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: Making multiplication meaningful: Teaching for conceptual understanding

authors: Mills, Judith Patricia

subjects: Conceptual understanding

abstract: The term numeracy is used widely in schools today and brings with it the expectation that students will be taught both how to do the mathematics, alongside an understanding of the concepts associated with the procedural application. One issue, which has arisen with the terminology ‘numeracy classroom’, is how to best support teachers to enhance their teaching of mathematics to allow this understanding to occur. This article stems from a larger research study that analysed the professional knowledge of teachers when teaching numeracy, and the impact their mathematics knowledge and procedural application had on children’s learning. This article presents observations of three teachers teaching a multiplication lesson (the first in a series of lessons over a six-week period) as they developed their students’ understanding of the mathematical concepts associated with the interpretation of the multiplication symbol. An analysis of the findings shows when the teachers used manipulatives, related word problems to the children’s lives, and promoted discussion in groups, a greater understanding of multiplication was apparent.

text: Making multiplication meaningful: Teaching for conceptual understanding The term numeracy is used widely in schools today and brings with it the expectation that students will be taught both how to do the mathematics, alongside an understanding of the concepts associated with the procedural application. One issue, which has arisen with the terminology ‘numeracy classroom’, is how to best support teachers to enhance their teaching of mathematics to allow this understanding to occur. This article stems from a larger research study that analysed the professional knowledge of teachers when teaching numeracy, and the impact their mathematics knowledge and procedural application had on children’s learning. This article presents observations of three teachers teaching a multiplication lesson (the first in a series of lessons over a six-week period) as they developed their students’ understanding of the mathematical concepts associated with the interpretation of the multiplication symbol. An analysis of the findings shows when the teachers used manipulatives, related word problems to the children’s lives, and promoted discussion in groups, a greater understanding of multiplication was apparent.

year: 2019

title: The Māori language curriculum for New Zealand schools: Spiral lesson/ lesson sequence design

authors: Johnson, Diane

subjects: Māori language teaching

abstract: A draft curriculum document for the teaching and learning of te reo Māori as a subject in mainstream schools in New Zealand (that is, in schools other than Kura Kaupapa Māori schools) was designed and trialled in 2004 and 2005. That draft is currently being reworked in line with the advice of those who trialled the document as well as that of a team of advisers set up by the Ministry of Education. The revised curriculum document will be submitted to the Ministry of Education in May 2006. As is the case with all new curriculum documents, the implementation phase will be critical. The extent to which this flexible, outcomes-focused curriculum document will genuinely inform new approaches to teaching and learning will depend not only upon the good will of teachers and communities, but also upon their ability to interpret the curriculum and to use it in a way that informs the design of language programmes, including the planning of units of work and of lessons and lesson sequences. In balancing language development and language practice, a communicative core and spiral approach is recommended, an approach in which there are core lessons (where the focus is language development) and spiral lessons (where the focus is language practice). In an earlier issue of this Journal (Johnson, 2003), one of us discussed core lesson design. Here, the design of spiral lessons is discussed and exemplified in the context of an outcomes-based curriculum.

text: The Māori language curriculum for New Zealand schools: Spiral lesson/ lesson sequence design A draft curriculum document for the teaching and learning of te reo Māori as a subject in mainstream schools in New Zealand (that is, in schools other than Kura Kaupapa Māori schools) was designed and trialled in 2004 and 2005. That draft is currently being reworked in line with the advice of those who trialled the document as well as that of a team of advisers set up by the Ministry of Education. The revised curriculum document will be submitted to the Ministry of Education in May 2006. As is the case with all new curriculum documents, the implementation phase will be critical. The extent to which this flexible, outcomes-focused curriculum document will genuinely inform new approaches to teaching and learning will depend not only upon the good will of teachers and communities, but also upon their ability to interpret the curriculum and to use it in a way that informs the design of language programmes, including the planning of units of work and of lessons and lesson sequences. In balancing language development and language practice, a communicative core and spiral approach is recommended, an approach in which there are core lessons (where the focus is language development) and spiral lessons (where the focus is language practice). In an earlier issue of this Journal (Johnson, 2003), one of us discussed core lesson design. Here, the design of spiral lessons is discussed and exemplified in the context of an outcomes-based curriculum.

year: 2005