Phylogenomic analysis of hemimetabolan insects with emphasis on the hemipteran suborder Auchenorrhyncha and the superorder Paraneoptera

Insects are the among the most diverse groups of organisms on the planet and understanding the factors contributing to their evolution has long been a goal of systematic entomology. However, despite efforts to reconstruct their evolutionary history using morphological and molecular Sanger sequencing data, many relationships in the insect tree of life remained uncertain, leading researchers to seek additional sources of phylogenetic information. The past two decades have seen an extraordinary expansion in the availability of genome-scale data from non-model organisms including insects due to increasing availability and affordability of high-throughput sequencing methods. One result of this expansion has been the incorporation of genomic and transcriptomic sequence data in phylogenetic analyses of many insect groups. These phylogenomic data sets were anticipated to resolve the remaining questions concerning insect relationships in the tree of life, although the reality has been more complicated. As data sets have increased in size, so too have the potential sources of incongruence between gene trees and the species tree that must be accounted for during phylogenetic inference. This thesis uses high-throughput sequencing to reconstruct evolutionary relationships of the hemimetabolan super order Paraneoptera (including Thysanoptera, Hemiptera, and Psocodea) and the hemipteran suborder Auchenorrhyncha, which have been hotly debated in the scientific literature due to differences in placement of large and small clades across analyses using different data types. Relationships between and within the auchenorrhynchan superfamilies were investigated using transcriptome and genome sequencing of preserved specimens, resulting in the highest taxonomic representation of any previous study of this group (Chapters 2 and 3). Chapter 2 identifies areas of poor support and explores the role of GC compositional heterogeneity on phylogenetic analyses of Auchenorrhyncha. Chapter 3 expands the taxonomic sampling of Chapter 2, resulting in increased support for the relationships of the auchenorrhynchan superfamilies. Chapter 3 again explores the relationship of GC content heterogeneity to auchenorrhynchan relationships and identifies regions of the tree which may be difficult to resolve due to ancient rapid radiations. Chapter 4 reinvestigates the results of a previous study of the Paraneoptera in which conflicting results between different analyses of the same phylogenomic data suggested that the unexpected placement of Psocodea sister to Holometabola in a maximum likelihood analysis was not robust. I have performed additional analyses of these data to identify putative sources of incongruence between analyses and identified incomplete lineages sorting and rate heterogeneity between lineages as putative sources of phylogenomic conflict in this group. The results of this thesis expand our knowledge of insect evolution and contribute to the growing body of knowledge concerning sources of conflict in phylogenomic analyses.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Entomology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Skinner, Rachel Kathleen

Contributors dc:contributor

• Dietrich, Christopher
• Johnson, Kevin
• Suarez, Andrew
• Whitfield, James

• phylogenomics
• insects
• Hemiptera
• phylogenetics

Statement dc:rights

• Copyright 2021 Rachel Skinner

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/113130

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/113130