Genomic insights into the evolution of the parasitoid Microctonus aethiopoides

Abstract

Parasitoids are used as biocontrol agents in classical biological control programmes for controlling invasive pest populations. In Aotearoa New Zealand, there are two strains of Microctonus aethiopoides that have been used against two serious pest weevils of the Sitona group. However, there is limited understanding of M. aethiopoides adaptability, particularly in the area of reproductive mode and host associations. My thesis explores these gaps, using population and comparative genomic approaches to investigate the adaptability of M. aethiopoides. Chapter 2 is a review that synthesises global research on parasitoid adaptation and identifies knowledge gaps across four key traits i.e., reproductive mode, olfaction, thermal tolerance, and microbiomes. Using the three Microctonus species in New Zealand as a focal example, this chapters explains why these traits matter for biocontrol and how genomic technologies reveal their underlying molecular mechanisms. Chapter 3 explores the adaptation of Irish asexual M. aethiopoides in New Zealand by analysing whole-genome resequencing data from 43 individuals representing historic (Ireland) and contemporary populations. The study reveals two distinct genetic clusters, most likely reflecting the genetic ancestry of introduced populations rather than post-introduction geographic isolation. All populations exhibit very low diversity and limited population expansion since release, consistent with their asexual nature and suggesting limited adaptation. Asexual M. aethiopoides show some heterozygosity across populations, supporting automictic thelytoky, likely via central fusion, as the primary reproductive mechanism. However, linkage disequilibrium patterns resemble those of sexual organisms, raising the possibility of facultative sex. This chapter sheds light on the adaptation, spread, and reproductive strategies of asexual M. aethiopoides in New Zealand. Chapter 4 further examines parasitoid adaptation, with a focus on host-associated divergence. Using eight newly assembled genomes from M. aethiopoides strains collected from three different hosts (Hypera postica, Sitona discoideus, S. obsoletus) and geographically distinct regions, this study investigates how host use and geography shape genomic structure. Comparative genomics reveals a clear host-associated phylogenetic split, with the H. postica lineage distinct from Sitona-associated lineages. Heterozygosity patterns support this separation, showing highest diversity in the H. postica group. However, gene families are mostly conserved across strains, with transposable element-related genes showing rapid evolution, suggesting their active role in genome restructuring. Chemosensory genes are also largely conserved, with only modest variation in odourant receptors that may reflect host-associated differences, although fragmentation and annotation bias cannot be ruled out. Overall, host association appears to be a key driver of divergence in M. aethiopoides, largely shaped by genome-level variation rather than major shifts in host-specific gene families. Finally, Chapter 5 assembles and characterises the first complete mitochondrial genome of M. aethiopoides, generated using a hybrid Oxford Nanopore-Illumina assembly. This study uncovers a long circular (33,173 bp) mitogenome with a unique gene arrangement, contributing a valuable genetic resource for future studies of mitochondrial evolution in parasitoids. Overall, my thesis demonstrates how genomic technologies can be used to provide a more comprehensive understanding of the evolutionary factors shaping a species’ genome and population structure. It provides a valuable genomic resource and sets a foundation of resources for continuing to build understanding of adaptation in the context of asexuality and host association in M. aethiopoides.