DOI: 10.5061/dryad.2tg34
title: Data from: When Darwin’s special difficulty promotes diversification in insects

description: Eusociality, Darwin’s special difficulty, has been widely investigated but
 remains a topic of great debate in organismal biology. Eusocial species
 challenge existing theories, and the impact of highly integrated societies
 on diversification dynamics is controversial with opposing assertions and
 hypotheses in the literature. Here, using phylogenetic approaches in
 termites – the first group that has evolved eusociality – we assessed the
 fundamental prediction that eusocial lineages have higher diversiﬁcation
 rates than non-eusocial clades. We found multiple lines of evidence that
 eusociality provided higher diversification as compared to
 non-eusociality. This is particularly exacerbated for eusocial species
 with ‘true’ workers as compared to species with ‘false’ workers. Because
 most species with ‘true’ workers have an entirely prokaryotic microbiota,
 the latter feature is also related to higher diversification rates, but it
 should be investigated further, notably in relation to angiosperm
 diversification. Overall, this study suggests that societies with ‘true’
 workers are not only more successful at ecological timescales but also
 over millions of years, which further implies that both organism- and
 species-level traits act on species selection.
description: Figure S1 - Partitioning
 Isoptera finalFigure S1. Partitioning
 the phylogeny of Dictyoptera into evolutionary scenarios. The null
 scenario is the entire dictyopteran tree. Then each time an evolutionary
 scenario is created, it consisted into a subclade and the rest of the tree
 composed of all dictyopterans without the subclade (i.e. here called the
 backbone). The numbers at nodes denotes all seven subclades. The first
 scenario excludes the entire termite (Isoptera, node 1). The second
 scenario excludes the Euisoptera (node 2). The third scenario excludes the
 Kalotermitidae + Neoisoptera (node 3). The fourth scenario excludes the
 Neoisoptera (node 4). The fifth scenario excludes the Neoisoptera minus
 the subfamily Rhinotermitinae (node 5). The sixth scenario excludes the
 Termitidae + Coptotermitinae + Heterotermitinae (node 6). The seventh
 scenario excludes the family Termitidae (node 7).Figure S2 - Prior and
 posterior probabilities for shiftsFigure S2. Frequency
 distribution of distinct macroevolutionary rate regimes estimated for the
 Dictyoptera using BAMM with a Poisson prior of 10. A scenario including
 five shifts of diversification has the highest posterior probability
 Similar results are obtained with different values of the Poisson prior
 (Fig. S6).Figure S3 - Marginal
 probabilities and marginal odds ratios of the BAMM runFigure S3. Two different
 metrics of weighing the relative evidence of a diversification shift
 occurring along any individual branch. (a) The phylogenetic tree has its
 branch lengths been replaced by the branch-specific marginal shift
 probabilities, i.e. the length of a given branch is equal to the
 percentage of samples from the posterior that contain a rate shift on that
 particular branch. (b) The phylogenetic tree has the branch lengths scaled
 to equal the corresponding marginal odds ratio accounting for the effects
 of the prior and branch length. The longest branch length, in both trees,
 is labelled for reference. In both cases, the longest branch is within the
 termites.Figure S4 - Credible set
 of diversification shifts in DictyopteraFigure S4. Credible set
 of configuration shifts for net diversification of Dictyoptera inferred
 with BAMM. Phylogenies show 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. Text labels (e.g. f=0.11) denote
 the posterior probability of each shift configuration.Figure S5 - Best shift
 configuration in diversification shifts in DictyopteraFigure S5. The best
 shift configuration for net diversification shifts inferred with BAMM. The
 phylogeny indicates five core rate shifts (indicated by red-filled circle)
 within the termites, two within the Mantodea, and two within the
 cockroaches (notably in Blaberidae, Panesthiinae). The first shift in
 mantises occurred early (166.8 Ma) and includes most of the mantises but
 leaves out all ancient and depauperate lineages near the root of the tree.
 The second shift within mantises is located at the base of a clade
 including notably the plant-mimicking mantises (Empusidae), the flower
 mantises (Hymenopodidae), and the core of praying mantises (Mantidae). The
 first shift in cockroaches is ancient (243 Ma), just after the
 Permian-Triassic extinction, corresponds to the divergence of the termite
 lineage (including Cryptocercidae and Lamproblattidae, two species-poor
 families of cockroaches) and the lineage leading to Blattidae. The second
 shift occurred at the K-Pg event (66 Ma), and involves an offshoot of the
 blaberid radiation (Panesthiinae, ca. 150 species). The most important
 shift occurred within termites, 66 Ma, at the node sustaining the
 radiation of Termitidae and a part of Rhinotermitidae. Interestingly this
 lineage is composed only by eusocial species with true workers (Fig.
