Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)
Data files
Mar 06, 2024 version files 36.31 MB
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BlanchardMoreau_PolyrhachisSpinesUCEs_DryadUpload.zip
36.29 MB
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README.md
11.25 KB
Abstract
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.
This revised README file was generated on 2024-03-04 by Benjamin D. Blanchard.
GENERAL INFORMATION
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Title of Dataset: Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)
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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 -
Date of data collection (single date, range, approximate date): 2017-2019
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Geographic location of data collection: Global
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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
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Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
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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
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Links to other publicly accessible locations of the data: None
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Links/relationshops to ancillary data sets: None
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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)
- 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
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.
- 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]
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Relationship between the files, if important: None
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Additional related data collected that was not included in the current data package: None
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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
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Number of variables: 7
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Number of cases/rows: 154
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Variable List:
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Taxon: Ant species name with appended specimen code (p = "Polyrhachis"; e.g. "p_abbreviata_CSM0776" = Polyrhachis abbreviata, with specimen code CSM0776)
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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)
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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
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Spines: Spine length, i.e., total length (millimeters) of one of each spine pair present in the corresponding species
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RelSpines: Relative spine length, i.e., "Spines" variable divided by "BodySize" variable
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MaxSpines: Maximum spine length, i.e., Length (millimeters) of the longest spine present in the corresponding species
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RelMaxSpines: Relative maximum spine length, i.e., "MaxSpines" variable divided by "BodySize" variable
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Missing data codes: None
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Specialized formats or other abbreviations used: None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: BodySizeSpinesSpeciesDist_ZeroSpinesRemoved.csv
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Number of variables: 7
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Number of cases/rows: 149
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Variable List:
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Taxon: Ant species name with appended specimen code (p = "Polyrhachis"; e.g. "p_abbreviata_CSM0776" = Polyrhachis abbreviata, with specimen code CSM0776)
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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)
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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
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Spines: Spine length, i.e., total length (millimeters) of one of each spine pair present in the corresponding species
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RelSpines: Relative spine length, i.e., "Spines" variable divided by "BodySize" variable
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MaxSpines: Maximum spine length, i.e., Length (millimeters) of the longest spine present in the corresponding species
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RelMaxSpines: Relative maximum spine length, i.e., "MaxSpines" variable divided by "BodySize" variable
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Missing data codes: None
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Specialized formats or other abbreviations used: None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: MacroevolutionaryAnalyses_RScript_NEW.R
- Description: R script detailing analyses
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DATA-SPECIFIC INFORMATION FOR: MaxCladeCredTree_100BEST_BEAST_3RunsCombined_Newick.tx
- 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
- Description: Time-scaled, Newick-formatted phylogenetic tree inferred in MCMCTree. See associated manuscript for phylogenetic inference details.
#########################################################################
DATA-SPECIFIC INFORMATION FOR: TreeFiles.zip
- 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
- 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/
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DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_filtered_176taxa_70pct.zip
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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
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Number of files (contigs): 1301
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Specialized formats or other abbreviations used: uce = ultra-conserved element
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DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_unfiltered_176taxa.zip
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Description: All trimmed UCE contigs captured for our 176 taxa, including 20 outgroup taxa, in NEXUS file format
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Number of files (contigs): 2510
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Specialized formats or other abbreviations used: uce = ultra-conserved element
#########################################################################
DATA-SPECIFIC INFORMATION FOR: Polyrhachis_154taxa_ultrametric_tree.tre
- 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
- 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
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Number of variables: 2
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Number of cases/rows: 154
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Variable List:
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[species]: 154 unique species names corresponding to pruned in-group phylogeny tip names
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[geographic range]: presence (1) or absence (0) from each of three biogeographic regions
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Missing data codes: None
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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
- 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
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 Polyrhachis diversification, spine evolution, and biogeography.
