DOI: 10.5061/dryad.3n5tb2rrt
title: Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale

description: 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.
description: 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.
description: **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)](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)](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.