DOI: 10.5061/dryad.0gb5mkm79
title: Data for: Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, or gall morphospace

description: 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.
description: # Additional files for "Speciation in kleptoparasites of oak gall
 wasps often correlates with shifts into new tree habitats, tree organs, or
 gall morphospace." 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.