Agaonidae_dataAgaonidae. Combined matrix of 6 genes. Two nuclear protein-coding genes [F2 copy of elongation factor-1a (EF1a, 516 bp), Wingless (Wg, 403 bp)]; two mitochondrial protein-coding genes [cytochrome c oxidase subunit I (COI, 1536 bp), cytochrome b (Cyt b, 749 bp)] and two ribosomal genes [28S rRNA (D2–D3 and D4–D5 expansion regions, 1520 bp), 18S rRNA (variable regions V3–5, 787 bp)].TreeRAxML_AgaonidaeML analyses and associated bootstrapping (1,000 replicates) using the MPI-parallelized RAxML 7.0.4 software (Stamatakis, 2006b). GTRCAT approximation of models (Stamatakis, 2006a) was used for ML boostrapping (1,000 replicates).Ficus_dataMatrix of using five genes: ITS (891 bp), ETS (528 bp), glyceraldehyde 3-phosphate dehydrogenase (G3pdh, 769 bp), chloroplast expressed glutamine synthetase region (ncpGS, 1630 bp) and granule-bound starch synthase (waxy region, 1734 bp).TreeRAxML_FicusML analyses and associated bootstrapping (1,000 replicates) using the MPI-parallelized RAxML 7.0.4 software (Stamatakis, 2006b). GTRCAT approximation of models (Stamatakis, 2006a) was used for ML bootstrapping (1,000 replicates.)Cruaud et al_SIThis document comprises the following items: - APPENDIX S1: Additional discussion relative to the phylogenetic position of the genus Tetrapus (Agaonidae). - APPENDIX S2: Review of the literature on fig fossils (leaves, woods, seeds and fruits). - SUPPORTING FIGURES S1-S14. - SUPPORTING TABLES S1-S6.BEAST_AgaonidaeBEAST control file for AgaonidaeBEAST_FicusBEAST control file for FicusAppendix S1-Ficus materialList of Ficus and outgroup species included in the present study. Voucher and taxonomic information, sampling localities and GenBank accession numbers are provided. Sequences produced for this study are indicated in bold font.Appendix S2- wasp materialList of Agaonidae and outgroup species included in this study. Voucher numbers, taxonomic information, natural host-fig, sampling localities and GenBank accession numbers are provided.Cruaud et al_SIThis document comprises the following items: - APPENDIX S3: Additional discussion relative to the phylogenetic position of the genus Tetrapus (Agaonidae). - APPENDIX S4: Review of the literature on fig fossils (leaves, woods, seeds and fruits). - SUPPORTING FIGURES S1-S14. - SUPPORTING TABLES S1-S6.TreeBASE:S13315A link to the related TreeBASE study

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant–insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant–insect interactions of coordinated dispersal and long-term codiversification.