Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using transcriptomes: examining controversial relationships via degeneracy coding and interrogation of gene conflict

Rachel K. Skinner, Christopher H Dietrich, Kimberly K.O. Walden, Eric Gordon, Andrew D. Sweet, Lars Podsiadlowski, Malte Petersen, Chris Simon, Daniela M. Takiya, Kevin Paul Johnson

Research output: Contribution to journalArticle

Abstract

The hemipteran suborder Auchenorrhyncha is a highly diverse, ecologically and agriculturally important group of primarily phytophagous insects which has been a source of phylogenetic contention for many years. Here, we have used transcriptome sequencing to assemble 2139 orthologues from 84 auchenorrhynchan species representing 27 families; this is the largest and most taxonomically comprehensive phylogenetic dataset for this group to date. We used both maximum likelihood and multispecies coalescent analyses to reconstruct the evolutionary history in this group using amino acid, nucleotide, and degeneracy-coded nucleotide orthologue data. Although many relationships at the superfamily level were consistent between analyses, several differing, highly supported topologies were recovered using different datasets and reconstruction methods, most notably the differential placement of Cercopoidea as sister to either Cicadoidea or Membracoidea. To further interrogate the recovered topologies, we explored the contribution of genes as partitioned by third-codon-position guanine-cytosine (GC) content and heterogeneity. We found consistent support for several relationships, including Cercopoidea + Cicadoidea, most often in genes that would be expected to be enriched for the true species tree if recombination-based dynamics in GC content have contributed to the observed GC heterogeneity. Our results provide a generally well-supported framework for future studies of auchenorrhynchan phylogeny and suggest that transcriptome sequencing is likely to be a fruitful source of phylogenetic data for resolving its clades. However, we caution that future work should account for the potential effects of GC content heterogeneity on relationships recovered in this group.

Original languageEnglish (US)
JournalSystematic Entomology
DOIs
StatePublished - Jan 1 2019

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Auchenorrhyncha
cytosine
guanine
Insecta
transcriptome
Hemiptera
Cercopoidea
Cicadoidea
phylogenetics
topology
gene
phylogeny
transcriptomics
Membracoidea
genes
nucleotides
recombination
phytophagous insects
amino acid
codons

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Insect Science

Cite this

Phylogenomics of Auchenorrhyncha (Insecta : Hemiptera) using transcriptomes: examining controversial relationships via degeneracy coding and interrogation of gene conflict. / Skinner, Rachel K.; Dietrich, Christopher H; Walden, Kimberly K.O.; Gordon, Eric; Sweet, Andrew D.; Podsiadlowski, Lars; Petersen, Malte; Simon, Chris; Takiya, Daniela M.; Johnson, Kevin Paul.

In: Systematic Entomology, 01.01.2019.

Research output: Contribution to journalArticle

Skinner, Rachel K. ; Dietrich, Christopher H ; Walden, Kimberly K.O. ; Gordon, Eric ; Sweet, Andrew D. ; Podsiadlowski, Lars ; Petersen, Malte ; Simon, Chris ; Takiya, Daniela M. ; Johnson, Kevin Paul. / Phylogenomics of Auchenorrhyncha (Insecta : Hemiptera) using transcriptomes: examining controversial relationships via degeneracy coding and interrogation of gene conflict. In: Systematic Entomology. 2019.
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