Data from: Testing cohesive selective paths and evaluating information loss while delimiting species of Brazilian wandering spiders
Data files
Jun 02, 2026 version files 2.59 GB
-
Analyses.7z
2.59 GB
-
DiscreteMorphoMatrix.7z
5 KB
-
DNA_alignments.7z
4.79 KB
-
README.md
28.75 KB
-
Trees.7z
90.35 KB
Abstract
Biodiversity is structured in nested Retrospective Reproductive Communities (RRCs) reflecting different levels of information about evolutionary processes. Ranking species involves deciding which level to emphasize, based on a trade-off in information gain and loss. Modeling the selective processes that maintain RRCs along distinct evolutionary paths can inform these trade-offs in species delimitation. We illustrate this approach using the Brazilian wandering spiders (Phoneutria). Integrating genetic markers, geometric morphometrics, color patterns, and environmental data, we applied both established and novel models to test historical natural and sexual selection driving divergence. We found evidence that selection on ecological niche and ventral abdominal coloration contributed to the formation of four distinct RRCs. Two of these RRCs also showed evidence of a Lock-and-Key mechanism influencing genital morphology evolution. Despite the distinct cohesive forces, gene flow modeling revealed incomplete reproductive isolation, with potential hybrid individuals. We evaluate the implications of lumping versus splitting these lineages and argue that recognizing all four as distinct species would better preserve evolutionary information and minimize downstream impacts on other research fields such as pharmacology, public health and conservation. Our approach provides a quantitative basis to ponder the implications of choosing between different species hypotheses.
Description of the data, directory structure and files
This repository contains the data matrices, custom scripts, software inputs and outputs used in the paper "Testing cohesive selective paths and evaluating loss of evolutionary information while delimiting species of Brazilian wandering spiders. Evolution, 2026." We generated Sanger sequencing data for Brazilian Wandering spiders (Phoneutria), as well as geometric morphometrics aligned coordinates and obtained 19 bioclimatic variables for curated locality records. For details on the DNA extraction, sequencing, geometric morphometrics and bioclimatic variables, please see the publication associated with this dataset.
Folders and Files
Folders are compressed with 7z
(./Analyses.7z):
Contains subfolders with inputs, scripts, and outputs for in the analyses described in the manuscript. Subfolders are organized by the name of the analyses in the manuscript. Names of the subfolder are structure as Software_AnalysisSpecificDatails. This information can be traced back to the Material And Methods sections in the publication. When necessary, README.md files with each subfolder provides additional information specific to each folder. Detailed of the subfolders content are shown below.
Folder BPP_GeneFlow_PopLevel.7z
This folder contains inputs, configuration files, and outputs for Bayesian Phylogenetics & Phylogeography (BPP) gene flow analysis conducted at the population level for Phoneutria species.
File Descriptions
- PhoBPP_A00.GF.r1.ctl - BPP control file for gene flow analysis, replicate 1
- PhoBPP_A00.GF.r2.ctl - BPP control file for gene flow analysis, replicate 2
- PhoBPP_A00.GF.Tree02.r1.ctl - BPP control file using Tree02 topology (Morphology Follows Population Tree), replicate 1
- PhoBPP_A00.GF.Tree02.r2.ctl - BPP control file using Tree02 topology, replicate 2
- PhoBPP_A00.GF.Tree03.r1.ctl - BPP control file using Tree03 topology (Molecular Only), replicate 1
- PhoBPP_A00.GF.Tree03.r2.ctl - BPP control file using Tree03 topology, replicate 2
- PhoBPP.Imap.txt - Individual-to-population mapping file; specifies which individuals belong to which populations
- PhoBPP_LociHeredity.txt - Locus heredity file; specifies heredity parameters for each genomic locus
- PhoBPP_ougroupFile.txt - Outgroup specification file; identifies which individuals/populations are designated as outgroups
- SeedUsed - Random seed value used for reproducibility of the analysis
- PhoBPP_GeneFlowSummary.csv - Summary spreadsheet of gene flow results across runs. NA means non-applicable.
