DOI: 10.5061/dryad.8pk0p2ntc
title: Back in black: concealed skin colour and skin colour polymorphism promotes diversification in birds

description: Evolutionary biologists have long been interested in understanding the
 factors that promote diversification in organisms, often focusing on
 distinct and/or conspicuous phenotypes with direct effects on natural or
 sexual selection such as body size and plumage colouration. However,
 multiple traits that potentially influence net diversification are not
 conspicuous and/or might be concealed. One such trait, the dark,
 melanin-rich skin concealed beneath the feathers, evolved more than 100
 times during avian evolution, frequently in association with white
 feathers on the crown and UV-rich environments, suggesting that it is a
 UV-photoprotective adaptation. Furthermore, multiple species are
 polymorphic, having both light and dark skin. Such polymorphisms might aid
 in species occupying different UV radiation environments with dark skin
 enabling their presence in high UV-rich areas, and light skin to cope with
 potential negative effects of melanised skin when this becomes redundant.
 As such these polymorphisms are predicted in species with large
 latitudinal variation in their distribution. Furthermore, via this
 polymorphism, and by alleviating evolutionary constraints on feather
 colour, the evolution of dark skin may promote net diversification. Here,
 using an expanded dataset on bird skin colouration of 3033 species (with
 all families and 99% of bird genera), we found that more than 19% of
 species had dark skin. Contrary to our prediction, dark-skinned birds have
 smaller distribution ranges. Furthermore, we show that the evolution of
 dark skin colours and polymorphism in skin colouration, promotes net
 diversification. These results suggest that even hidden or concealed
 traits can influence large-scale evolutionary events such as
 diversification in birds.
description: See main manuscript.
description: Raw data is provided as a supplementary file. These files contain: 3
 supplementary files \- Supplementary file 1: a list of all specimens
 sample\, their order\, family\, skin colour\, feather colour\, baldness\,
 sex\, age\, collection number and collection\. \- Supplementary file 2: a
 species list of all dark skinned birds along with their family and order\.
 \- Supplementary file 3: a list of all families samples\, the number of
 species per family\, the number of species sampled and the number of
 species with dark skin\. In addition this file also contains 4 scripts:
 -black\_skinplotter.R is used to plot the geographic distribution of black
 skin and polymorphisms. It requires species\_final.csv,
 blackspecies\_final.csv and variation\_final2.csv -SSE models.R is used to
 run the different SSE models. It requires Final\_table\_SSE\_input2.csv,
 birdtree.tre, EricsonStage1full\_1.tre -Ancestral\_state\_estimation is
 used to test whether polymorphism is an intermediate between dark skinned
 and not dark skinned. It requires Final\_table\_SSE\_input2.csv and
 birdtree.tre -polymorphism vs lat max\_lat\_range\_final.R is used to
 perform phylogenetic regressions. It requires variation\_final2.csv,
 birdtree.tre, and BirdzillaEricson3.tre Addtional input files are:
 -birdtree.tre a MCC tree based on the Jetz et al. 2012 tree
 -BirdzillaEricson3.tre a subset of 1000 trees obtained by Jetz et al.,
 2012 -EricsonStage1full\_1.tre a subset of 1000 trees obtained by Jetz et
 al., 2012 only containing genetic data only trees. -variation\_final2.csv
 an excel file that for each specieswith dark skin mentions whether: -there
 are polymorphims -there are different synonyms according to different
 taxonomies -it's mean breeding latitude -the minimum, maximum and
 range of latitudes a species is found -species\_final.csv a list of all
 species sampled -blackspecies\_final.csv a list of all dark skinned
 species \- Final\_table\_SSE\_input2\.csv the input data or the SSE models
 with scores for black skin and skin polymorphisms\. Note that
 polymorphisms also contains NA values when polymorphism could not be
 determined \(i\.e\. frequency &lt;2\)\. This table also contains the
 values used for ace where 1 corresponds to no black skin\, 3 to
 polymorphism and 2 to black skin\.