DOI: 10.5281/zenodo.14642353
title: Data and scripts supporting the manuscript: 'Why the long "horns"? Fine-scale morphology suggests tactile demands contributed to the exaggeration of male longhorned beetle antennae (Coleoptera: Cerambycidae)'

description: Contents (copied from README.md):

 

# Raw and processed data and scripts supporting the manuscript 'Why the long "horns"? Fine-scale morphology suggests tactile demands contributed to the exaggeration of male longhorned beetle antennae (Coleoptera: Cerambycidae)'

 

## List of Contents: 

 

 

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### Phylogeny  (folder)

 

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######### Input_SuperCrunch (folder)

- Anoplistes_allseqs_LK_plus_outgroups-FINAL.fasta: fasta file of raw COI sequences (including previously published sequences and the new A. tuvensis sequence)

- Anoplistes_supercrunch_bash_COIOnly_FINAL.sh: custom bash script used to run SuperCrunch program

- Anoplistes_taxa_FINAL.txt: list of target taxa for SuperCrunch

- COI-refseqs.fasta: reference COI sequences from GenBank; used for target sequence filtration

- Locus-Search-Terms_Markers_Anoplistes_COIOnly_2022.10.31.txt: search terms for the target locus (COI); used to filter out non-COI sequences from the .fasta file

 

 

######### Input_Mesquite (folder)

- Concatenated_Alignment_namesupdated.nex: final COI alignment produced by SuperCrunch; used as input for Mesquite (which we used to concatenate the morpho & COI matrices before running MrBayes)

- Morpho_matrix_trimmed_2_specimen-level_FINAL.txt: final morphological character matrix

 

 

 

######### Input_MrBayes (folder)

- COI-morpho-fusediffDataTypes_MrBayesInput_1outgroup_2024-07-17_trimmed.nex: concatenated alignment of COI and morphological data from Mesquite, with an added MrBayes block

 

######### Output_MrBayes (folder)

- infile.nex.con.tre: 50% majority rule consensus tree from MrBayes analysis of the concatenated morphological and COI alignment (used to create Fig. S10a)

- infile.nex.run1.p: log file from run 1 of MrBayes

- infile.nex.run1.t: trees produced by run 1 of MrBayes

- infile.nex.run2.p: log file from run 2 of MrBayes

- infile.nex.run2.t: trees produced by run 2 of MrBayes

- infile.nex.run3.p: log file from run 3 of MrBayes

- infile.nex.run3.t: trees produced by run 3 of MrBayes

- infile.nex.run4.p: log file from run 4 of MrBayes

- infile.nex.run4.t: trees produced by run 4 of MrBayes

 

 

 

######### Input_BEAST (folder)

- BEAST_unconst_A-150mill.xml: BEAST 2 xml run file (generated using BEAUti) for the analysis of a concatenated alignment of Anoplistes COI sequences

- COI-morpho-fusediffDataTypes_BeastInput_1outgroup_2024-10-26_trimmed_MolecularOnly_a.nex: alignment of Anoplistes COI sequences; adapted from the SuperCrunch output by selecting a single sequence (the longest) for each (sub-)species

 

######### Output_BEAST (folder)

- Beast-4runs-combined (folder)

- Beast-unconst-A-150mill-combined-burnin25_mcc.tre: maximum clade credibility tree based on the 4 combined runs (see below), after removing 25% burnin from each run (used to create Fig. S10b)

- Beast-unconst-A-150mill-combined-burnin25.log: log file based on the 4 combined runs (see below), after removing 25% burnin from each run

- Beast-unconst-A-150mill-combined-burnin25.trees: trees produced by the 4 combined runs (see below), after removing 25% burnin from each run

- Beast-unconst-A-150mill-run1 (folder)

- infile-COI-morpho-fusediffDataTypes_BeastInput_1outgroup_2024-10-26_trimmed_MolecularOnly_a_run1.trees: trees produced by run 1 of BEAST 2 on the COI alignment; .trees files for runs 2-4 are in separate folders (see below)

- infile_run1.log: log file for run 1 of BEAST 2 on the COI alignment; .log files for runs 2-4 are in separate folders (see below)

- infile_run1.xml: xml run file for run 1 of BEAST 2 on the COI alignment; .xml files for runs 2-4 are in separate folders (see below)

- Beast-unconst-A-150mill-run2 (folder)

- infile-COI-morpho-fusediffDataTypes_BeastInput_1outgroup_2024-10-26_trimmed_MolecularOnly_a_run2.trees

- infile_run2.log

- infile_run2.xml

- Beast-unconst-A-150mill-run3 (folder)

- infile-COI-morpho-fusediffDataTypes_BeastInput_1outgroup_2024-10-26_trimmed_MolecularOnly_a_run3.trees

- infile_run3.log

- infile_run3.xml

- Beast-unconst-A-150mill-run4 (folder)

- infile-COI-morpho-fusediffDataTypes_BeastInput_1outgroup_2024-10-26_trimmed_MolecularOnly_a_run4.trees

- infile_run4.log

- infile_run4.xml

 

 

 

 

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### Stat_analyses

 

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######### R_scripts (folder)

