Data from: Tempo and mode of winter diapause evolution in butterflies
Data files
Sep 23, 2024 version files 7.39 MB
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butterfly_phylogeny_pruned.trees
85.94 KB
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ButterflyPhyloMulti_pruned.trees
5.73 MB
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Counting_transitions___rate_through_time.Rmd
32.57 KB
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diapause_classification_data_PROCESSED.xlsx
66.99 KB
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diapause_classification_data_RAW.xlsx
86.35 KB
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Fitting_hidden_rate_models_corHMM.Rmd
35.02 KB
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Fitting_Mk_models__simmap___ancestral_state_estimation_phytools.Rmd
54.27 KB
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getRates_modified_Etka_Yapar.R
5.69 KB
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Plotting_uncertainty_in_ancestral_estimation.Rmd
14.07 KB
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Preprocessing_data___some_plots.Rmd
11.43 KB
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README.md
3.73 KB
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S_3b_core_analysis_median_ages.tre
1.26 MB
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source_rate_through_time_Hughes_et_al_2021.R
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Abstract
Quantifying the tempo and mode via modern phylogenetic comparative methods can provide key insights into how selection and constraints shape trait evolution on a macroevolutionary time scale. Here we elucidate the evolution of hibernation (winter) diapause, a complex and defining life-history trait that allows temporal escape from harsh winters in temperate regions in many insects, including our model system, butterflies. Butterflies can diapause in all major life-stages and availability of global-scale phylogenies makes them an ideal model system for studying diapause evolution. First, using a thorough literature survey, we scored the developmental stage of hibernation diapause (egg, larva, pupa, adult) vs. absence of diapause. We find that larval diapause is most common while pupal, egg, and adult diapause are relatively rare. Next, we determined that the loss of diapause occurred at a much higher rate, and that gains primarily occurred from the non-diapause state. While ancestral state estimation at deeper nodes remained uncertain, we found consistent patterns for some families and strong evidence for extensive convergence in diapause evolution. Contrary to expectations, we find no support for increased gain of diapause during the Eocene-Oligocene glaciation (~35 MYA). Overall, the evolution of diapause in butterflies has a complex history, has evolved convergently, and has likely pre-dated the major glaciation event consistent with the deep history of diapause evolution in insects. This study advances our understanding of the evolution of a complex and important life-history trait and establishes a macroevolutionary base for future studies on the ultimate and proximate basis of diapause evolution.
README: Tempo and mode of diapause evolution in butterflies
Sridhar Halali, Etka Yapar, Christopher W Wheat, Niklas Wahlberg, Karl Gotthard, Nicolas Chazot, Sören Nylin, Philipp Lehmann
Dataset and R codes for modelling diapause evolution in butterflies
Summary of the contents
Trait data
diapause_classification_data_RAW.xlsx
: This file contains raw data for five, three and binary diapause classification along with the data on tree id (as in the phylogeny), species, genus, and references used for diapause classification. Note that the full citations corresponding to these references are provided in the supplementary information. All the columns are self-explanatory and contain information on the tip labels in the phylogeny, genus, species and species family followed by five, three and two-state diapause classification. Note that there are ’NA’ rows in the ‘tree_species’ column which simply means that the species name for that specific genus is not known.diapause_classification_data_PROCESSED.xlsx
: This file contains the data on diapause classification but has been processed (e.g. by removing ‘skip’ and ‘skip_high_altitude’ rows from ‘diapause_classification_data_RAW.xlsx’ file) for phylogenetic comparative analyses. Note that there are ’NA’ rows in the ‘tree_species’ column which simply means that the species name for that specific genus is not known.
Phylogenies
S_3b_core_analysis_median_ages.tre
: Global genus-level phylogeny obtained from Chazot et al. [1]butterfly_phylogeny_pruned.trees
: This is a pruned phylogeny (from the global phylogeny from Chazot et al [1]) consisting of 952 tips ready for running the comparative analyses.ButterflyPhyloMulti_pruned.trees
: This is a pruned phylogeny with 952 tips consisting of 200 posterior trees from Chazot et al. [1]
R Scripts
Preprocessing data & some plots.Rmd
: Code for processing raw data (e.g. renaming some columns/diapause classification), pruning phylogeny and making some basic plotsFitting Mk models, simmap & ancestral state estimation_phytools.Rmd
: Code for fitting the Mk models, extracting transition rates, carrying out stochastic mapping and ancestral state estimation using both maximum likelihood and stochastic mapping in phytools R packageCounting transitions & rate through time.Rmd
: Code for counting number of state transition (using 1000 stochastic maps) and calculating rate through timeFitting hidden rate models_corHMM.Rmd
: Code for fitting several hidden rate models using the corHMM R package.Plotting uncertainty in ancestral estimation.Rmd
: Code for calculating the uncertainty in ancestral state estimation across methods and root priors using the sum of squares metricsource_rate_through_time_Hughes_et_al_2021.R
: R code provided by Hughes et al. 2 for calculating rate through time for both single and using posterior trees.getRates_modified_Etka_Yapar.R
: modified function from Hughes et al. [2], mainly to plot 95% CI on points, when stochastic maps are generates for a single best (e.g. consensus) tree.
[1] Chazot, N., Wahlberg, N., Freitas, A. V. L., Mitter, C., Labandeira, C., Sohn, J. C., ... & Heikkilä, M. (2019). Priors and posteriors in Bayesian timing of divergence analyses: the age of butterflies revisited. Systematic biology, 68(5), 797-813.
[2] Hughes, J. J., Berv, J. S., Chester, S. G., Sargis, E. J., & Field, D. J. (2021). Ecological selectivity and the evolution of mammalian substrate preference across the K–Pg boundary. Ecology and Evolution, 11(21), 14540-14554.
Methods
The data comprises the developmental stage in which butterflies diapause (i.e. egg, larva, pupa, adult) or do not diapause, and was collected by literature search. The diapause classification was scored at the genus level. Next, using the phylogenetic comparative methods, mainly models for modelling the evolution of discrete traits or Mk models, a range of analyses were performed, for example, quantifying the rate of transition between states, ancestral state estimation, rate through time, etc. Please refer to the Methods section in the paper for more details. All analyses data analyses were performed in R.