Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale
Data files
Apr 15, 2024 version files 37.03 MB
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environmental_niche_modelling.zip
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phylogenetic_comparative_analyses.zip
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README.md
Abstract
Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the Late Miocene and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity due to them experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modelling, and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We show that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments, and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.
README
README: Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale
This repository contains all the data and R scripts used to perform the analyses. The files are grouped (as two folders) according to the type of data and analyses. Details are as follows:
Environmental_niche_modelling folder
Species location data
Bicyclus_all_non_duplicated_presence_points.csv - raw data containing lat-long records for Bicyclus species. This data is the finalised version after doing all the checks for duplicate coordinates and other obvious errors (see Methods for details).
Bicyclus_rarefied_for_maxent_input.csv - raw data containing lat-long records for Bicyclus species after performing thinning (see ‘plotting_location_points_and_rarefaction.Rmd’ script). The rarefaction level used for each species is provided in Table S1.
Koppen_clipping_mask.asc - Koppen climate mask used for clipping Bioclim rasters, for example, to remove deserts where Bicyclus species do not occur.
Predicted niche occupancy (PNO) data
PNO files for each climatic layer used in the analyses: Data file containing PNO values for each climatic layer (produced using script ‘extracting_PNO_values.Rmd’). The names of files are as follows: PNO_Bio02.csv, PNO_Bio11.csv, PNO_Bio12.csv, PNO_Bio15.csv, PNO_Bio17.csv, PNO_Bio89.csv, PNO_Bio1011.csv
R scripts for processing species distribution data and obtaining PNO values
climate_layer_evaluations_and_input_file_generation.Rmd - Script for reading, cropping and selecting Bioclim climate rasters based on the correlation score and variable inflation factor.
plotting_location_points_and_rarefaction.Rmd - Script for plotting species distribution points and carrying out thinning at different resolutions resulting in the file (“Bicyclus_rarefied_for_maxent_input.csv”) used for MaxEnt analyses.
extracting_PNO_values.Rmd - Script for calculating predicted niche occupancy values using phyloclim R package
extracting_pno_quantiles.Rmd - Script for extracting required PNO quantiles (15, 20, 25, 75, 80, 85%). See Methods and Table1 for details.
Note: Please note that some of the raster files for environmental data (which are quite heavy) and output files from MaxEnt (which are numerous) have not been deposited here. Please free to contact the authors if you would need access to these files.
Phylogenetic_comparative_analyses folder
Butterfly phylogenies
bicyclus_phylogeny.tre - Consensus tree of Bicyclus species obtained from Aduse-Poku et al. (2022, https://doi.org/10.1093/sysbio/syab066) for running comparative analyses
Bicyclus_phylogeny_multi.tre - A set of posterior trees (~3000 trees) of Bicyclus species obtained from Aduse-Poku et al. (2022, https://doi.org/10.1093/sysbio/syab066) for running comparative analyses
Phenotypic and environmental data
raw_eyespot_wing_length_measurements.xlsx - The datafile contains raw measurements on the absolute eyespot size and wing length in mm along with the species names. Note that this file contains 'NA' values which are the cases when the accurate species identification was not possible.
eyespot_range_85sps.xlsx - The datafile contains maximum, minimum and range of the relative eyespot size along with species names and plasticity categories (see Methods)
PNO_all_quantiles.xlsx - Data file contains 15, 20, 25, 75, 80, and 85% quantiles of PNO values for all climatic layers (produced using script ‘extracting_pno_quantiles.Rmd’)
R scripts for processing phenotypic data and running phylogenetic comparative analyses
calculating_eyespot_size_plasticity.Rmd - Script for calculating range of the relative eyespot size, other alternative measures of eyespot size plasticity and exploring allometry (see Methods and Supplementary Figures for details)
core_phylogenetic_comparative_analyses.Rmd - Script for calculating phylogenetic signal, ancestral state estimation, running phylogenetic generalised least squares regression and a a suite of sensitivity analyses (see Methods and Supplementary Figures for details)
PGLS_sensitivity_analyses.Rmd - Script for performing sensitivity analyses for robustness of PGLS for different PNO quantiles and sample size.
Methods
The dataset has two components: (1) phenotypic data- the data was collected by measuring the eyespot size and wing length (which was then used to calculate relative eyespot size) from the photographed museum specimens of African Bicyclus butterflies. (2) distribution data- this is the distribution/location data for the African Bicyclus butterflies collated from museum records and citizen science online platforms. All the data (in .csv and .xlsx) has been processed in R statistical software, except the environmental niche modelling which was carried out using the Maxent software.