Data for: The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome
Data files
Dec 19, 2023 version files 1.36 GB
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Prebus_et_al_2023_dryad.tar.gz
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README.md
Abstract
Parasitism is ubiquitous across the tree of life, comprising approximately half of all animal species. Social insect colonies attract many pathogens, endo- and ectoparasites, and are exploited by social parasites, which usurp the social environment of their hosts for survival and reproduction. Exploitation by parasites and pathogens versus social parasites may cause similar behavioral and morphological modifications. Ants possess two overlapping syndromes: the social parasite and endoparasite syndromes. Upon rediscovering two populations of the putative social parasite Manica parasitica in the Sierra Nevadas, we test the hypothesis that M. parasitica is an independently evolving social parasite species relative to its host M. bradleyi. We evaluate traits used to discriminate M. parasitica from M. bradleyi, and examine the morphology and behavior of M. parasitica in the context of ant parasitic syndromes. We find that M. parasitica is not a social parasite species. Instead, M. parasitica individuals represents cestode-infected M. bradleyi workers. We propose that Manica parasitica should be regarded as a junior synonym of Manica bradleyi. Our results emphasize that an integrative approach is essential for unraveling the complex life histories of social insects and their symbionts.
README
This README file was generated on 2023-12-15 by Matthew Prebus
GENERAL INFORMATION
Title of Dataset: Data for "The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome"
Author information
A. Principal Investigator Contact Information
Name: Christian Rabeling
Institution: University of Hohenheim
Adress: Hohenheim, Germany
Email: crabeling@gmail.com
B. Associate or Co-investigator Contact Information
Name: Matthew Prebus
Institution: Arizona State University
Adress: Tempe, AZ USA
Email: mprebus@gmail.com
Date of data collection: 2018-2022
Geographic location of data collection: Clark Fork and Camp Wolfeboro, CA USA
Information about funding sources that supported the collection of the data: NSF CAREER DEB-1943626
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
Links to publications that cite or use the data:
Prebus, M. M., Georgiev, B. B., van de Kamp, T., Hamann, E., Baker, I., Rabeling, C. (2023). The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome. Biology Letters. https://dx.doi.org/10.1098/rsbl.2023.0399.
Links to other publicly accessible locations of the data: None
Links/relationships to ancillary data sets: None
Was data derived from another source? No
A. If yes, list source(s): NARecommended citation for this dataset:
Prebus, M. M., Georgiev, B. B., van de Kamp, T., Hamann, E., Baker, I., Rabeling, C. (2023). Data from: The rediscovery of the putative ant social parasite Manica parasitica syn. nov.
(Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome. Dryad Digital Repository. https://doi.org/10.5061/dryad.9s4mw6mnz
DATA & FILE OVERVIEW
- File list:
A) mct_final.Mbradleyi_gaster_cropped.smooth_cs.nrrd
B) mct_final.Mparasitica_gaster_cropped.smooth_cs.nrrd
C) mct_Mbradleyi_gaster_cropped.nrrd
D) mct_Mparasitica_gaster_cropped.zip
E) mor_Manica_morphometrics.csv
F) phy_Manica_36t_2186l_BS10.tre
G) phy_Manica_36t_2186l_BS10_astral.tre
H) phy_Manica_36t.phylip
I) phy_SWSCEN_input.nex
J) phy_Manica_36t_SWSCEN_partitions.txt
K) phy_Manica_36t.treefile
L) mor_Manica_morphometrics.R
- Relationship between files, if important:
A) "mct_final.Mbradleyi_gaster_cropped.smooth_cs.nrrd" is a segmentation file containing all segmentations which can be layered over the raw micro computed tomography (microCT) output, which is "mct_Mbradleyi_gaster_cropped.nrrd". Both files were used as input for the reconstruction of the gaster of Manica bradleyi in Slicer v5.0.3.
B) "mct_final.Mparasitica_gaster_cropped.smooth_cs.nrrd" is a segmentation file containing all segmentations which can be layered over the raw microCT output, which is "mct_Mparasitica_gaster_cropped.zip". Both files were used as input for the reconstruction of the gaster of Manica bradleyi in Slicer v5.0.3.
