title: Genomic insights into the evolution of the parasitoid Microctonus aethiopoides

authors: Hussain, Meeran

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.

text: Genomic insights into the evolution of the parasitoid Microctonus aethiopoides 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.

year: 2026

title: Streptococcus equi subsp. zooepidemicus in New Zealand horses

authors: Patty, Olivia Anne

subjects: Streptococcus zooepidemicus

abstract: Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is an opportunistic commensal bacterium of the horse mucosa causing disease in susceptible populations.  This research sets out to enhance the understanding of S. zooepidemicus infections within the New Zealand horse population through strain-associated genomic and phenotypic characteristics.  Retrospectively, S. zooepidemicus is the second most frequently isolated bacterium in New Zealand horses, being mainly associated with respiratory and urogenital tract infections.  However, it also has the ability to colonise and or infect a diverse range of other anatomical regions of New Zealand horses.  S. zooepidemicus isolates were shown to be genetically diverse via strain typing using either the single polymorphic gene, szp or standard multilocus sequence typing (MLST). Both typing schemes were shown to lack the discriminatory power needed to completely separate the isolates which was resolved by employing core genome MLST.  Importantly, none of these typing methods could link a particular strain to disease status or anatomical region.  However, when disease occurred the number of colonising strains tended to reduce to just the infective strain, indicating bacterial competition and strain fitness advantages.  Factors available to S. zooepidemicus to colonise and persist in the horse include biofilm formation and cellular invasion with the majority of strains tested in vitro, able to form biofilms and all tested strains capable of invasion.  
Bioinformatic analysis showed that the pangenome of S. zooepidemicus is open, which demonstrates the ability of species to accessorise its genome enabling the species to diversify and exploit different hosts and environment.  An average of 45 new genes are discovered with the addition of each new genome.  Unfortunately, no single feature of the accessory genome analysed was able to differentiate the New Zealand horse S. zooepidemicus strains as commensals or pathogens or differentiate strains from respiratory disease or uterine infection.  As a result, this study defines S. zooepidemicus as an opportunistic pathogen that can reside in the healthy equine population and infect susceptible hosts and are not anatomically, geographically or host bound.

text: Streptococcus equi subsp. zooepidemicus in New Zealand horses Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is an opportunistic commensal bacterium of the horse mucosa causing disease in susceptible populations.  This research sets out to enhance the understanding of S. zooepidemicus infections within the New Zealand horse population through strain-associated genomic and phenotypic characteristics.  Retrospectively, S. zooepidemicus is the second most frequently isolated bacterium in New Zealand horses, being mainly associated with respiratory and urogenital tract infections.  However, it also has the ability to colonise and or infect a diverse range of other anatomical regions of New Zealand horses.  S. zooepidemicus isolates were shown to be genetically diverse via strain typing using either the single polymorphic gene, szp or standard multilocus sequence typing (MLST). Both typing schemes were shown to lack the discriminatory power needed to completely separate the isolates which was resolved by employing core genome MLST.  Importantly, none of these typing methods could link a particular strain to disease status or anatomical region.  However, when disease occurred the number of colonising strains tended to reduce to just the infective strain, indicating bacterial competition and strain fitness advantages.  Factors available to S. zooepidemicus to colonise and persist in the horse include biofilm formation and cellular invasion with the majority of strains tested in vitro, able to form biofilms and all tested strains capable of invasion.  
Bioinformatic analysis showed that the pangenome of S. zooepidemicus is open, which demonstrates the ability of species to accessorise its genome enabling the species to diversify and exploit different hosts and environment.  An average of 45 new genes are discovered with the addition of each new genome.  Unfortunately, no single feature of the accessory genome analysed was able to differentiate the New Zealand horse S. zooepidemicus strains as commensals or pathogens or differentiate strains from respiratory disease or uterine infection.  As a result, this study defines S. zooepidemicus as an opportunistic pathogen that can reside in the healthy equine population and infect susceptible hosts and are not anatomically, geographically or host bound.

year: 2020

title: Taonga maioha: (Born this way) The in-depth stories of three Māori, Pasifika, and Indigenous Queens

authors: Tamuera Ariki, Paikea

abstract: Who else has the right to define these, Queens? 

This thesis provides a vital platform for the voices of three Māori, Pasifika, and Indigenous Queens, allowing them to share their transformation stories in their own words. Their experiences and feelings about in their words “being born into the wrong bodies” highlight the complex realities of identity and the struggle for acceptance by others. 

These Queens are unified in their desire for dignity and respect. Dignity and respect underscore a fundamental human right. They seek recognition in all areas of their lives, from healthcare to education, housing, employment, and beyond. By articulating their needs, they advocate for themselves and all marginalized individuals, seeking fairness and understanding within systems that often overlook them. 

