DOI: 10.5061/dryad.32bp4
title: Data from: Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies

description: In macroevolution, the Red Queen (RQ) model posits that biodiversity
 dynamics depend mainly on species-intrinsic biotic factors such as
 interactions among species or life-history traits, while the Court Jester
 (CJ) model states that extrinsic environmental abiotic factors have a
 stronger role. Until recently, a lack of relevant methodological
 approaches has prevented the unraveling of contributions from these two
 types of factors to the evolutionary history of a lineage. Here we take
 advantage of the rapid development of new macroevolution models that tie
 diversification rates to changes in paleoenvironmental (extrinsic) and/or
 biotic (intrinsic) factors. We inferred a robust and fully-sampled
 species-level phylogeny, as well as divergence times and ancestral
 geographic ranges, and related these to the radiation of Apollo
 butterflies (Parnassiinae) using both extant (molecular) and extinct
 (fossil/morphological) evidence. We tested whether their diversification
 dynamics are better explained by a RQ or CJ hypothesis, by assessing
 whether speciation and extinction were mediated by diversity-dependence
 (niche filling) and clade-dependent host-plant association (RQ) or by
 large-scale continuous changes in extrinsic factors such as climate or
 geology (CJ). For the RQ hypothesis, we found significant differences in
 speciation rates associated with different host-plants but detected no
 sign of diversity-dependence. For CJ, the role of Himalayan-Tibetan
 building was substantial for biogeography but not a driver of high
 speciation, while positive dependence between warm climate and
 speciation/extinction was supported by continuously varying
 maximum-likelihood models. We find that rather than a single factor, the
 joint effect of multiple factors (biogeography, species traits,
 environmental drivers, and mass extinction) is responsible for current
 diversity patterns, and that the same factor might act differently across
 clades, emphasizing the notion of opportunity. This study confirms the
 importance of the confluence of several factors rather than single
 explanations in modeling diversification within lineages.
description: Appendix 1 - GenBank
 sequencesAll sequence data used
 for this study (a file is generated per gene).Appendix 2 - Gene
 alignments and treesThe individual gene
 alignments as recovered by MAFFT. Results of the Bayesian phylogenetic
 analyses for each gene, and an explanation of the
 results.Appendix 3 -
 Parnassiinae_Fossils_MBThe total-evidence
 matrix (including molecular and morphological data) used for the
 phylogenetic placement of fossils with MrBayes.Appendix 4 - BEAST files
 for the dating analysesThe BEAST files for the
 Bayesian dating analyses (the tree prior can be a Yule process or a
 birth-death model, and the dataset can include or not the morphological
 data).Appendix 5 -
 Parnassiinae DistributionThe current geographic
 species distribution data of all Parnassiinae as coded present (1) or
 absent (0) in all ten geographic areas (Western Palearctic, North Africa,
 Turkey, Central Asia, Himalaya, India, Mongolia, Siberia, China-Japan, and
 Western Nearctic).Appendix 6 - Adjacency
 matrices through timeThe time-stratified
 biogeographic model used for DEC analyses (time slices represent
 geological epochs or stages in the Cenozoic).Appendix 7 - Himalaya
 and Tibetan paleoaltimetryPaleo-elevation for the
 Himalayan and Tibetan compiled from the literature.Appendix 8 - Bayesian
 paleoenvironmental modelDescription of the
 Bayesian episodic environment-dependent birth-death
 model.Appendix 9 -
 PartitionFinder analyses and resultsResults of
 PartitionFinder performed on the concatenated molecular
 dataset.Appendix 10 -
 Time-calibrated trees of ParnassiinaeTime-calibrated trees of
 Parnassiinae as estimated by BEAST following four different
 analyses.Appendix 11 - Bayes
 factors DatingResults of the model
 comparison for the dating analyses based on marginal likelihood estimates
 and Bayes factors.Appendix 12 -
 Parnassiinae DECBiogeographic history of
 Parnassiinae as estimated by DEC.Appendix 13 - DDD
 ParnassiinaeResults from the
 diversity-dependence diversification analyses in DDD.Appendix 14 - SSE
 modelsResults of the MuSSE and
 GeoSSE analyses performed on 200 trees randomly taken from the Bayesian
 dating analysis. Models are ranked by AICc.Appendix 15 - MuSSE MCMC
 difference on speciation ratesPlot of the difference
 between speciation rates between all traits. When the difference overlaps
 zero (vertical red bar), the speciation rates are not significantly
 different.Appendix 16 - Robustness
 of SSE analysesRobustness of the SSE
 models with simulation tests, HiSSE analyses and an implementation in
 RevBayes. For the simulation, the difference of fit between the best model
 and the reference model is shown with the red vertical line for real data,
 and in black for simulated data. HiSSE and RevBayes agree with the MuSSE
 models on host plants.Appendix 17 - BAMM
 analysesSummary of
 diversification models in BAMM compared across a gradient of values for
 the Poison process governing the number of rate shifts.Appendix 18 - Credible
 set of speciation shifts in ParnassiinaeCredible set of
 configuration shifts inferred with BAMM and five different values of the
 Poison prior. It shows the distinct shift configurations with the highest
 posterior probability. For each shift configuration, the locations of rate
 shifts are shown as black circles, with circle size proportional to the
 marginal probability of the shift.Appendix 19 - BAMM-like
 RevBayes analysesRate-through-time plot
 as inferred with RevBayes for Parnassiinae. Net diversification rates
 significantly changed and increased along the stem of the genus
 Parnassius, in agreement with the rates as estimated with
 BAMM.Appendix 20 - CoMET
 analysesRate-through-time plot
 as inferred with CoMET for Parnassiinae. The analyses detected one
 possible mass extinction around 15 Ma and one speciation rate shift around
 3.5 Ma, in agreement with two TreePar analyses allowing or not the mass
 extinction.Appendix 21 -
 Correlation parameters for Bayesian modelsCredibility intervals of
 the correlation parameters for the Bayesian (RevBayes)
 environment-dependent diversification models.Appendix 22 - Relation
 butterfly diversification and host-plant diversityCorrelation (linear
 regression) between speciation rates as inferred with MuSSE (a) and BAMM
 (b) and the species richness of host plants on which each parnassiine
 clade is feeding. In both cases, a strong and positive correlation is
 found.Scripts and R codes for
 diversification analysesScripts for diversification
 analyses.zip