands the visual sensory niche, increasing the number of achievable colours. (2) Structural colouration diverges more readily across the body than pigment-based colouration, enabling an increase in colour complexity. (3) Novel colour mechanisms might minimize trade-offs between natural and sexual selection such that colour can function both as camouflage and conspicuous signal. (4) Despite structural colours being more colorful and mobile, only melanin-based colouration is positively correlated with net diversification. Together, these findings explain why colour distances increase with increasing number of sympatric species, even though packing of colour space would predict otherwise.
README: Evolution of multiple colour mechanisms enhances opportunities for diversification in sunbirds (Nectariniidae)
https://doi.org/10.5061/dryad.7h44j0zxp
Data
This repository contains 4 supplementary tables. Throughout the files and scripts,are shown by "?" or NA. This can be because there are no values, or in the case of specimen data, missing values (either not readable or erroneously not noted).
Supplementary data 1 contains all specimens investigated. Data shown (i.e. columns) are: Collection where measured, Label used for processing, Genus name, Species (and subspecies name), sex, Genus+species name (without subspecies), specimen number (i.e. label number).
Supplementary data 2 shows the how we classified colour mechanisms for both sexes using two methods: 1) reflectance measurements (plots). Within the excel file this is shown in the first two sheets (for male and female). 2) by visually looking at photos (photos). These are shown in the latter two sheets (for male and female). In each sheet we score for each species what the colour mechanism is for MA (mantle), TH (throat), PR (primaries), SH (shoulder), BA (breast 1), BD (Breast 2), BE (belly) and CR (crown). Mechanisms identified are iridescent, melanin-based, carotenoid-based, structural white, grey and olive green colouration. 'NA's' indicate that colour mechanisms was not clear.
Supplementary data 3 Voucher numbers for the specimens used in the reconstruction of the phylogeny
Supplementary data 4 This is the output of the biogeographic analyses. This consists of 4 sheets, where we have a sheet listing the different parameters for all models run for the single mechanism and combination mechanism dataset. In addition, there are "Best model ..." sheets, that highlight the parameters for the best model only per dataset and for each colour mechanism. In each sheet the following parameters are shown: sex, colour mechanism investigated, distance model tested, biogeographic model tested, LnL (log likelihood), number of parameters, dispersal paramter (d), extinction parameter (e), jump dispersal parameter (j), distance parameter (x) and AICc. Best AICc values are highlighted in green.
In addition, there are two zip files.
Supplementary data_5.zip contains the input and output files for the biogeographic analyses. These are organised per model, per colour mechanism and per sex. Within each final folder, input files follow the organisation of the BioGeoBEARS template, as does the output. All these data structures are explained at a dedicated wiki: http://phylo.wikidot.com/biogeobears.
R_files.7z contains R code used in this manuscript and the associated files necessary to run it.
Code:
Files 1-7 are all prep-files, i.e. they create the numerous datasets necessary to run subsequenct analyses:
0a. color distance_calculator_F_final.R calculates colour distances for female data.
0b. color distance_calculator_M_final.R calculates colour distances for male data.
1.interpatch contrast and sexual dimorphism calculator_final calculates interpatch contrast and sexual dichromatism for all species
2.a degree_sympatric_overlap_M_calculator_final.R calculates the degree of overlap between species for male data
2.b degree_sympatric_overlap_F_calculator_final.R calculates the degree of overlap between species for female data
3.b. number of sympatric species calculator_final.R calculates per species how many species are sympatric
4.a sympatric_coldist_calculator_F_notweighed_sympatryonly_f calculates colour distance between sympatric species without taking the degree of overlap (weighing factor) into account and this for female data, but only for sympatric species pairs.
4.b sympatric_coldist_calculator_F_notweighed_sympatryonly_m calculates colour distance between sympatric species without taking the degree of overlap (weighing factor) into account and this for male data, but only for sympatric species pairs.
5.a sympatric_coldist_calculator_F_notweighed_F calculates colour distance between sympatric species taking the degree of overlap (weighing factor) into account and this for female data.
5.b sympatric_coldist_calculator_F_weighed_Mcalculates colour distance between sympatric species taking the degree of overlap (weighing factor) into account and this for male data.
6a. maxvolcalculator_M_final.R calculates the maximal attainable colour volume for male sunbirds
6b. maxvolcalculator_F_final.R calculates the maximal attainable colour volume for female sunbirds
7a. sympatric_col_vol_F_final.R calculates the colour volume obtained by all sympatric species for female data.
7b. sympatric_col_vol_M_final.R calculates the colour volume obtained by all sympatric species for male data.
8.dichromatism vs contrast_final.R is used to investigate the correlation between dichromatism and contrast.
9.a sympatric_coldist_calculator_F_notweighed_sympatryonly_f calculates colour distance between sympatric species without taking the degree of overlap (weighing factor) into account and this for female data,
9.b sympatric_coldist_calculator_F_notweighed_sympatryonly_m calculates colour distance between sympatric species without taking the degree of overlap (weighing factor) into account and this for male data
10.sympatric colour volume in function of number of species.R investigates the correlation between sympatric colour volume and the number of species.
11.ACE sexual dichromatism and interpatch contrast.R is used for ancestral state estimations for sexual dichromatism and interpatch contrast.
SSE-models are run using the example scripts.
Input files are:
colour_X_Y.csv, where X is the sex and Y the colour patch. These contain for all species pairs the colour distances for that combination of sex and colour patch.
contrast_sexualdichromatism.txt contains per species the sexual dichromatism in all patches and averaged across all patches.
degree_sympatric_overlap_x_b.txt (where x is sex), contains the degree of sympatric overlap for all species pairs.
x_contrast_sexualdichromatism (where x is sex), contains for each species the dichromatism for all patches and averaged acrossed all patches. It also contains the interpatch contrast.
sunbirds.ave.csv contains the raw reflectance spectra
mechanism_x.csv (where x is sex) contains the raw data for the assigned colour mechanism
sympatric_coldist_x_Y.txt (where x is sex and y is a subcondition, e.g. weighed or not) contains the colour distances for all patches per species.
sympatric_col_vol_x.txt (where x is sex) contains for each species, the sympatric colour volume.
sympatric_col_vol_x_max.txt (where x is sex) contains for each species, the max sympatric colour volume.
sympatric_overlap.txt contains the degrees of overlap for all species pairs and whether they are sympatric or allopatric