DOI: 10.5061/dryad.ffbg79crt
title: Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

description: Several prominent evolutionary theories propose mechanisms whereby the
 evolution of a defensive trait or suite of traits causes significant
 shifts in species diversification rate and niche evolution. We investigate
 the role of cuticular spines, a highly variable morphological defensive
 trait in the hyperdiverse ant genus Polyrhachis, on species
 diversification and geographic range size. Informed by key innovation
 theory and the escape-and-radiate hypothesis, we predicted that clades
 with longer spines would exhibit elevated rates of diversification and
 larger range sizes compared to clades with shorter spines. To address
 these predictions, we estimated phylogenetic relationships with a
 phylogenomic approach utilizing ultra-conserved elements (UCEs) and
 compiled morphological and biogeographic trait databases. In contrast to
 the first prediction, we found no association between diversification rate
 and any trait (spine length, body size, and range size). However, we
 recovered a positive correlation between spine length and geographic range
 size, suggesting that spines promote expanded geographic range. Notably,
 these results were consistent across analyses using different phylogenetic
 inference approaches and spine trait measurement schemes. This study
 provides a rare investigation of the role of a defensive trait on
 geographic range size, and ultimately supports the hypothesis that
 defensive spines are a factor in increased range size in Polyrhachis ants.
 Furthermore, the lack of support for an association between spines and
 diversification, which contrasts with previous work demonstrating a
 positive association between spines and diversification rate, is
 intriguing and warrants further study.
description: UCE contig files (including .zip for trimmed-unfiltered contigs
 and .zip for trimmed-filtered contigs [70% taxon complete contigs]), tree
 files, data, and R script associated with the manuscript by Blanchard and
 Moreau (submitted) on <em>Polyrhachis</em> diversification,
 spine evolution, and biogeography.
description: This revised README file was generated on 2024-03-04 by Benjamin D.
 Blanchard. GENERAL INFORMATION 1. Title of Dataset: Defensive spines are
 associated with large geographic range but not diversification in spiny
 ants (Hymenoptera: Formicidae: Polyrhachis) 2. Author Information A.
 Corresponding Author Contact Information Name: Benjamin D. Blanchard
 Institution: Xishuangbanna Tropical Botanical Garden Address: CAS Key
 Laboratory of Tropical Forest Ecology, XTBG, Chinese Academy of Sciences,
 Menglun, Mengla, Yunnan 666303, China Email:
 [benjamin@xtbg.ac.cn](mailto:benjamin@xtbg.ac.cn) 3. Date of data
 collection (single date, range, approximate date): 2017-2019 4. Geographic
 location of data collection: Global 5. Information about funding sources
 that supported the collection of the data: NSF DEB-1701352, NSF
 IOS-1916995, NSF DEB-1900357, CAS PIFI 2021PB0085, grant from the
 University of Chicago Henry Hinds Fund for Evolutionary Research, and a
 Field Museum of Natural History Brown Graduate Fellowship
 \##SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data:
 CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that
 cite or use the data: Blanchard, B. D., & Moreau, C. S. (2023).
 Defensive spines are associated with large geographic range but not
 diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis).
 Systematic Entomology, 48:328-340. DOI: 10.1111/syen.12578 1. Links to
 other publicly accessible locations of the data: None 2.
 Links/relationshops to ancillary data sets: None 3. Was data derived from
 another source? If yes, list source(s): * Outgroup taxa UCE sequences
 obtained via NCBI's Sequence Read Archive, associated with Blaimer et
 al. (2015, BMC Evolutionary Biology) * Geographic range size data derived
 from Kass et al. (2022, Science Advances) 1. Recommended citation for this
 dataset: Blanchard, B. D., & Moreau, C. S. (2023). Data from:
 Defensive spines are associated with large geographic range but not
 diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis).
 Dryad Digital Repository.
