title: How can genomic data inform biological invasions?

authors: Matheson, Paige

subjects: Genomics

abstract: Rates of biological invasions are increasing, with global trade and climate change causing significant damage to biodiversity, human well-being, primary industries, and economies around the world. However, our ability to predict and prevent future invasions is limited by significant gaps in our mechanistic understanding of the invasion process. Advances in next generation sequencing technologies and bioinformatics make it possible to investigate potential genomic factors that drive invasion success with much higher resolution and accuracy than prior research based on a small number of genetic loci. My thesis argues for the value of population genomic data in invasion biology, first examining the uptake of genomics in invasion research and then providing a case study for using genomic data to understand invasion patterns of pink bollworm (Pectinophora gossypiella).

The first analysis (Chapter 2) compares the extent to which population genetic data versus population genomic data, including reference genomes, have been used or are publicly available to study globally invasive species from the International Union for Conservation of Nature (IUCN) “100 of the World’s Worst Invasive Alien Species” (WAS) list. In this chapter, I demonstrate that ‘invasion genomics’ is still in its infancy with respect to research uptake: while 82% of species on the WAS list have been studied using some form of population genetic data, just 32% have been studied using population genomic data. Further, 55% of the WAS list species lack a reference genome, however 18% of these were sequenced in the last three years, indicating a growing investment in genomic resources that looks promising for future invasion genomics research.

The second analysis (Chapter 3) showcases population genomic data being used as a tool to inform a biological invasion. Pink bollworm is one of the most destructive global pests of cotton, costing farmers millions of dollars each year in productivity losses and management efforts. A small population of pink bollworm is currently established in North West Australia, where it poses a significant threat to the expanding cotton industry there. In this chapter, I analysed genomic data in the form of single nucleotide polymorphisms (SNPs) – obtained through a reduced representation, genotyping-by- sequencing technique (DArTseq) – for global populations of pink bollworm to elucidate the population structure and connectivity patterns of the pest. My results show that pink bollworm populations in my dataset have low genetic diversity and strong differentiation between populations from different continents. Importantly, the high genetic differentiation between Australia and other continents reduces concerns about gene flow to North West Australia, particularly from populations in India and Pakistan that have evolved resistance to transgenic insecticidal cotton.

As species continue to move globally beyond their natural ranges, understanding how genome-driven processes facilitate invasion is critical. Genomic data can enhance our mechanistic understanding of the invasion process and inform proactive management of invasive species. Yet, despite progress in this space, there remain limitations to the breadth and depth of such studies that are highlighted throughout my thesis. These represent valuable research opportunities. With the cost of generating genomic data constantly decreasing and long-read sequencing bridging the gap for many taxon-specific challenges, genomic data is starting to address many previously intractable research questions and has the potential to improve overall biosecurity outcomes worldwide.

text: How can genomic data inform biological invasions? Rates of biological invasions are increasing, with global trade and climate change causing significant damage to biodiversity, human well-being, primary industries, and economies around the world. However, our ability to predict and prevent future invasions is limited by significant gaps in our mechanistic understanding of the invasion process. Advances in next generation sequencing technologies and bioinformatics make it possible to investigate potential genomic factors that drive invasion success with much higher resolution and accuracy than prior research based on a small number of genetic loci. My thesis argues for the value of population genomic data in invasion biology, first examining the uptake of genomics in invasion research and then providing a case study for using genomic data to understand invasion patterns of pink bollworm (Pectinophora gossypiella).

The first analysis (Chapter 2) compares the extent to which population genetic data versus population genomic data, including reference genomes, have been used or are publicly available to study globally invasive species from the International Union for Conservation of Nature (IUCN) “100 of the World’s Worst Invasive Alien Species” (WAS) list. In this chapter, I demonstrate that ‘invasion genomics’ is still in its infancy with respect to research uptake: while 82% of species on the WAS list have been studied using some form of population genetic data, just 32% have been studied using population genomic data. Further, 55% of the WAS list species lack a reference genome, however 18% of these were sequenced in the last three years, indicating a growing investment in genomic resources that looks promising for future invasion genomics research.

