DOI: 10.5061/dryad.9s4mw6mnz
title: Data for: The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome

description: 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.
description: This README file was generated on 2023-12-15 by Matthew Prebus GENERAL
 INFORMATION 1. Title of Dataset: Data for "The rediscovery of the
 putative ant social parasite Manica parasitica syn. nov. (Hymenoptera:
 Formicidae) reveals an unexpected endoparasite syndrome" 2. Author
 information A. Principal Investigator Contact Information Name: Christian
 Rabeling Institution: University of Hohenheim Adress: Hohenheim, Germany
 Email: B. Associate or Co-investigator Contact
 Information Name: Matthew Prebus Institution: Arizona State University
 Adress: Tempe, AZ USA Email: 1. Date of data
 collection: 2018-2022 2. Geographic location of data collection: Clark
 Fork and Camp Wolfeboro, CA USA 3. Information about funding sources that
 supported the collection of the data: NSF CAREER DEB-1943626
 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: 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.
 . 1. Links to other
 publicly accessible locations of the data: None 2. Links/relationships to
 ancillary data sets: None 3. Was data derived from another source? No A.
 If yes, list source(s): NA 4. Recommended 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.
 DATA & FILE OVERVIEW
 1. 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 1. 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&gt; 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. 1. Additional related data
 collected that was not included in the current data package: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR:
 mct_final.Mbradleyi_gaster_cropped.smooth_cs.nrrd 1. File format: .nrrd
 ("nearly raw raster data") is a library and file format for the
 representation and processing of n-dimensional raster data. 2. Software
 used to generate this file: Slicer v5.0.3, Biomedisa web portal. 3.
 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. 4. Missing data codes: None 5. Specialized formats or
 other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR:
 mct_final.Mparasitica_gaster_cropped.smooth_cs.nrrd 1. File format: .nrrd
 ("nearly raw raster data") is a library and file format for the
 representation and processing of n-dimensional raster data. 2. Software
 used to generate this file: Slicer v5.0.3, Biomedisa web portal. 3.
 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. 4. Missing data codes: None 5. Specialized formats or
 other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: mct_Mbradleyi_gaster_cropped.nrrd 1. File
 format: .nrrd ("nearly raw raster data") is a library and file
 format for the representation and processing of n-dimensional raster data.
 2. Software used to generate this file: Slicer v5.0.3. 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. 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: mct_Mparasitica_gaster_cropped.zip 1. File
 format: .zip, an archive file format that supports lossless data
 compression. 2. Software used to generate this file: Slicer v5.0.3. 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. 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: mor_Manica_morphometrics.csv 1. File
 format: .csv, comma-separated values file, which allows data to be saved
 in a tabular format. 2. Software used to generate this file: LibreOffice
 v7.5.2.2. 3. Number of variables: 27 4. Number of rows: 82 5. 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. 6. Missing data codes: None. Entries were left blank if the
 voucher specimen was missing the body part specified to be measured. 7.
 Specialized formats or other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_2186l_BS10.tre 1. File
 format: .tre, NEWICK tree file. 2. Software used to generate this file:
 IQTREE v2.1.2, newick_utils. 3. 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 &lt;10 were collapsed using nw_ed from the newick_utils
 package in an effort to reduce noise in the dataset. 4. Missing data
 codes: None 5. Specialized formats or other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_2186l_BS10_astral.tre 1.
 File format: .tre, NEWICK tree file. 2. Software used to generate this
 file: ASTRAL-III. 3. Description: NEWICK tree file containing output from
 the ASTRAL-III analysis above. Node support values are in local posterior
 probability. 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t.phylip 1. 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. 2. Software used to generate this file: PHYLUCE. 3.
 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. 4. Missing data
 codes: None 5. Specialized formats or other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_SWSCEN_input.nex 1. File format: .nex,
 NEXUS file format. 2. Software used to generate this file: PHYLUCE. 3.
 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. 4. Missing
 data codes: None 5. Specialized formats or other abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t_SWSCEN_partitions.txt 1.
 File format: .txt, text file format. 2. Software used to generate this
 file: SWSC-EN. 3. 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. 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: phy_Manica_36t.treefile 1. File format:
 .treefile, NEWICK tree file. 2. Software used to generate this file:
 IQTREE v2.1.2. 3. Description: NEWICK tree file containing output from the
 IQTREE v2.1.2 analysis above. Node support values are in ultrafast
 bootstraps. 4. Missing data codes: None 5. Specialized formats or other
 abbreviations used: None
 \#######################################################################
 DATA-SPECIFIC INFORMATION FOR: mor_Manica_morphometrics.R 1. File format:
 .R, R script. 2. Software used to generate this file: Atom text editor. 3.
 Description: this is the script that was used to analyze
 "mor_Manica_morphometrics.csv". To run, the "ggpubr"
 library with dependencies must be installed. 4. Missing data codes: None
 5. Specialized formats or other abbreviations used: None