- GeneFlowTree01_MorphoHemiplasy.tre - Population tree topology assuming morphology evolves under coalescent (Topology 1)
- GeneFlowTree02_MorphoFollowsSpeciesTREE.tre - Population tree topology where morphology follows molecular phylogeny (Topology 2)
- GeneFlowTree03_MolecularOnly.tre - Population tree topology based on molecular data only (Topology 3)
- outGF_r01/ - Output results from gene flow analysis using Tree01, replicate 1
- outGF_r02/ - Output results from gene flow analysis using Tree01, replicate 2
- outGFTree2_r01/ - Output results from gene flow analysis using Tree02 (Morphology Follows Species), replicate 1
- outGFTree2_r02/ - Output results from gene flow analysis using Tree02, replicate 2
- outGFTree3_r01/ - Output results from gene flow analysis using Tree03 (Molecular Only), replicate 1
- outGFTree3_r02/ - Output results from gene flow analysis using Tree03, replicate 2
Output Contents (in outGF*/outGFTree*/ directories)
Each output directory typically contains:
- Log files (.log) with summary statistics and convergence diagnostics
Folder BPP_GeneFlow_PutativeSpeciesLevel.7z
This folder contains inputs, configuration files, and outputs for Bayesian Phylogenetics & Phylogeography (BPP) gene flow analysis conducted at the putative species level for Phoneutria species.
File Descriptions
- PhoBPP_A00.GFSpecies.r1.ctl - BPP control file for species-level gene flow analysis, replicate 1
- PhoBPP_A00.GFSpecies.r2.ctl - BPP control file for species-level gene flow analysis, replicate 2
- PhoBPP_A00.GFSpecies.r3.ctl - BPP control file for species-level gene flow analysis, replicate 3
- PhoBPP.Imap.txt - Individual-to-species mapping file; specifies which individuals belong to which putative species
- PhoBPP_LociHeredity.txt - Locus heredity file; specifies heredity parameters for each genomic locus
- SeedUsed - Random seed value used for reproducibility of the analysis
- geneFlowSpecies_results.csv - Summary spreadsheet of gene flow results across species-level replicates. NA means non-applicable.
- outGFSp_r01/ - Output results from species-level gene flow analysis, replicate 1
- outGFSp_r02/ - Output results from species-level gene flow analysis, replicate 2
- outGFSp_r03/ - Output results from species-level gene flow analysis, replicate 3
Output Contents (in outGFSp*/ directories)
Each output directory typically contains:
- Log files (.log) with summary statistics and convergence diagnostics
Folder BPP_population_limits.7z
This folder contains inputs, configuration files, and outputs for Bayesian Phylogenetics & Phylogeography (BPP) population delimitation analysis for Phoneutria species. This analysis tests alternative hypotheses for population boundaries using molecular data.
File Descriptions
- PhoBPP_A11.alg0.r1.ctl - BPP control file for population delimitation (A11 model) using algorithm 0, replicate 1
- PhoBPP_A11.alg0.r2.ctl - BPP control file for population delimitation using algorithm 0, replicate 2
- PhoBPP_A11.alg1.r1.ctl - BPP control file for population delimitation using algorithm 1, replicate 1
- PhoBPP_A11.alg1.r2.ctl - BPP control file for population delimitation using algorithm 1, replicate 2
- PhoBPP.Imap.txt - Individual-to-population mapping file; specifies which individuals belong to which populations being tested
- PhoBPP_LociHeredity.txt - Locus heredity file; specifies heredity parameters for each genomic locus
- PhoBPP_ougroupFile.txt - Outgroup specification file; identifies which individuals/populations are designated as outgroups
- SeedUsed - Random seed value used for reproducibility of the analysis
- outAlg0Run01/ - Output from algorithm 0, run 1 (population delimitation results using algorithm 0)
- outAlg0Run02/ - Output from algorithm 0, run 2
- outAlg1Run01/ - Output from algorithm 1, run 1 (population delimitation results using algorithm 1)
- outAlg1Run02/ - Output from algorithm 1, run 2
Output Contents (in outAlgRun/ directories)
Each output directory typically contains:
- Log files (.log) with summary statistics, species delimitation results, and posterior probabilities
Folder ENMTools_NicheOverlap.7z
This folder contains scripts, input data, and results for ENMTools (Ecological Niche Modeling Tools) analyses of niche overlap between Phoneutria species.
