Data for: Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, or gall morphospace
Data files
Nov 09, 2023 version files 119.52 KB
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cergendist.txt
4.04 KB
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Ceroptres_eMPRess-Tree.nwk
926 B
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Ceroptres_Putative-Species.nwk
867 B
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Ceroptres-Data.csv
3.52 KB
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certraitdist.txt
4.63 KB
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Cynipini_Ceroptres-eMPRess-Tree.nwk
840 B
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Cynipini_Master-Tree.nwk
1.65 KB
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Cynipini_Synergus-eMPRess-Tree.nwk
921 B
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Cynipini-Data.csv
7.46 KB
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cyntraits.txt
2.28 KB
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distinq.txt
28 KB
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inqclustA.txt
2.74 KB
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inqclustB.txt
13.08 KB
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inqtrait.txt
4.35 KB
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inqtraitclust.txt
2.55 KB
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Master-Data.csv
18.78 KB
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README.md
8.60 KB
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Synergus_eMPRess-Tree.nwk
1.16 KB
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Synergus_Putative-Species.nwk
926 B
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Synergus-Data.csv
4.06 KB
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syngendist.txt
3.77 KB
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syntraitdist.txt
4.39 KB
Abstract
Host shifts to new plants can drive speciation for plant-feeding insects, but how commonly do host shifts also drive diversification for the parasites of those same insects? Oak gall wasps induce galls on oak trees, and shifts to novel tree hosts and new tree organs have been implicated as drivers of oak gall wasp speciation. Gall wasps are themselves attacked by many insect parasites, which must find their hosts on the correct tree species and organ, but which also must navigate the morphologically variable galls with which they interact. Thus, we ask whether host shifts to new trees, organs, or gall morphologies correlate with gall parasite diversification. We delimit species and infer phylogenies for two genera of gall kleptoparasites, Synergus and Ceroptres, reared from a variety of North American oak galls. We find that most species were reared from galls induced by just one gall wasp species, and no parasite species was reared from galls of more than four species. Most kleptoparasite divergence events correlate with shifts to non-ancestral galls. These shifts often involved changes in tree habitat, gall location, and gall morphology. Host shifts are thus implicated in driving diversification for both oak gall wasps and their kleptoparasitic associates.
Anna K.G. Ward, Y. Miles Zhang, Guerin E. Brown, Alaine C. Hippee, Kirsten M. Prior, Shannon Rollins, Nicolas Sierra, Sofia I. Sheikh, Carly M. Tribull, Andrew A. Forbes
Files include the comma seperated value files for morphological data, phylogenies, and Rmarkdown scripts
For additional information about samples see supplemental tables
Post-SODA phylogenetic trees. Trees have been rooted on a midpoint and the outgroup and duplicate putative species have been pruned.
- Ceroptres_Putative-Species.nwk
Newick file for the Ceroptres phylogeny - Synergus_Putative-Species.nwk
Newick file for the Synergus phylogeny
eMPRess-specific phylogenetic trees
- Ceroptres_eMPRess-Tree.nwk
Ceroptres phylogeny for eMPRess calculations, includes duplicated species - Synergus_eMPRess-Tree.nwk
Synergus phylogeny for eMPRess calculations, includes duplicated species - Cynipini_Ceroptres-eMPRess-Tree.nwk
Cynipini tree for Ceroptres eMPRess calculations, includes only hosts of Ceroptres - Cynipini_Synergus-eMPRess-Tree.nwk
Cynipini tree for Synergus eMPRess calculations, includes only hosts of Synergus
Cynipini_Master-Tree.nwk
Cynipini phylogeny created from all COI sequences available to the Forbes Laboratory at the University of Iowa, see Materials and Methods for more details
Comma Seperated Value Dataframes
- Master-Data.csv
Tidy dataframe of all kleptoparasites in both Synergus and Ceroptres along with their hosts, host morphologies, and host generation. All subsequent dataframes are derived from Master-Data.csv and headers are retained. - Cynipini-Data.csv
Dataframe created from Master-Data.csv with all unique Cynipini in our analysis along with all morphologies and generations - Synergus-Data.csv
Dataframe created from Master-Data.csv with all unique Synergus kleptoparasites, their Cynipini host, and the range of morphologies from multiple hosts seperated by ‘+’ - Ceroptres-Data.csv
Dataframe created from Master-Data.csv with all unique Ceroptres kleptoparasites, their Cynipini host, and the range of morphologies from multiple hosts seperated by ‘+’
Header descriptions for .csv files
- Inquiline
Post-UCE and SODA putative species identification for samples - inq_genus
Genus each specimen belongs to - eMPRess
Modified label from the Inquiline column adjusted to fit eMPRess anlaysis. See methods and supplementary materials for more details - new_inquiline_acronym
Shortened label from the Inquiline column - dendrogram_clusters