The second analysis (Chapter 3) showcases population genomic data being used as a tool to inform a biological invasion. Pink bollworm is one of the most destructive global pests of cotton, costing farmers millions of dollars each year in productivity losses and management efforts. A small population of pink bollworm is currently established in North West Australia, where it poses a significant threat to the expanding cotton industry there. In this chapter, I analysed genomic data in the form of single nucleotide polymorphisms (SNPs) – obtained through a reduced representation, genotyping-by- sequencing technique (DArTseq) – for global populations of pink bollworm to elucidate the population structure and connectivity patterns of the pest. My results show that pink bollworm populations in my dataset have low genetic diversity and strong differentiation between populations from different continents. Importantly, the high genetic differentiation between Australia and other continents reduces concerns about gene flow to North West Australia, particularly from populations in India and Pakistan that have evolved resistance to transgenic insecticidal cotton.

As species continue to move globally beyond their natural ranges, understanding how genome-driven processes facilitate invasion is critical. Genomic data can enhance our mechanistic understanding of the invasion process and inform proactive management of invasive species. Yet, despite progress in this space, there remain limitations to the breadth and depth of such studies that are highlighted throughout my thesis. These represent valuable research opportunities. With the cost of generating genomic data constantly decreasing and long-read sequencing bridging the gap for many taxon-specific challenges, genomic data is starting to address many previously intractable research questions and has the potential to improve overall biosecurity outcomes worldwide.

year: 2022

title: Examining therapeutic approaches towards injurious behaviours in adolescents: Perspectives on influence, efficacy & prevention

authors: Parsons, Abby

subjects: NSSI

abstract: This qualitative research investigates professional perspectives on adolescent non- suicidal self-injury (NSSI) and outward-directed injurious (ODI) behaviours through in-depth interviews with twelve professionals across mental health, education, and social services in New Zealand. Utilising thematic analysis, the study reveals insights into how these behaviours represent interconnected manifestations of underlying emotional regulation challenges shaped by individual vulnerabilities, relationship dynamics, and systemic factors. Four key themes emerged: The Duality of Aggressive Expression, Environmental and Developmental Influences, Building Therapeutic Connections, and System Complexities and Bridge-Building. The research extends theoretical understanding by examining how risk factors influence behavioural expression, highlighting the connection between neurodevelopmental differences, trauma histories, and family dynamics. By challenging traditional conceptual frameworks, the study identifies significant gaps between evidence- based interventions and real-world implementation, ultimately offering recommendations for more integrated treatment protocols, enhanced professional support systems, and comprehensive care pathways for vulnerable youth.

text: Examining therapeutic approaches towards injurious behaviours in adolescents: Perspectives on influence, efficacy & prevention This qualitative research investigates professional perspectives on adolescent non- suicidal self-injury (NSSI) and outward-directed injurious (ODI) behaviours through in-depth interviews with twelve professionals across mental health, education, and social services in New Zealand. Utilising thematic analysis, the study reveals insights into how these behaviours represent interconnected manifestations of underlying emotional regulation challenges shaped by individual vulnerabilities, relationship dynamics, and systemic factors. Four key themes emerged: The Duality of Aggressive Expression, Environmental and Developmental Influences, Building Therapeutic Connections, and System Complexities and Bridge-Building. The research extends theoretical understanding by examining how risk factors influence behavioural expression, highlighting the connection between neurodevelopmental differences, trauma histories, and family dynamics. By challenging traditional conceptual frameworks, the study identifies significant gaps between evidence- based interventions and real-world implementation, ultimately offering recommendations for more integrated treatment protocols, enhanced professional support systems, and comprehensive care pathways for vulnerable youth.

year: 2025

title: An evaluation of the Raukawa Health Services Kaumatua Mirimiri Programme

authors: Gregg, Lisa

subjects: Maori

abstract: The Kaumatua Mirimiri Programme was funded as a Service to Improve Access project under a contract which ran from 1st September 2004 to 30th June 2005. Its aim was to provide a “culturally based treatment and recovery programme to restore the health and independence” of people aged 40 years and over (Pinnacle Group Ltd, 2004a, p.1). However, as the service specification in the contract made clear, the programme was not designed be exclusive: it has attracted younger as well as older people, non-Māori as well as Māori, and people seeking help for a wide range of ailments and pain.

text: An evaluation of the Raukawa Health Services Kaumatua Mirimiri Programme The Kaumatua Mirimiri Programme was funded as a Service to Improve Access project under a contract which ran from 1st September 2004 to 30th June 2005. Its aim was to provide a “culturally based treatment and recovery programme to restore the health and independence” of people aged 40 years and over (Pinnacle Group Ltd, 2004a, p.1). However, as the service specification in the contract made clear, the programme was not designed be exclusive: it has attracted younger as well as older people, non-Māori as well as Māori, and people seeking help for a wide range of ailments and pain.

year: 2006-03