 [https://doi.org/10.5061/dryad.ffbg79crt](https://doi.org/10.5061/dryad.ffbg79crt) DATA & FILE OVERVIEW These data include the necessary sequence data, phylogenetic tree files, and trait databases necessary to reproduce the results reported in Blanchard and Moreau (Systematic Entomology, accepted 2022). *Exception: Due to data size, raw UCE (ultra-conserved elements) sequences are uploaded to NCBI's Sequence Read Archive repository. See TableS2 of the associated manuscript for the list of SRA accession numbers. 1. File list: A. BodySizeSpinesSpeciesDist.csv [Trait data associated with each Polyrhachis species included in the trait-based analyses] B. BodySizeSpinesSpeciesDist_ZeroSpinesRemoved.csv [Trait data with zero-spine-length taxa removed] C. MacroevolutionaryAnalyses_RScript_NEW.R [R script detailing analyses] D. MaxCladeCredTree_100BEST_BEAST_3RunsCombined_Newick.txt [Time-scaled phylogenetic tree inferred in BEAST] E. MCMCtreeFiveRunsCombinedIndepRates_176taxa_70p_Newick_tree.txt [Time-scaled phylogenetic tree inferred in MCMCTree] F. TreeFiles.zip [Direct output of five tree files inferred in ASTRAL-III, BEAST, ExaBayes, MCMCTree, and RAxML] G. BAMM_files [directory - contains files necessary to run BAMM diversification rate-shift analyses] bamm_BEAST_phylo [subdirectory] bamm_MCMCTree_phylo [subdirectory] \#within each subdirectory: control.txt sample_probs myPriors.txt Polyrhachis_BEAST_154taxa_ultrametric_tree.tre H. contigs_trimmed_filtered_176taxa_70pct.zip [trimmed UCE contigs filtered to 70% completeness, i.e. 70% of taxa must be included in a given locus alignment for that alignment to be retained] I. contigs_trimmed_unfiltered_176taxa.zip [All trimmed UCE contigs captured for our 176 taxa, including 20 outgroup taxa] J. Polyrhachis_154taxa_ultrametric_tree.tre [MCMCTree phylogeny pruned to 154 in-group taxa] K. Polyrhachis_BEAST2_154taxa_ultrametric_tree.tre [BEAST phylogeny pruned to 154 in-group taxa] L. Polyrhachis_geog.data [Presence-absence in each included large biogeographic region, for 154 Polyrhachis taxa, used in BioGeoBEARS] M. UCEmatrix_phyluce_mafft-nexus-internal-trimmed-gblocks-clean-176taxa-70p.phylip [sequence matrix of our 70% taxon-complete dataset, used as input for RAxML, ExaBayes, BEAST, and MCMCTree] 1. Relationship between the files, if important: None 2. Additional related data collected that was not included in the current data package: None 3. Are there multiple version of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA \######################################################################### DATA-SPECIFIC INFORMATION FOR: BodySizeSpinesSpeciesDist.csv 1. Number of variables: 7 2. Number of cases/rows: 154 3. Variable List: * Taxon: Ant species name with appended specimen code (p = "Polyrhachis"; e.g. "p_abbreviata_CSM0776" = Polyrhachis abbreviata, with specimen code CSM0776) * SpeciesDistribution: Species distribution, i.e., geographic range size in square kilometers, extracted from Kass et al. (2022) data (TIF files imported into QGIS v3.22.10) * BodySize: Body size, i.e., Weber's length measurement (millimeters) of specimen body size; numbers are averages from 1-3 specimen images for the species, obtained from AntWeb and/or AntWiki * Spines: Spine length, i.e., total length (millimeters) of one of each spine pair present in the corresponding species * RelSpines: Relative spine length, i.e., "Spines" variable divided by "BodySize" variable * MaxSpines: Maximum spine length, i.e., Length (millimeters) of the longest spine present in the corresponding species * RelMaxSpines: Relative maximum spine length, i.e., "MaxSpines" variable divided by "BodySize" variable 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: BodySizeSpinesSpeciesDist_ZeroSpinesRemoved.csv 1. Number of variables: 7 2. Number of cases/rows: 149 3. Variable List: * Taxon: Ant species name with appended specimen code (p = "Polyrhachis"; e.g. "p_abbreviata_CSM0776" = Polyrhachis abbreviata, with specimen code CSM0776) * SpeciesDistribution: Species distribution, i.e., geographic range size in square kilometers, extracted from Kass et al. (2022) data (TIF files imported into QGIS v3.22.10) * BodySize: Body size, i.e., Weber's length measurement (millimeters) of specimen body size; numbers are averages from 1-3 specimen images