DOI: 10.5061/dryad.4j0zpc8m9
title: Data from: Evolutionary déjà vu? A case of convergent evolution in an ant-plant association

description: Obligatory ant-plant symbioses often appear to be single evolutionary
 shifts within particular ant lineages; however, convergence can be
 revealed once natural history observations are complemented with molecular
 phylogenetics. Here we describe a remarkable example of convergent
 evolution in an ant-plant symbiotic system. Exclusively arboreal,
 Myrmelachista species can be generalized opportunists nesting in several
 plant species or obligately symbiotic, live-stem nesters of a narrow set
 of plant species. Instances of specialization within Myrmelachista are
 known from northern South America and throughout Middle America. In Middle
 America, a diverse radiation of specialists occupies understory treelets
 of lowland rainforests. The morphological and behavioural uniformity of
 specialists suggests that they form a monophyletic assemblage,
 diversifying after a single origin of specialization. Using ultraconserved
 element phylogenomics and ancestral state reconstruction, we show that
 shifts from opportunistic to obligately symbiotic evolved independently in
 South and Middle America. Furthermore, our analyses strongly support a
 remarkable case of convergence within the Middle American radiation, with
 two independently evolved specialist clades, arising nearly simultaneously
 from putative opportunistic ancestors during the late Pliocene. This
 repeated evolution of a complex phenotype suggests similar mechanisms
 behind trait shifts from opportunists to specialists, generating further
 questions about the selective forces driving specialization.
description: # Data for: Evolutionary déjà vu? A case of convergent evolution in an
 ant-plant association
 [https://doi.org/10.5061/dryad.4j0zpc8m9](https://doi.org/10.5061/dryad.4j0zpc8m9) #### Complete set of UCE contigs The file includes the complete set of 2103 aligned UCE contigs for 45 taxa. The alignments are provided as invidual FASTA files (i.e., one file per specimen). File name: uce-contigs.zip File list: *Brachymyrmex_admotus_EXRP163.contigs.fasta Brachymyrmex_cf._aphidicola_EXRP168.contigs.fasta Brachymyrmex_depilis_EXRP169.contigs.fasta Brachymyrmex_heeri_EXRP182.contigs.fasta Brachymyrmex_nebulosus_EXRP181.contigs.fasta Brachymyrmex_pilipes_EXRP174.contigs.fasta Lasius_sitiens_EX1585.contigs.fasta Myrmelachista_RSP011_EXRP166.contigs.fasta Myrmelachista_RSP014_EXRP56.contigs.fasta Myrmelachista_RSP020_EXRP137.contigs.fasta Myrmelachista_RSP024_EXRP97.contigs.fasta Myrmelachista_RSP026_EX819.contigs.fasta Myrmelachista_RSP027_EXRP1.contigs.fasta Myrmelachista_RSP056_EXRP6.contigs.fasta Myrmelachista_RSP057_EXRP63.contigs.fasta Myrmelachista_RSP063_EXRP21.contigs.fasta Myrmelachista_RSP065_EXRP179.contigs.fasta Myrmelachista_bambusarum_EXRP100.contigs.fasta Myrmelachista_brevicornis_EXRP49.contigs.fasta Myrmelachista_bruchi_EXRP177.contigs.fasta Myrmelachista_catharinae_EXRP180.contigs.fasta Myrmelachista_cf._zeledoni_EXRP44.contigs.fasta Myrmelachista_cooperi_EXRP17.contigs.fasta Myrmelachista_flavocotea_EXRP71.contigs.fasta Myrmelachista_flavoguarea_EXRP28.contigs.fasta Myrmelachista_gagates_EXRP124.contigs.fasta Myrmelachista_haberi_EXRP42.contigs.fasta Myrmelachista_hoffmanni_EXRP103.contigs.fasta Myrmelachista_lauroatlantica_EXRP4.contigs.fasta Myrmelachista_lauropacifica_EXRP74.contigs.fasta Myrmelachista_longiceps_EXRP41.contigs.fasta Myrmelachista_longiceps_EXRP43.contigs.fasta Myrmelachista_mayri_EXRP170.contigs.fasta Myrmelachista_meganaranja_EXRP64.contigs.fasta Myrmelachista_mexicana_EXRP58.contigs.fasta Myrmelachista_nigrocotea_EXRP29.contigs.fasta Myrmelachista_nodigera_EXRP175.contigs.fasta Myrmelachista_osa_EXRP65.contigs.fasta Myrmelachista_plebecula_EXRP30.contigs.fasta Myrmelachista_reclusi_EXRP50.contigs.fasta Myrmelachista_schumanni_EXRP48.contigs.fasta Myrmelachista_schumanni_EXRP68.contigs.fasta Myrmelachista_schumanni_EXRP77.contigs.fasta Myrmelachista_skwarrae_EXRP22.contigs.fasta Myrmelachista_zeledoni_EXRP7.contigs.fasta* #### Concatenated matrix of aligned UCE loci The primary DNA sequence matrix analyzed in this study. The matrix contains 2104 aligned, filtered (matrix generated with Phyluce for 75% completeness), and trimmed (using GBlocks) UCE loci. Includes by-locus character partitions. File name: uce-contigs-unaligned-untrimmed.zip File list: *align-nexus-gblocks-names-75.phylip align-nexus-gblocks-names-75.charsets* #### BEAST xml data file The BEAST xml data file used in this study. Includes one file for the 45 sample analysis, comprising of 500 randomly chosen UCE loci and lognormal distribution priors set for the Myrmelachistini tribe (i.e., root of analysis). File name: beast_xml_file.zip File list: *Myrmelachista_500loci_tribelognormal2* #### Tree files Main phylogenetic tree results provided in .tre format (edited NEXUS). Includes best IQ-Tree output trees with