C) "phy_Manica_36t_2186l_BS10.tre" was used as input for ASTRAL III v5.7.4, using the command "java -jar astral.5.7.4.jar -t 1 -i phy_Manica_36t_2186l_BS10.tre -o phy_Manica_39t_2186l_BS10_astral.tre 2> phy_Manica_39t_2186l_BS10_astral.log". "phy_Manica_36t_2186l_BS10_astral.tre" is the output of the above analysis.
D) "mor_Manica_morphometrics.R" is the R script that was used to analyze the "mor_Manica_morphometrics.csv" dataset.
D) "phy_Manica_36t_SWSCEN_partitions.txt" is the partition file extracted from the output of the SWSCEN partitioning analysis (see below), which was used as partial input for IQTREE2 v2.1.2. "phy_Manica_36t.phylip" is the alignment file used as partial input for IQTREE2 v2.1.2. We used the command "iqtree2 -mrate E,I,G,R -rclusterf 10 -bnni -s phy_Manica_36t.phylip -B 1000 --prefix phy_Manica_36t -m MFP+MERGE -p phy_Manica_36t_SWSCEN_partitions.txt" to begin the analysis. "phy_Manica_36t.treefile" is the (unrooted) output tree file from the IQTREE2 analysis above, in NEWICK format. "phy_SWSCEN_input.nex" was used as input for the SWSCEN partitioning analysis. We used the command "python SWSCEN.py SWSCEN_input.nex" to begin the analysis.
- Additional related data collected that was not included in the current data package: None
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DATA-SPECIFIC INFORMATION FOR: mct_final.Mbradleyi_gaster_cropped.smooth_cs.nrrd
File format: .nrrd ("nearly raw raster data") is a library and file format for the representation and processing of n-dimensional raster data.
Software used to generate this file: Slicer v5.0.3, Biomedisa web portal.
Description: segmentations of raw microCT scans of the gaster of a Manica bradleyi worker. Segmentation is a method in which a target structure in microCT scans is differentiated from the background image, often with the goal of clarifying the relationships of structures in a three dimensional reconstruction.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: mct_final.Mparasitica_gaster_cropped.smooth_cs.nrrd
File format: .nrrd ("nearly raw raster data") is a library and file format for the representation and processing of n-dimensional raster data.
Software used to generate this file: Slicer v5.0.3, Biomedisa web portal.
Description: segmentations of raw microCT scans of the gaster of a Manica parasitica worker. Segmentation is a method in which a target structure in microCT scans is differentiated from the background image, often with the goal of clarifying the relationships of structures in a three dimensional reconstruction.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: mct_Mbradleyi_gaster_cropped.nrrd
File format: .nrrd ("nearly raw raster data") is a library and file format for the representation and processing of n-dimensional raster data.
Software used to generate this file: Slicer v5.0.3.
Description: cropped microCT scans of the gaster of a Manica bradleyi worker. These are the microCT scans which the segmentations in "mct_final.Mbradleyi_gaster_cropped.smooth_cs.nrrd" were derived from.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: mct_Mparasitica_gaster_cropped.zip
File format: .zip, an archive file format that supports lossless data compression.
Software used to generate this file: Slicer v5.0.3.
Description: cropped microCT scans of the gaster of a Manica parasitica worker. These are the microCT scans which the segmentations in "mct_final.Mparasitica_gaster_cropped.smooth_cs.nrrd" were derived from.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: mor_Manica_morphometrics.csv
File format: .csv, comma-separated values file, which allows data to be saved in a tabular format.
Software used to generate this file: LibreOffice v7.5.2.2.
Number of variables: 27
Number of rows: 82
Description: all raw measurements taken from specimens as described in the methods section of the original article. Variable list:
*SpecimenCode: unique specimen identifiers, which are unique alpha-numerical codes that are physically associated with voucher specimens (mounted on the same pins) used in this study.
*CollectionCode: collection codes are alpha-numerical codes that identify unique collection events. In this case they denote collections of worker ants from separate nests.
*Locality: name of each collection locality where voucher specimens were collected.
*Genus: genus of the voucher specimen.
*morphotype: putative species of the voucher specimen.
*WL: Weber’s length: distance between the caudal most point of propodeal lobe to the inflection point between the pronotal neck and the pronotal declivity.
*SL: Scape length: maximum scape length excluding the basal neck and the articular condyle.