Cluster identification label. See methods and supplementary materials for more details - cynipid_acronym
Shortened name for the gallforming Cynipid wasp inquilines were reared from - cynipid_code_names
Name of the gallforming Cynipid wasp inquilines were reared from but names do not have spaces - cynipid
Name of the gallforming Cynipid wasp inquilines were reared from but names do have spaces - cell_clustering_morphology
Clustering based on dendrogram analysis. See methods and supplementary materials for more details - oak_section
Taxonomic section (subgenus) for oak trees (Quercus sp) - oak_subsection
Taxonomic classification below section for oak trees (Quercus sp) - generation
Sexual or asexual generation of the Cynipid gall wasp the inquiline was reared from - polythalamous
A gall has more than one individual cell, or larval chamber. 1 implies this is true 0 implies that there is one chamber or cell per gall - cluster
Galls appear in clusters. 1 implies true, 0 implies false - gall_size
Size of the gall structure where 1 is the smallest and 3 is the largest - detachable
Gall is detechable from the plant material and is not integrated into the plant material. 1 implies true, 0 implies false - spines
The gall has protruding spines or plant material. 1 implies true, 0 implies false - textured
The gall is course or rough in texture. 1 implies true, 0 implies false - hairs_or_pubescence
The gall has thin plant fibers surrounding it that resemble thin hair. 1 implies true, 0 implies false - wool
The gall has thick plant fibers surrounding it that resembles wool. 1 implies true, 0 implies false - nectar
The gall produces or releases plant nectar. - fiber
The internal structure of the gall has radiating fibers. - bract
The gall resembles a plant bract and produces or is part of a structure that produces leaves or flowers. - fleshy early
The gall is fleshy at the early parts of its development. 1 implies true, 0 implies false - fleshy late
The gall is fleshy at the later parts of its development. 1 implies true, 0 implies false - woody late
The gall is woody or dense at the later parts of its development. 1 implies true, 0 implies false - fleshy
The gall is fleshy for the entirety of its development. 1 implies true, 0 implies false - fl woody
The gall is fleshy or woody depending on the time of its development. 1 implies true, 0 implies false - woody
The gall is dense and woody for the entirety of its development. 1 implies true, 0 implies false - none-external
The gall does not have any external ecological defensive structures. 1 implies true, 0 implies false - none internal
The gall does not have any internal ecological defensive structures. 1 implies true, 0 implies false - location
The location of the plant the gall is formed on. - hollow
The gall is entirely hollow or near hollow on the inside - spatial defense
Clustering of spatial defense from dendrogram and PCA analysis - internal defense
Clustering of internal defense from dendrogram and PCA analysis - external defense
Clustering of external defense from the dendrogram and PCA analysis - walls
The walls of the gall are either thick or thin
Dataframes for Principle Component and Cluster Analysis
- inqtrait.txt
parasite * gall host * gall trait matrix# - cyntraits.txt
gall host species * gall trait matrix - cergendist.txt
distance matrix of genetic distances for Ceroptres species - certraitdist.txt
distance matrix of Euclidian distances for Ceroptres species plotted in host gall trait space - syngendist.txt
distance matrix of genetic distances for Synergus species - syntraitdist.txt
distance matrix of Euclidian distances for Synergus species plotted in host gall trait space - distinq.txt
distance matrix of Euclidian distances for parasites plotted in centroids of host galls in host gall trait space - inqclustA.txt
cluster A (determined by primary cluster analysis for secondary cluster analysis - inqclutB.txt
cluster B for secondary cluster analysis - inqtraitclust.txt
traits of host gall species for each parasite species (combined across hosts) as predictor variables for regression model
Rmarkdown scripts for PACo, ParaFit, and Ancestral State Reconstructions for both Synergus and Ceroptres
- ASR-Script.rmd
Rmarkdown file with script used for Ancestral State Reconstruction - Ceroptres_PACo-Script.rmd
Rmarkdown file with script used for PACo and Parafit calculations for Ceroptres - Synergus_PACo-Script.rmd
Rmarkdown file with script used for PACo and Parafit calculations for Synergus
RFunctions.R
R file containing functions for non-polymorphic Ancestral State Reconstructions, polymorphic Ancestral State Reconstructions, and ASR ordered model comparison
Ancestral reconstruction of host tree association.
- ASR.r
R file with script used for the Ancestral reconstruction - Cynipini.nwk
Newick file used as input for the Ancestral reconstruction. Paired down to one individual per species - Cynipini_ASR.csv
file containing host associations for each Cynipini species
PCoA-and-Cluster-Analysis.R
R script performing a principle component analysis, constructing a biplot for traits of gall hosts, performing the mantel tests for both genera of kleptoparasites, and computing the cluster analysis for morphological traits of gall hosts
NA, missing, or ambiguous data
Some .csv files will have NA for present in some cells. This implies that the data is either no present for that particular gall or that the specific trait in question is ambiguous and cannot be represented by a particular value either due to natural variation or unclear definitions between specimens.