10.5061/DRYAD.5R6D5KC
Johnson, Andrew
University of Florida
McKenna,, Duane D
University of Memphis
Jordal, Bjarte H.
University of Bergen
Cognato, Anthony I.
Michigan State University
Smith, Sarah M.
Michigan State University
Lemmon, Alan R.
Florida State University
Moriarty Lemmon, Emily L.
Florida State University
Hulcr, Jiri
University of Florida
Data from: Phylogenomics clarifies repeated evolutionary origins of
inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)
Dryad
dataset
2019
Entomology
phylogenetics
Scolytinae
bark beetles
Curculionidae
Cryphalini
Ambrosia beetles
National Science Foundation
1256968
2019-03-07T00:00:00Z
en
doi:10.1016/j.ympev.2018.05.028
43193416 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Bark and ambrosia beetles (Curculionidae, Scolytinae) display a
conspicuous diversity of unusual genetic and ecological attributes and
behaviors. Reconstructing the evolution of Scolytinae, particularly the
large and ecologically significant tribe Cryphalini (pygmy borers), has
long been problematic. These challenges have not adequately been addressed
using morphological characters, and previous research has used only DNA
sequence data from small numbers of genes. Through a combination of
anchored hybrid enrichment, low-coverage draft genomes, and
transcriptomes, we addressed these challenges by amassing a large
molecular phylogenetic dataset for bark and ambrosia beetles. The
resulting DNA sequence data from 251 protein coding genes (114,276 bp of
nucleotide sequence data) support inference of the first robust phylogeny
of Scolytinae, with a special focus on the species rich tribe Cryphalini
and its close relatives. Key strategies, including inbreeding mating
systems and fungus farming, evolved repeatedly across Scolytinae. We
confirm 12 of 16 hypothesized origins of fungus farming, 6 of 8 origins of
inbreeding polygyny and at least 11 independent origins of a
super-generalist host range. These three innovations are statistically
correlated, but their appearance within lineages was not necessarily
simultaneous. Additionally, the evolution of extreme host plant generalism
often preceded, rather than succeeded, fungus farming. Of the
high-diversity tribes of Scolytinae, only Xyleborini is monophyletic,
Corthylini is paraphyletic and Cryphalini is highly polyphyletic.
Cryphalini sensu stricto is part of a clade containing the genera
Hypothenemus, Cryphalus and Trypophloeus, and the tribe Xyloterini.
Stegomerus and Cryptocarenus (Cryphalini) are part of a clade otherwise
containing all Corthylini. Several other genera, including Ernoporus and
Scolytogenes (Cryphalini), make up a distantly related clade. Several of
the genera of Cryphalini are also intermixed. For example, Cryphalus and
Hypocryphalus are intermingled, as well as Ernoporicus, Ptilopodius and
Scolytogenes. Our data are consistent with widespread polyphyly and
paraphyly across Scolytinae and within Cryphalini, and provides new
insights into the evolution of inbreeding mating systems and fungus
farming in the species rich and ecologically significant weevil subfamily
Scolytinae.
annotated assembliesAssemblies automatically generated in GenBank flat
file format.annotated_assemblies.zipConcatenated alignment used in
phylogeny inference251 concatenated genes (introns and low coverage areas
removed).alltaxa_concatenated_nothird.phylipAlignmentsalignments.zipTree
from Bayesian inference with posterior probability
supportexabayes_tree_with_pp_rerooted.newickTree from Bayesian inference
with ML bootstrap supportTree inferred with Exabayes with node support
taken from a analyses of bootstrapped alignment with trees estimated using
Maximum Likelihoodexabayes_tree_with_bootstraps_rerooted.newickcustom
scripts usedScripts used in sequence preparation. This contains one bash
script "master_raw_to_alignment.sh" which undertakes simple bash
commands which acts as a wrapper for various pieces of software and custom
scripts. The rest of the files are specific python 3 scripts to complete
specific tasks.scripts.zip