Focusing on their lived experiences is crucial for fostering empathy and promoting systemic change, as it brings attention to the disparities they face and the importance of inclusivity in society. By sharing their truths, these Queens contribute to a broader dialogue about identity, respect, and the pursuit of equality for all. 

This thesis aims to illuminate the transformation stories or pūrākau of ten Māori and Pasifika Queens, to foster understanding of their unique experiences. The focus on those who identify as wahine despite being born biologically male allows the reader to highlight the rich diversity of gender identity within these cultures and groups. 

The Māori Ethics Committee granted ethics approval for the study, thereby paving the way for the Queens to tell their stories or pūrākau from their truths and perspectives. 

Taonga Maioha details the in-depth transformation stories of three Māori-Pasifika Queens aged 60 plus, supported by a contextual and cultural analysis of their generation. The voices and stories of the Queens are central to this thesis. These stories are thematically analyzed to unpack the cultural and generational influences impacting their identities. The core identity constructs of whakapapa, tinana, hinengaro, and wairua are used to frame and organize their transformation stories according to their instructions. Above all, this thesis is anchored in their rights to define themselves on the premise that they have the mana to define themselves irrespective of others who define them from the sidelines of their lives. Their definitions are theirs alone. The storytellers call themselves Queen, Wahine, or women. This is based on the assertion that it is their right to be called a Queen. In certain contexts, they may refer to themselves as takatāpui and transgender for the sake of acceptance by others. This thesis is written to enhance the mana of the storytellers. These are their stories and their truths. 

The late Dame Georgina Beyer, was one of the original participants in this thesis. Many interviews were conducted with her. Instructed by Georgina before her passing to publish elements of her story as part of this thesis. Unfortunately, the Ethics Committee at Waikato University did not accept this due to her passing. Hence, the reason ‘First Lady’ was introduced, where Liz Roberts gives exclusive details of her change, both legally and physically.

text: Taonga maioha: (Born this way) The in-depth stories of three Māori, Pasifika, and Indigenous Queens Who else has the right to define these, Queens? 

This thesis provides a vital platform for the voices of three Māori, Pasifika, and Indigenous Queens, allowing them to share their transformation stories in their own words. Their experiences and feelings about in their words “being born into the wrong bodies” highlight the complex realities of identity and the struggle for acceptance by others. 

These Queens are unified in their desire for dignity and respect. Dignity and respect underscore a fundamental human right. They seek recognition in all areas of their lives, from healthcare to education, housing, employment, and beyond. By articulating their needs, they advocate for themselves and all marginalized individuals, seeking fairness and understanding within systems that often overlook them. 

Focusing on their lived experiences is crucial for fostering empathy and promoting systemic change, as it brings attention to the disparities they face and the importance of inclusivity in society. By sharing their truths, these Queens contribute to a broader dialogue about identity, respect, and the pursuit of equality for all. 

This thesis aims to illuminate the transformation stories or pūrākau of ten Māori and Pasifika Queens, to foster understanding of their unique experiences. The focus on those who identify as wahine despite being born biologically male allows the reader to highlight the rich diversity of gender identity within these cultures and groups. 

The Māori Ethics Committee granted ethics approval for the study, thereby paving the way for the Queens to tell their stories or pūrākau from their truths and perspectives. 

Taonga Maioha details the in-depth transformation stories of three Māori-Pasifika Queens aged 60 plus, supported by a contextual and cultural analysis of their generation. The voices and stories of the Queens are central to this thesis. These stories are thematically analyzed to unpack the cultural and generational influences impacting their identities. The core identity constructs of whakapapa, tinana, hinengaro, and wairua are used to frame and organize their transformation stories according to their instructions. Above all, this thesis is anchored in their rights to define themselves on the premise that they have the mana to define themselves irrespective of others who define them from the sidelines of their lives. Their definitions are theirs alone. The storytellers call themselves Queen, Wahine, or women. This is based on the assertion that it is their right to be called a Queen. In certain contexts, they may refer to themselves as takatāpui and transgender for the sake of acceptance by others. This thesis is written to enhance the mana of the storytellers. These are their stories and their truths. 

The late Dame Georgina Beyer, was one of the original participants in this thesis. Many interviews were conducted with her. Instructed by Georgina before her passing to publish elements of her story as part of this thesis. Unfortunately, the Ethics Committee at Waikato University did not accept this due to her passing. Hence, the reason ‘First Lady’ was introduced, where Liz Roberts gives exclusive details of her change, both legally and physically.

year: 2024