Data from: Evolutionary déjà vu? A case of convergent evolution in an ant-plant association
Data files
Jun 06, 2024 version files 924.98 MB
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align-nexus-gblocks-names-75.phylip.zip
17.49 MB
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ASR_BayesTraits_Myrmelachista.zip
9.62 MB
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ASR_R_Myrmelachista.zip
1.86 MB
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beast_xml_file.zip
4.15 MB
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README.md
8.03 KB
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Tree_files.zip
178.42 MB
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UCE_contigs.zip
713.43 MB
Aug 30, 2024 version files 924.99 MB
Abstract
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.
README: Data for: Evolutionary déjà vu? A case of convergent evolution in an ant-plant association
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").