 S1).Figure S6 - BAMM
 analyses to check for prior effectFigure S6. All the
 results for the BAMM analyses using a range of values for the Poisson
 prior process (0.1/0.5/1/5/10/50). The figures are ranked as follows: (1)
 prior and posterior distribution, and (2) best configuration. Overall, the
 results indicate a similar macroevolutionary mixture of rate shifts and
 diversification rates, with a significant shift within termites and a
 higher net diversification for termites.Figure S7 - Differences
 BiSSE MCMCDifferences between
 speciation (a), extinction (b), and net diversification rates (c),
 computed from the MCMC analyses using the best BiSSE model. No posterior
 distribution overlaps with the red line, indicating that the differences
 between all rates are significant. Eusocial lineages diversified faster
 than non-eusocial lineages.Figure S8 - Differences
 MuSSE worker states macroevolutionary rates MCMCDifferences in rates
 computed from the MCMC analyses using the best MuSSE model for the ‘true’
 workers. The compound figure shows: 1) the differences between speciation
 rates as made by pair comparisons; 2) the differences between extinction
 rates; and 3) the differences between net diversification rates. Only the
 lineages with ‘true’ workers have a significant different speciation,
 extinction, and net diversification rates (i.e. no posterior distribution
 overlaps with the red line). Eusocial lineages with ‘true’ workers
 diversified faster than non-eusocial lineages and eusocial lineages with
 pseudergates.Figure S9 - Differences
 MuSSE hindgut microbiota macroevolutionary rates MCMCDifferences in rates
 computed from the MCMC analyses using the best MuSSE model for the gut
 microbiota. The compound figure shows: 1) the differences between
 speciation rates as made by pair comparisons; 2) the differences between
 extinction rates; and 3) the differences between net diversification
 rates. Only the lineages with an entirely prokaryotic gut microbiota have
 a significant different net diversification rates (i.e. no posterior
 distribution overlaps with the red line). Eusocial lineages with an
 entirely prokaryotic hindgut microbiota diversified faster than other
 lineages (cellulolytic flagellates or no specialized microbiota for
 lignocellulose digestion).Figure S10 - Simulations
 with SSE modelsRandomization tests for
 (a) BiSSE, (b) MuSSE on the worker state, and (c) MuSSE on the hindgut
 microbiota. The difference of fit between the best model and the reference
 model is shown with the red vertical line for real data, and in vertical
 coloured bars for the distribution of simulated data. The tests show that
 our results are robust to type-I error.Figure S11 - MuSSE
 hindgut microbiota Wood-feeding non-eusocialResults for the MuSSE
 analyses with the wood-feeding non-eusocial lineages re-coded as
 cellulolytic flagellates along with plots of the differences in rates
 computed from the MCMC analyses using the best MuSSE model. The compound
 figure shows: 1) the differences between speciation rates as made by pair
 comparisons; 2) the differences between extinction rates; and 3) the
 differences between net diversification rates. Only the lineages with an
 entirely prokaryotic hindgut microbiota have a significant different net
 diversification rates (i.e. no posterior distribution overlaps with the
 red line). Eusocial lineages with an entirely prokaryotic hindgut
 microbiota diversified faster than other lineages (cellulolytic
 flagellates or no specialized microbiota for lignocellulose
 digestion).Figure S12 - MuSSE
 hindgut microbiota rates MacrotermitinaeResults for the MuSSE
 analyses with the Macrotermitinae re-coded with ‘lower’ termites, due to
 their simple hindgut structure, along with plots of the differences in
 rates computed from the MCMC analyses using the best MuSSE model. The
 compound figure shows: 1) the differences between speciation rates as made
 by pair comparisons; 2) the differences between extinction rates; and 3)
 the differences between net diversification rates. Only the lineages with
 a complex hindgut structure have a significant different net
 diversification rates (i.e. no posterior distribution overlaps with the
 red line). Eusocial lineages with a complex hindgut structure diversified
 faster than other lineages (eusocial and non-eusocial organisms with
 simple hindgut structure)Table S1 - BAMM
 analysesSummary of
 diversification models in BAMM compared across a gradient of values for
 the Poison process governing the number of rate shifts. The analyses show
 that a scenario with either four, five or six shifts of diversification
 best explained the macroevolution of Dictyoptera. Although it might
 suggest that the Poison prior has some effect on the analyses, it is
 important to note that all shifts are in common between the analyses (see
 Fig. S6 for more details). Based on the effective sample size (ESS) and
 the highest posterior distribution per number of shifts for the Poisson
 rate prior, we selected the model with a Poison prior of 10 (highlighted
 in bold). In addition this model represents an intermediary among the
 analyses (i.e. we did not favour a model with more shifts or a model with
 few shifts).Table S2 - SSE
 analysesSupports for
 eusociality, eusocial lineages with ‘true’ workers, and eusocial lineages
 with entirely prokaryotic microbiota as driver(s) of diversification.
 Tables (a), (c) and (e) report the means for each value estimated based on
 100 dated trees, for each diversification model applied under the BiSSE
 approach, their number of parameters (NP), the log-likelihood (logL), the
 corrected Akaike Information Criterion (AICc), the difference of AICc
 (ΔAIC) between the best model (lowest AIC) and a given model. The best
 model is highlighted in bold and determined by ∆AIC. Tables (b), (d) and
 (f) report the standard errors for each parameter estimated by the
 diversification models and listed in the tables (a), (c) and
 (e).