DOI: 10.5061/dryad.7h44j0zxp
title: Data from: Evolution of multiple colour mechanisms enhances opportunities for diversification in sunbirds (Nectariniidae)

description: 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.
description: # Evolution of multiple colour mechanisms enhances opportunities for
 diversification in sunbirds (Nectariniidae)
 ## 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:
 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