File Descriptions
- Pho_nicheoverlap.R - R script that runs the ENMTools niche overlap analysis, calculates overlap metrics, and generates output files
- climate/ - Folder containing climate/environmental variable raster files or processed climate data used in the niche modeling
- datapoints/ - Folder containing occurrence point data coordinates
- key_per_pvalues.txt - P-values from statistical tests comparing niche overlap between P. keyserlingi and P. pertyi against null expectations
- nig_eic_pvalues.txt - P-values from statistical tests comparing niche overlap between P. nigriventer and P. eickestedtae
- key_per_dataframe.txt - Replications for null distribution for P. keyserlingi vs P. pertyi comparison
- nig_eic_dataframe.txt - Replications for null distribution for P. nigriventer vs P. eickestedtae comparison
- bg_dm_key_per.pdf - Histogram for the null distribution for P. keyserlingi vs P. pertyi niche comparison
- nig_eic_bg_dm.pdf - Histogram for the null distribution for P. nigriventer vs P. eickestedtae niche comparison
Folder PhuUNC_ColorFixationProbabilities.7z
This folder contains input data, commands, and results for analyses of color fixation probabilities in Phoneutria species using the PhuUNC framework.
File and Folder Descriptions
- commands_used.txt - Log of commands or scripts used to run the analyses in this folder. This file is useful for reproducing the analysis workflow.
- speciestree.nex - Primary species tree in NEXUS format for the full dataset analysis.
- speciestree_key_per.nex - Species tree in NEXUS format for the P. keyserlingi vs. P. pertyi comparison.
- speciestree_nig_eic.nex - Species tree in NEXUS format for the P. nigriventer vs. P. eicestedtae comparison.
- all_sp/
- Contains results for the color fixation analysis across all Phoneutria species included in the study. This includes simulated gene trees, fixation probability results, and summary files.
- key_per/
- Contains results for analyses focusing on the P. keyserlingi and P. pertyi pair.
- nig_eic/
- Contains input data and results for analyses focusing on the P. nigriventer and P. eicestedtae pair.
Folder RevBayes_SeDHiSSE.7z
This folder contains the scripts, data, and output files for the SeDHiSSE analyses implemented in RevBayes. SeDHiSSE is a state-dependent diversification model that evaluates how sexually dimorphic phenotypic states affect speciation and extinction rates while allowing hidden rate variation.
Folder Structure
- data/ - Input data for the analysis, including phenotype matrices and phylogenetic trees.
- scripts/ - RevBayes scripts and R plotting scripts used to run the model and summarize results.
- outputs/ - Primary output from the main analysis run.
- outputs_tree1/ - Output from the analysis run on the alternative Tree 1 topology.
- outputs_tree3/ - Output from the analysis run on the alternative Tree 3 topology.
Input Files
- data/Pho_PolyColorMatrix.csv - Color phenotype matrix in CSV format. Contains state coding for species or populations across color morphs.
- data/Pho_PolyColorMatrix.tsv - Same data in TSV format.
- data/Pho_Trees.tre - File with all three trees in Nexus format.
- data/Pho_Trees.newick - File with all three trees in Newick format.
Scripts
- scripts/Pho_SeDHiSSE.Rev - Main RevBayes script for running the SeDHiSSE model on the primary tree topology.
- scripts/SeDHiSSE_DAG.dot - Graphviz representation of the RevBayes graphical model structure.
- scripts/SeDHiSSE_DAG.png - Rendered DAG image.
- scripts/SeDHiSSE_DAG.svg - Vector graphic of the DAG.
- scripts/plotTrees.R - R script for plotting phylogenetic trees and tree-related results.
- scripts/plot_model_probs.R - R script for plotting posterior model probabilities.
- scripts/plot_rates.R - R script for plotting diversification and transition rates.
- scripts/plot_rates_ridgeline.R - R script for ridgeline-style visualization of rate distributions.