bootstrap scores using different input matrices (*concatenated.tre*: tree from UCE matrix treated as concatenated alignment; *bylocus-UFB_gCF_and_sCF.tre*: tree from UCE matrix partitioned by UCE locus and including calculation of gene concordance factor (gCF) and site concordance factor (sCF); *bylocus.tre*: tree from UCE matrix partitioned by UCE locus; *ry-coding.tre*: tree from UCE matrix with all purines (A or G) coded as Rs and all pyrimidines (C or T) coded as Ys; *binary(0-1).tre*: tree from UCE matrix with all purines (A or G) coded as 0s and all pyrimidines (C or T) coded as 1s; *SWSC.treefile*: tree from UCE matrix partitioned using the entropy-based Sliding-Window Site Characteristics (SWSC-EN), a sliding-window approach to divide each UCE into three data blocks (left/core/right); *symtest-SWSC_partition-not_merged.tre*, *symtest-SWSC_partition-merged.tre* and *symtest-partitionbylocus.tre*: trees performing tests of symmetry on the UCE matrix partitioned using the entropy-based Sliding-Window Site Characteristics (SWSC-EN) for every ungermed and every merged partition of the alignment, respectively, and on the partition by locus matrix), *astral-tree.tre*: ASTRAL species tree with bootstrap scores, BEAST outputs (a file combining 4 independent runs totaling 12,000 trees with a lognormal distribution and 25% burn-in (*BEAST_combined4runs_lognormal2_burnin25.tre*), a file with the maximum clade credibility or MCC tree, summarized by BEAST’s TreeAnnotator tool (*BEAST_mcc_combined_burnin25.tre*), and a file comprising of 1000 randomly chosen trees from the 12,000 posterior distribution, used for downstream ancestral reconstruction analyses (*1000random_trees_pruned_from_posterior.tre*) and the MCMCTree chronogram (*MCMCTree_gamma_0.146.tre*: tree from MCMCTree using a gamma value of 0.146). File name: Tree_files.zip File list: *concatenated.tre* *bylocus-UFB_gCF_and_sCF.tre* *bylocus.tre* *ry-coding.tre* *binary(0-1).tre* *SWSC.treefile* *symtest-SWSC_partition-merged.tre* *symtest-SWSC_partition-not_merged.tre* *symtest-partitionbylocus.tre* *astral-tree.tre* *BEAST_combined4runs_lognormal2_burnin25.tre* *BEAST_mcc_combined_burnin25.tre* *1000random_trees_pruned_from_posterior.tre* *MCMCTree_gamma_0.146.tre* #### Trait reconstruction analysis files R scripts and trait data for inferring nesting habit (opportunist vs. specialist) ancestral states for R analyses. Files correspond to R script file for ancestral state reconstructions (ASRs) (*Script_for_chronogram_and_asr_updated_pruned_tree.R*), simmap trees for equal rates (ER) and all-rates different (ARD) models using 1,000 trees, MCMC algorithm, and *Myrmelachista cooperi* labeled as opportunist.The *mcc_combined4runs_lognormal2_burnin25.tre* is equivalent to the *BEAST_mcc_combined_burnin25.tre* above besides having outgroups ladderized. The file *tip_labels_mcmc.txt* correspond to ASR coding for all terminals included in the analyses. The file *tree_pruned_random1000* corresponds to the *1000random_trees_pruned_from_posterior.tre* by pruning the species *Lasius sitiens* and duplicates of *Myrmelachista schumanni* out of the analyses. File name: ASR_R_Myrmelachista.zip File list: *Script_for_chronogram_and_asr_updated_pruned_tree.R MyrmelachistaARD_cooperi_opportunist.1000MCMCsimmap MyrmelachistaER_cooperi_opportunist.1000MCMCsimmap mcc_combined4runs_lognormal2_burnin25.tre tip_labels_mcmc.txt tree_pruned_random1000* Trait data for inferring nesting habit (opportunist vs. specialist) ancestral states for BayesTraits analyses. Each subfolder (1\_ to 6_) contains the input tree file (1,000 random trees as per *tree_pruned_random1000* above), log files, nesting habit coding for all terminals, command-line file utilized for the analyses, and stepping-stone output. For each run, nomenclature is as follows: *1_MCMC_Tree_cooperi_opport_all_nodes*: *M. cooperi* labeled as opportunist, all tree nodes unfixed *2_MCMC_Tree_cooperi_unk*: *M. cooperi* labeled as unknown, all tree nodes unfixed *3_MCMC_Tree_cooperi_opport_root_fixed_opp*: *M. cooperi* labeled as opportunist, tree root fixed as opportunist *4_MCMC_Tree_cooperi_unk_root_fixed_opp*: *M. cooperi* labeled as unknown, tree root fixed as opportunist *5_MCMC_Tree_cooperi_opport_fixed_nodeX_opp*: *M. cooperi* labeled as opportunist, Node X fixed as opportunist *6_MCMC_Tree_cooperi_opport_fixed_nodeX_spec*: *M. cooperi* labeled as opportunist, Node X fixed as specialist File name: ASR_BayesTraits_Myrmelachista.zip File list: *1_MCMC_Tree_cooperi_opport_all_nodes 2_MCMC_Tree_cooperi_unk 3_MCMC_Tree_cooperi_opport_root_fixed_opp 4_MCMC_Tree_cooperi_unk_root_fixed_opp 5_MCMC_Tree_cooperi_opport_fixed_nodeX_opp 6_MCMC_Tree_cooperi_opport_fixed_nodeX_spec* #### Voucher information file The file *Voucher_table.xlsx* includes the complete voucher information for all 45 taxa included in the present study, linking extraction data for all specimens and additional pertinent information (check Tab "Notes").