*HW: Head width: maximum width of the head, including the compound eyes
*HL: Head length: the head must be carefully tilted to the position, providing the true maximum. If excavations of the posterior margin of the head capsule and/or anterior margin of the clypeus are present, then the measurement is taken from an imaginary line that spans the excavations from the posterior- or anterior-most margins.
*PrdH: Propodeum height: the maximum height of the propodeum in profile, measured as the perpendicular distance from the space between the meso- and metacoxae to the highest point of the propodeum.
*PEH: Petiole height: the longest distance measured from the ventral petiolar profile at node level (perpendicular to the chord length of the petiolar sternum) to the distal most point of the dorsal profile of the petiolar node.
*NOH: Petiolar node height: Maximum height of the petiolar node, measured in lateral view from the uppermost point of the petiolar node perpendicular to a reference line set from the petiolar spiracle to the imaginary midpoint of the transition between the dorso-caudal slope and dorsal profile of caudal cylinder of the petiole.
*PEW: Petiole width: maximum width of petiole in dorsal view, measured across the posteriormost margin.
*PPW: Postpetiole width: Maximum width of postpetiole in dorsal view.
*HFL: Hind femur length: maximum length of the metafemur in dorsal view.
*CS: Cephalic size: mean of head length and head width (HL + HW)/2.
*SI: Scape index: SL/WL*100.
*SI2: Scape index 2: SL/HW*100:
*CSI: Cephalic size index: CS/WL*100.
*PrdHI: Propodeum height index: PrdH/WL*100.
*PEHI: Petiole height index: PEH/WL*100.
*NOHI: Petiolar node height index: NOH/WL*100.
*NOHI2: Petiolar node height index 2: NOH/PEH*100.
*PPWI: Postpetiole width index: PPW/WL*100.
*PPWI2: Postpetiole width index 2: PPW/PEW*100.
*HFLI: Hind femur length index: HFL/WL*100.
*HWI: Head width index: HW/WL*100.
*HLI: Head length index: HL/WL*100.
Missing data codes: None. Entries were left blank if the voucher specimen was missing the body part specified to be measured.
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_2186l_BS10.tre
File format: .tre, NEWICK tree file.
Software used to generate this file: IQTREE v2.1.2, newick_utils.
Description: NEWICK tree file containing 2,186 gene trees calculated from the phylogenomic dataset using IQTREE v2.1.2 to be used as input into ASTRAL-III. Before input, nodes with bootstrap support <10 were collapsed using nw_ed from the newick_utils package in an effort to reduce noise in the dataset.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_2186l_BS10_astral.tre
File format: .tre, NEWICK tree file.
Software used to generate this file: ASTRAL-III.
Description: NEWICK tree file containing output from the ASTRAL-III analysis above. Node support values are in local posterior probability.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t.phylip
File format: .phy, PHYLIP is a plain text format containing two sections: a header describing the dimensions of the alignment, followed by a multiple sequence alignment.
Software used to generate this file: PHYLUCE.
Description: PHYLIP file containing aligned, trimmed and concatenated ultraconserved element (UCE) sequence data, which was used as input for maximum likelihood phylogeny inference in IQTREE v2.1.2.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_SWSCEN_input.nex
File format: .nex, NEXUS file format.
Software used to generate this file: PHYLUCE.
Description: NEXUS file containing aligned, trimmed and concatenated ultraconserved element (UCE) sequence data, partitioned by UCE locus. This file was used as input for the SWSC-EN partitioning method.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_SWSCEN_partitions.txt
File format: .txt, text file format.
Software used to generate this file: SWSC-EN.
Description: text file containing multiple sequence alignment partitioning position data for from the SWSC-EN analysis, which was used as input for maximum likelihood phylogeny inference in IQTREE v2.1.2.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t.treefile
File format: .treefile, NEWICK tree file.
Software used to generate this file: IQTREE v2.1.2.
Description: NEWICK tree file containing output from the IQTREE v2.1.2 analysis above. Node support values are in ultrafast bootstraps.
Missing data codes: None
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: mor_Manica_morphometrics.R
File format: .R, R script.
Software used to generate this file: Atom text editor.
Description: this is the script that was used to analyze "mor_Manica_morphometrics.csv". To run, the "ggpubr" library with dependencies must be installed.
Missing data codes: None
Specialized formats or other abbreviations used: None