- scripts/summary_stats_from_trace.R - R script for summarizing trace statistics from MCMC output.
- scripts/trace_plot_probs_function.R - R helper function to plot posterior probability traces.
- scripts/trace_ridgeline_plot_function.R - R helper function for ridgeline trace visualizations.
- scripts/trace_violin_plot_function.R - R helper function for violin plot visualizations of MCMC traces.
Output Files
Each output folder contains the same basic suite of SeDHiSSE result files produced by the RevBayes MCMC run.
Common outputs include:
- Pho_SeDHiSSE.BirthDeathBrRates.log - Trace file of birth/death rate parameters for each state and hidden rate class.
- Pho_SeDHiSSE.model.log - Trace file of all model parameters.
- Pho_SeDHiSSE.cond.states.log - Trace file of conditional ancestral state probabilities.
- Pho_SeDHiSSE.stoch.log - Stochastic mapping trace.
- Pho_SeDHiSSE.ase.cond.tre - Tree file containing conditional ancestral state estimates.
- Pho_SeDHiSSE.ase.marg.tre - Tree file containing marginal ancestral state estimates.
- Pho_SeDHiSSE.char.map.marg.target.tre - Tree file with marginal character maps.
- Pho_SeDHiSSE.pp.map.marg.Target.tre - Tree file with posterior probabilities.
- Pho_SeDHiSSEcharmapTarget.tsv - Tabular stochastic character mapping results.
- Pho_SeDHiSSE.tre - Sampled phylogenetic trees from the MCMC run.
- Pho_SeDHiSSE.checkpoint - Checkpoint file for resuming the MCMC run.
- Pho_SeDHiSSE_mcmc.checkpoint - MCMC-specific checkpoint.
- Pho_SeDHiSSE_moves.checkpoint - Checkpoint file for sampler moves/proposals.
Folder RevBayes_OU_ClimaticPCA.7z
This folder contains scripts, data, and outputs from RevBayes analyses of phenotypic evolution on a phylogenetic tree using an Ornstein-Uhlenbeck (OU) model in relation to climatic principal components. This analysis tests whether phenotypic traits show evolutionary adaptation to climatic gradients.
File Descriptions
- Pho_OU_EnvPC1.Rev - RevBayes script for OU model analysis with Environmental PC1 as the environmental gradient (main analysis, Tree Topology 02)
- Pho_OU_EnvPC1_tree01.Rev - OU model analysis with Environmental PC1 using Tree Topology 01
- Pho_OU_EnvPC1_tree03.Rev - OU model analysis with Environmental PC1 using Tree Topology 03
- Pho_OU_EnvPC2.Rev - RevBayes script for OU model analysis with Environmental PC2 (second climatic principal component)
- Pho_OU_EnvPC2_tree01.Rev - OU model analysis with Environmental PC2 using Tree Topology 01
- Pho_OU_EnvPC2_tree03.Rev - OU model analysis with Environmental PC2 using Tree Topology 03
- PhoplotOUEnv.R - R script for visualizing OU model results and creating diagnostic plots
- plot_tree_color_branches_function.R - R helper function for plotting phylogenetic trees with branch colors
- data/Pho_EnvPCA.nexus - Phenotypic trait data in NEXUS format (complete dataset)
- data/Pho_EnvPCA_withMissing.nexus - Phenotypic trait data with missing values included (Not used in analyses. Kept for record)
- data/Pho_Trees.tre - Phylogenetic trees in Newick format (complete dataset)
- data/Pho_Trees_withMissing.tre - Phylogenetic trees with taxa having missing phenotypic data (Not used in analyses. Kept for record)
- data/README.md - Information about datapoints removed.
