Back in black: concealed skin colour and skin colour polymorphism promotes diversification in birds
Data files
Oct 20, 2023 version files 773.70 MB
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Ancestral_state_estimation.R
1.20 KB
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birdtree.tre
459.88 KB
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BirdzillaEricson3.tre
463.70 MB
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black_skinplotter.R
6.27 KB
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blackspecies_final.csv
40.92 KB
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EricsonStage1Full_1.tre
308.73 MB
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Final_table_SSE_input2.csv
94.48 KB
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polymorphism_vs_lat_max_lat_range_v2.R
3.10 KB
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README.md
2.28 KB
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species_final.csv
187.48 KB
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SSE_models.R
12.26 KB
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Suppelementary_file_2.xlsx
43.42 KB
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Supplementary_file_1.xlsx
237.25 KB
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supplementary_file_3.xlsx
31.11 KB
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variation_final2.csv
150.13 KB
Abstract
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.
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 <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.
See main manuscript.