- AnoplistesSensilla-DataPrep-Final-CLEAN.R: R script used to process raw data (trees, antennal measurements, and sensilla data)

- AnoplistesSensilla-Models-Final-CLEAN.R: R script used to create and run brms models across 100 phylogenetic trees

- AnoplistesSensilla-ModelSummaries-Final-CLEAN.R: R script used to pool brms model results across 100 phylogenetic trees; also used to test for phylogenetic signal in antennal data

- AnoplistesSensilla-Plots-Final-CLEAN.R: R script used to generate plots for the main text and supplementary material

 

######### DataPrep_input (folder): input files for the AnoplistesSensilla-DataPrep-Final-CLEAN.R script

- Anoplistes_segmentDimensions_2024-02-27.csv: raw data on the lengths and widths of individual flagellomeres 

- Anoplistes_sensilla_data_v3_2024-03-20b.csv: raw data on the abundance of (a) all sensillum types (pooled together) within quadrats overlaid on general (low-magnification) images and (b) the abundance of long chemosensory sensilla in apical and basal regions of the ninth flagellomere

- Anoplistes_sensillabasiconica_2024-03-24.csv: raw data on the abundance of short olfactory and mechanosensory sensilla within quadrats overlaid on detailed (high-magnification)images of the ninth flagellomere

- AnoplistesRelativeAntennaLength_v2.csv: raw antenna length/elytral length data collected by measuring images of specimens

- Beast-unconst-A-150mill-combined-burnin25.trees: same tree file as in the Beast-4runs-combined folder; copied here for convenience

 

######### DataPrep_output (folder): output files from the AnoplistesSensilla-DataPrep-Final-CLEAN.R script; files used as input for the other three scripts

- antennaSegDimensions_spsexmean_2024-06-05.csv: Mean lengths & widths of individual antennal segments (one mean per sex and species)

- relativeAntennaLengthSD_spsexmean_2024-06-05.csv: Relative antenna lengths and antenna length sexual dimorphism from specimen images (one mean per sex and species) 

- sensilla_detImages_ind_2024-06-05.csv: individual-level data on the abundances of mechanosensory hairs, short olfactory hairs from detailed images 

- sensilla_detImages_spsexmean_2024-06-05.csv: sex and taxon-specific means for the abundances of mechanosensory hairs, short olfactory hairs from detailed images 

- sensilla_genImages_AL_spsexmean_2024-06-05.csv:sex and taxon-specific means for total sensilla abundance and density from general images 

- sensilla_genImages_ind_2024-06-05.csv: individual-level data on total sensilla abundance and density from general images 

- sensilla_genImages_longchemo_ind_2024-06-05.csv: individual-level data on the estimated abundance of long chemosensory sensilla in the apical and basal halves of the ninth flagellomere; estimates from general images

- sensilla_genImages_longchemo_spsexmean_2024-06-05.csv: sex and taxon-specific means for the estimated abundance of long chemosensory sensilla in the apical and basal halves of the ninth flagellomere; estimates from general images

- trees_beast_100_grafted_2024-10-31.nwk: list of 100 randomly sampled BEAST phylogenies with A. agababiani and A. mongolicus grafted on; used this list for downstream phylogenetic comparative analyses

 

 

######### Model_output (folder): brms model results outputted in list format by the AnoplistesSensilla-Models-Final-CLEAN.R script; objects used as input for the AnoplistesSensilla-ModelSummaries-Final-CLEAN.R and AnoplistesSensilla-Plots-Final-CLEAN.R scripts

- LongChemosensorySensillaAbund_brmsfitted_100trees_2024-11-22.rds: long chemosensory model (Fig. 5a)

- MechanosensorySensillaAbund_brmsfitted_100trees_2024-11-22.rds: mechanosensory model (Fig. 5b)

- segmentArea_brmsfitted_100trees_2024-11-24.rds: segment area model (Fig. S12)

- ShortOlfactorySensillaAbund_brmsfitted_100trees_2024-11-22.rds: short olfactory model (Fig. 5c)

- totalsensillaAbund_brmsfitted_100trees_2024-11-19.rds: sensilla abundance model (Fig. 4a)

- totalsensillaDens_brmsfitted_100trees_2024-11-22.rds: sensilla density model (Fig. 4b)

 

######### ModelSummary_output (folder): brms model results pooled across 100 iterations by the AnoplistesSensilla-ModelSummaries-Final-CLEAN.R script; objects used as input for the AnoplistesSensilla-Plots-Final-CLEAN.R script

- brm.abund.gen_100models_combined_2024-11-28.RDS: sensilla abundance model (Fig. 4a)

- brm.chaetica.det_100models_combined_2024-11-28.RDS: mechanosensory model (Fig. 5b)

- brm.contactchemo.gen_100models_combined_2024-11-28.RDS: long chemosensory model (Fig. 5a)

- brm.dens.gen_100models_combined_2024-11-28.RDS: sensilla density model (Fig. 4b)

- brm.sb.det_100models_combined_2024-11-28.RDS: short olfactory model (Fig. 5c)

- brm.segarea_100models_combined_2024-11-28.RDS: segment area model (Fig. S12)