- PhoOUEnvPC1Out/ - Output from OU analysis with Environmental PC1 (main analysis, Tree02 topology)
- PhoOUEnvPC1_Tree01Out/ - Output from OU analysis with Environmental PC1 using Tree01 topology
- PhoOUEnvPC1_Tree03Out/ - Output from OU analysis with Environmental PC1 using Tree03 topology
- PhoOUEnvPC2Out/ - Output from OU analysis with Environmental PC2 (all data)
- PhoOUEnvPC2_Tree01Out/ - Output from OU analysis with Environmental PC2 using Tree01 topology
- PhoOUEnvPC2_Tree03Out/ - Output from OU analysis with Environmental PC2 using Tree03 topology
- outfigs/ - Generated figures from R visualization scripts
Output Contents (in PhoOUEnv*Out/ directories)
Each output directory typically contains:
- MCMC trace files (.log) with parameter posterior distributions
- Tree files with inferred parameter values at nodes
- Summary statistics on evolutionary parameters (alpha, sigma, optimum)
Folder RevBayes_OU_RWFemaleGenitalia
This folder contains scripts, data, and outputs from RevBayes analyses of phenotypic evolution of female reproductive morphology (epigyne/genitalia) using an Ornstein-Uhlenbeck (OU) model. This analyzes how female genitalic traits have evolved across the Phoneutria phylogeny.
File Descriptions
- Pho_OU_FemalesRW1.Rev - RevBayes script for OU model analysis of female genitalic trait (Relative Warps 1)
- Pho_OU_FemalesRW1_tree01.Rev - OU model for female genitalic trait (RW1) using Tree Topology 01
- Pho_OU_FemalesRW1_tree03.Rev - OU model for female genitalic trait (RW1) using Tree Topology 03
- Pho_OU_FemalesRW2.Rev - RevBayes script for OU model analysis of female genitalic trait (Relative Warps 2)
- Pho_OU_FemalesRW2_tree01.Rev - OU model for female genitalic trait (RW2) using Tree Topology 01
- Pho_OU_FemalesRW2_tree03.Rev - OU model for female genitalic trait (RW2) using Tree Topology 03
- PhoplotOUFemales.R - R script for visualizing OU model results for female genitalic evolution
- plot_tree_color_branches_function.R - R helper function for plotting phylogenetic trees with branch colors
- data/ - Folder containing morphometrics and phylogenetic trees
- PhoOUFemalesRW1Out/ - Output from OU analysis of female genitalic trait (RW1) using main tree
- PhoOUFemalesRW1_Tree01Out/ - OU analysis of female genitalic trait (RW1) using Tree Topology 01
- PhoOUFemalesRW1_Tree03Out/ - OU analysis of female genitalic trait (RW1) using Tree Topology 03
- PhoOUFemalesRW2Out/ - Output from OU analysis of female genitalic trait (RW2) using main tree
- PhoOUFemalesRW2_Tree01Out/ - OU analysis of female genitalic trait (RW2) using Tree Topology 01
- PhoOUFemalesRW2_Tree03Out/ - OU analysis of female genitalic trait (RW2) using Tree Topology 03
- outfigs/ - Generated figures and visualizations
Output Contents (in PhoOUFemalesRW*Out/ directories)
Each output directory typically contains:
- MCMC trace files (.log) with posterior distributions of evolutionary parameters
- Tree files with parameter estimates
- Summary statistics for evolutionary parameters (alpha = selection strength, sigma = evolutionary rate)
Folder RevBayes_OU_RWMaleGenitalia.7z
This folder contains scripts, data, and outputs from RevBayes analyses of phenotypic evolution of male reproductive morphology (palpal/genitalic structures) using an Ornstein-Uhlenbeck (OU) model. This analyzes how male genitalic traits have evolved across the Phoneutria phylogeny.
File Descriptions
- Pho_OU_MalesRW1.Rev - RevBayes script for OU model analysis of male genitalic trait (Relative Warps 1) using Tree Topology 02
- Pho_OU_MalesRW1_tree01.Rev - OU model for male genitalic trait (RW1) using Tree Topology 01
- Pho_OU_MalesRW1_tree03.Rev - OU model for male genitalic trait (RW1) using Tree Topology 03
- Pho_OU_MalesRW2.Rev - RevBayes script for OU model analysis of male genitalic trait (Relative Warps 2)
- Pho_OU_MalesRW2_tree01.Rev - OU model for male genitalic trait (RW2) using Tree Topology 01
- Pho_OU_MalesRW2_tree03.Rev - OU model for male genitalic trait (RW2) using Tree Topology 03
- PhoplotOUMales.R - R script for visualizing OU model results for male genitalic evolution
- plot_tree_color_branches_function.R - R helper function for plotting phylogenetic trees with branch colors
- data/ - Folder containing geometric morphometric (Relative Warps) data and phylogenetic trees.