for the species, obtained from AntWeb and/or AntWiki * Spines: Spine length, i.e., total length (millimeters) of one of each spine pair present in the corresponding species * RelSpines: Relative spine length, i.e., "Spines" variable divided by "BodySize" variable * MaxSpines: Maximum spine length, i.e., Length (millimeters) of the longest spine present in the corresponding species * RelMaxSpines: Relative maximum spine length, i.e., "MaxSpines" variable divided by "BodySize" variable 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None \######################################################################### DATA-SPECIFIC INFORMATION FOR: MacroevolutionaryAnalyses_RScript_NEW.R 1. Description: R script detailing analyses \######################################################################### DATA-SPECIFIC INFORMATION FOR: MaxCladeCredTree_100BEST_BEAST_3RunsCombined_Newick.tx 1. Description: Time-scaled, Newick-formatted phylogenetic tree inferred in BEAST. See associated manuscript for phylogenetic inference details. \######################################################################### DATA-SPECIFIC INFORMATION FOR: MCMCtreeFiveRunsCombinedIndepRates_176taxa_70p_Newick_tree.txt 1. Description: Time-scaled, Newick-formatted phylogenetic tree inferred in MCMCTree. See associated manuscript for phylogenetic inference details. \######################################################################### DATA-SPECIFIC INFORMATION FOR: TreeFiles.zip 1. Description: Direct output of five tree files inferred in ASTRAL-III, BEAST, ExaBayes, MCMCTree, and RAxML. See associated manuscript for phylogenetic inference details. \######################################################################### DATA-SPECIFIC INFORMATION FOR: BAMM_files 1. Description: Directory containing files necessary to run BAMM diversification rate-shift analyses. See detailed description of variables for BAMM analyses at [http://bamm-project.org/](http://bamm-project.org/) \######################################################################### DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_filtered_176taxa_70pct.zip 1. Description: Trimmed UCE contigs in NEXUS file format filtered to 70% completeness, i.e. 70% of taxa must be included in a given locus alignment for that alignment to be retained 2. Number of files (contigs): 1301 3. Specialized formats or other abbreviations used: uce = ultra-conserved element \######################################################################### DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_unfiltered_176taxa.zip 1. Description: All trimmed UCE contigs captured for our 176 taxa, including 20 outgroup taxa, in NEXUS file format 2. Number of files (contigs): 2510 3. Specialized formats or other abbreviations used: uce = ultra-conserved element \######################################################################### DATA-SPECIFIC INFORMATION FOR: Polyrhachis_154taxa_ultrametric_tree.tre 1. Description: Ultrametric MCMCTree phylogeny pruned to 154 in-group taxa, in Newick file format. See associated manuscript for phylogenetic inference details. \######################################################################### DATA-SPECIFIC INFORMATION FOR: Polyrhachis_BEAST2_154taxa_ultrametric_tree.tre 1. Description: Ultrametric BEAST phylogeny pruned to 154 in-group taxa, in Newick file format. See associated manuscript for phylogenetic inference details. \######################################################################### DATA-SPECIFIC INFORMATION FOR: Polyrhachis_geog.data 1. Number of variables: 2 2. Number of cases/rows: 154 3. Variable List: * \[species]: 154 unique species names corresponding to pruned in-group phylogeny tip names * \[geographic range]: presence (1) or absence (0) from each of three biogeographic regions 4. Missing data codes: None 5. Specialized formats or other abbreviations used: A = Afrotropical, O = Oriental, P = Australasian \######################################################################### DATA-SPECIFIC INFORMATION FOR: UCEmatrix_phyluce_mafft-nexus-internal-trimmed-gblocks-clean-176taxa-70p.phylip 1. Description: Sequence matrix of our 70% taxon-complete dataset with 176 taxa including 20 outgroup taxa, in Phylip file format, used as input for RAxML, ExaBayes, BEAST, and MCMCTree