- PhoOUMalesRW1Out/ - Output from OU analysis of male genitalic trait (RW1) using main tree
- PhoOUMalesRW1_Tree01Out/ - OU analysis of male genitalic trait (RW1) using Tree Topology 01
- PhoOUMalesRW1_Tree03Out/ - OU analysis of male genitalic trait (RW1) using Tree Topology 03
- PhoOUMalesRW2Out/ - Output from OU analysis of male genitalic trait (RW2) using main tree
- PhoOUMalesRW2_Tree01Out/ - OU analysis of male genitalic trait (RW2) using Tree Topology 01
- PhoOUMalesRW2_Tree03Out/ - OU analysis of male genitalic trait (RW2) using Tree Topology 03
- outfigs/ - Generated figures and visualizations
Output Contents (in PhoOUMalesRW*Out/ directories)
Each output directory typically contains:
- MCMC trace files (.log) with posterior distributions of evolutionary parameters
- Tree files with parameter estimates
- Summary statistics for evolutionary parameters (alpha = selection strength, sigma = evolutionary rate)
Folder StarBeast2_PopLevel_approach02_MolecularAndMorpho.7z
This folder contains input files and outputs from BEAST/StarBeast2 joint phylogenetic-demographic analyses at the population level. This "Approach 02" combines both molecular and morphological data to jointly infer species trees and population parameters.
File Descriptions
- TaxonMap.txt - Taxon mapping file that specifies which individuals belong to which populations.
- run01/ - Output files from first independent MCMC run
- run02/ - Output files from second independent MCMC run
Output Contents (in run01/ and run02/ directories)
Each run directory typically contains:
- XML configuration files (.xml) - BEAST input specifications
- Log files (.log) - MCMC trace files with parameter values at each iteration
- Tree files (.trees, .species.trees) - MCMC samples of phylogenetic trees
- State files (.xml.state) - Final state for resuming analysis if needed
- Summary statistics and diagnostic files
Folder StarBeast3_PopLevel_approach01_Molecular.7z
This folder contains input files and outputs from BEAST2 with StarBeast3 joint phylogenetic-demographic analyses at the population level.
File Descriptions
- StarBeastMapFileGeoPop.txt - Taxon-to-population mapping file specifying which individuals/sequences belong to which populations.
- run01/ - Output files from first independent MCMC run
- run02/ - Output files from second independent MCMC run
Output Contents (in run01/ and run02/ directories)
Typical contents include:
- PhoGeoPop_r1.xml - BEAST/StarBeast3 configuration file (input specification)
- PhoGeoPop_r1.species.trees - MCMC samples of the species tree
- PhoGeoPop_r1.trees - MCMC samples of gene trees (by locus)
- PhoGeoPop_r1.log - MCMC trace file with parameter values
- PhoGeoPop_r1.xml.state - Final MCMC state (for resumption if needed)
- Pho_COI.trees - Gene tree samples from Cytochrome Oxidase I locus
- Pho_H3_Phased.trees - Gene tree samples from H3 locus (phased haplotypes)
- Pho_ITS2_Phased.trees - Gene tree samples from ITS2 locus (phased haplotypes)
Folder StarBeast3_PopLevel_approach03_MolAndILSforMorph.7z
This folder contains input files and outputs from BEAST2 with StarBeast3 joint phylogenetic-demographic analyses at the population level. This "Approach 03" combines molecular data with morphological data modeled under an Incomplete Lineage Sorting (ILS) framework to jointly infer species trees and population parameters.
File Descriptions
- run01/ - Output files from first independent MCMC run
- run02/ - Output files from second independent MCMC run
Output Contents (in run01/ and run02/ directories)
Typical contents include:
- XML configuration files (.xml) - BEAST/StarBeast3 specification
- Log files (.log) - MCMC trace files with parameter posteriors
- Tree files (.trees, .species.trees) - Sampled species and gene trees
- State files (.xml.state** ) - Final MCMC state for potential resumption
- Gene tree files by locus
- Summary statistics and diagnostics
Folder StarBeast3_PutativeSpecies.7z
This folder contains input files and outputs from BEAST2 with StarBeast3 joint phylogenetic-demographic analysis at the putative species level for Phoneutria. This analysis infers species trees and population parameters treating the current taxonomical groups as distinct species.
File Descriptions
- run01/ - Output files from first independent MCMC run
- run02/ - Output files from second independent MCMC run
Output Contents (in run01/ and run02/ directories)
Each run directory typically contains:
- XML configuration files (.xml) - StarBeast3 analysis specification
- Log files (.log) - MCMC trace files with posterior distributions of parameters
- Tree files (.species.trees, .trees) - Sampled species trees and gene trees
- State files (.xml.state) - Final MCMC state for potential resumption
- Gene tree samples by locus
- Summary statistics and convergence diagnostics
Folder tps_RW.7z
This folder contains morphometric data, analysis files, and compiled results from Thin-Plate Spline (TPS) morphometric analyses of Phoneutria spider reproductive structures. TPS is a geometric morphometrics method used to quantify and analyze shape variation in biological structures.
File Descriptions
Female reproductive morphology (epigyne/genitalic) analyses:
- analises TPS/ - Folder containing TPS-specific analysis files, landmark coordinates, and computed morphometric variables
- epigyne_images/ - Folder containing digital images of female genitalic structures (epigynes) used for landmark placement
Male reproductive morphology (palpal/genitalic) analyses:
- analises TPS/ - Folder containing TPS-specific analysis files, landmark coordinates, and computed morphometric variables
- male_images/ or similar - Folder containing digital images of male genitalic structures (palps) used for landmark placement
Output Contents
- Files with suffix ...alinhado... contains all species landmarks and semi-landmarks aligned coordinates either in TPS or CSV format.
- Files with suffix ...lista.csv contains list of image files used
- Files with suffix ...partial warps.NTS contains the partial warps results.
- Files with suffix ...relative warps.NTS contains the relative warps results.
- Files with suffix ...report.txt contains the log of the analyses
- Files with suffix ...link.NTS contains the connection between landmarks (for visualization only)
- Files with suffix ...slider.NTS contains the slider file to identify semi-landmarks.
- Digital photographs of reproductive structures (.tiff) and TPS file with raw landmarks and semi-landmarks (.TPS)
Results
The higher level CSV files contains Geometric Morphometric Data and Results Compilation from the TPS analyses output files.
- MalesRelativeWarps.csv: The relative warps results for the male landmarks and semi-landmarks
- FemalesRelativeWarps.csv: The relative warps results for the femamale landmarks and semi-landmarks
- MalesPartialWarps.csv: The partial warps results for the male landmarks and semi-landmarks
- FemalesPartialWarps.csv: The partial warps results for the female landmarks and semi-landmarks
- MalesAlignedLandmarks.csv: The procrustes aligned lendmarks and semi-landmarks for males.
- FemalesAlignedLandmarks.csv: The procrustes aligned lendmarks and semi-landmarks for females.
(./DiscreteMorphoMatrix.7z)
Contains the data matrix with the scorings for the discrete character data used. There is one file which traits are scored by population in species tree, and one scored for each individual examined.
(./DNA_alignments.7z)
Contains the DNA sequence alignments, in fasta format, for each of the three markers used in the study. Names of the files contains the name of the markers. Sequence names are given by SpeciesCode_PopulationCode_ColectionNumber_GeneAndAllele. Each of the elements separated by "_" can be trace back to the Supplementary Material Table S1 associated with the publication.
(./Trees.7z)
Contains the files with the MCC trees used for the figures in the paper and in the supplementary material. There is also two R scripts. "plot_dated_tree_function.R" is a custom function used to plot dated "tress. Pho_plotDated.R" is a script that uses the custom function to plot the trees using the files in the folder as input.