UC Research Repository
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The UC Research Repository collects, stores and makes available original research from postgraduate students, researchers and academics based at the University of Canterbury.
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Recent Submissions
Lonely on limestone? A conservation genomics study of the Gentianella calcis complex.
(2024) Eastman-Densem, Robb William
Naturally fragmented or rare ecosystems are important components of terrestrial plant
biodiversity. Unfortunately, many are also threatened through anthropogenic activities
leading to increased extinction risk for their flora. In Aotearoa / New Zealand, the limestone
areas of the eastern South Island / Te Waipounamu are a naturally fragmented and rare
ecosystem of particular concern as they contain many highly threatened plant taxa. To assist
with the ongoing conservation management of limestone endemic plants in New Zealand, the
overall aim of this thesis was to explore patterns of genetic diversity and connectivity within
a group of threatened limestone gentians (subspecies of Gentianella calcis and G. astonii) as
well as investigate the interspecific taxonomic delimitation of G. calcis and G. astonii and
infraspecific taxonomic delimitation of G. calcis. In Chapter 2, using Single Nucleotide
Polymorphisms (SNPs) from 174 G. calcis and G. astonii samples genotyped through
genotyping-by-sequencing (GBS), I aimed to determine the amount of genetic diversity in
each subspecies and sampled population of G. calcis and G. astonii, assess the extent of
genetic connectivity among them, and understand the geographic structuring of genetic
diversity and its relationship to the environment. I show that all taxa are characterised by high
population structure and limited genetic connectivity, with the presence of three main genetic
groups corresponding to the South Canterbury and North Otago, Waipara, and North
Canterbury and Marlborough regions. Although Isolation-By-Distance appeared to explain
the observed patterns of genetic connectivity, potential adaptation to local climate and habitat
soils was also seen. Patterns of observed heterozygosity potentially reflect past demographic
histories as well as the effects of polyploidy-induced paralogy in some SNPs. Based on these
findings, I designate conservation Management Units to assist with current and future
conservation of G. calcis.
DiscoSNP-RAD represents a novel SNP discovery approach that claims to not require the
same parameter optimisation as other commonly used programs such as Stacks. There are
very few published comparisons of its output to other SNP discovery programs, however,
illustrating the need for empirical studies. Considering these factors, in Chapter 3 I aimed to
assess the importance of using similarity-based parameters in SNP discovery by comparing
both SNP discovery methods (i.e. Stacks and DiscoSNP-RAD) in terms of RAD loci
assembled, data error, and population genetic inferences (e.g., estimates of population
structure and genetic diversity). While both approaches provided similar patterns of
population structure, estimates of genetic diversity and pairwise Fst differed between the two
approaches. Using sample replicates, I show that this is likely due to increased SNP error in
the DiscoSNP-RAD dataset, potentially reflecting a greater proportion of paralogy-induced
SNPs caused by lower user control over the formation of RAD loci. Despite this, considering
it has faster run-time and does not need extensive parameter optimisation, I suggest
DiscoSNP-RAD is still a useful SNP discovery program.
In Chapter 4, synthesising the learnings from Chapter 2 and Chapter 3, I make populationspecific management recommendations for each Gentianella calcis population along with
taxonomic delimitation recommendations using knowledge of the genetic patterns in G.
calcis and G. astonii. Considering that to date no conservation genetics or genomics studies
have considered limestone plants in New Zealand at the population level, this research
represents an important step towards the integration of genomic data into their conservation
management.
Applying behavioural science to understand and support biosecurity risk assessments.
(2024) Bain, Dominic
Invasive species threaten the health, safety, sustainability, wellbeing, and prosperity of Aotearoa New Zealand. A key function of the biosecurity system is to comprehensively assess the risks posed by invasive species. This study investigated the psychological dimensions of biosecurity risk assessments and explored potential targets and mechanisms for improvement. Twenty participants were recruited from Aotearoa New Zealand’s biosecurity workforce. Policy capturing, multiple-criteria decision analysis, and the behaviour change wheel were used as investigative frameworks. Results from the policy capturing analysis indicated that risks to economic, environmental, sociocultural, and te ao Māori values all significantly increased participants’ perception of invasive species’ overall biosecurity risk. Risks to economic values had the largest effect and risks to sociocultural and te ao Māori values had the smallest effects. Results from multiple-criteria decision analysis indicated that participants consciously allocated the most importance to risks to economic values followed by risks to environmental, then sociocultural, and then te ao Māori values. Results from the behaviour change wheel analysis indicated that participants were motivated to incorporate te ao Māori values into their biosecurity risk assessments but perceived that they lacked the capability and opportunity to do so. Key intervention targets and mechanisms were discussed to address these areas and support comprehensive biosecurity risk assessments.
Japanese junior high school teachers’ perspectives on teaching English as a foreign language.
(2024) Tomita, Hanako
How do language teachers position grammar instruction and interaction in their teaching?
This study postulated that, in a context where a communicative approach to language
teaching is promoted over a structuralist/behaviourist approach, teacher perception of
grammar instruction and interaction might be where the tension between the two approaches
would surface. Exploration in this scope is relevant in Japan, where it has been twenty years
since an action plan to nurture the national communicative skills in English was announced
by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in 2003. The
action plan prescribed the incorporation of learner-centred interactive teaching approaches,
and the principles of the action plan continue to be enacted in the present Japanese national
curriculum standards of junior and senior high schools (MEXT, 2017a; MEXT, 2018). Yet
statistics indicate that Japanese students struggle in expressing themselves in writing and
speaking (MEXT, 2019; MEXT, 2022). This study focused in on teacher perception on
grammar instruction because extant literature suggests that language teachers hold persistent
belief in transmitting explicit grammar rules for students’ deductive application, when
research indicates that consciously attained explicit knowledge does not equate to language
proficiency (Krashen & Terrell, 1983). Furthermore, the current study enquired into teacher
views on interaction and bilingualism. Not only must teachers balance grammar instruction
with dialogic activities, but their views of students as potential bi-/multilingual speakers
might impact how they design a lesson. Based on a constructionist epistemology, relativism
ontology, and a theoretical underpinning of Blumer’s (1969) symbolic interactionism, I
conducted semi-structured interviews with 11 Japanese junior high school English-language
teachers. A thematic analysis (Braun & Clarke, 2022) on the collected data demonstrated that
teacher perceptions regarding grammar instruction, interaction, and bi-/multilingualism were
varied, depicting fluidity and uncertainty around pedagogical choices among the participant
teachers, but a tendency toward communicative language teaching and scepticism toward
monolingual instruction. I conclude that more theory-based discussions would lead to teacher
confidence in their practice.
The biofactory : implementing a life cycle sustainability assessment decision making tool for quantifying integral sustainability benefits of the wastewater circular economy in Chile.
(2023) Furness, Madeline
The “Biofactory” is a circular economy-based concept for wastewater treatment that improves
water quality, promotes efficient use of materials and energy, recovering resources, generating
stakeholder collaboration, and decreasing both emissions and costs. This proposes a solution for
the global challenge of integrated water and sanitation management. Due to socio-economic
bottlenecks, such as typical high costs and low public acceptance of novel resource recovery
scenarios in wastewater treatment, realizing the Biofactory goals becomes a difficult task. Decision
makers are currently unable to appreciate the environmental and social benefits of the Biofactory,
as most decision-making tools focus on mainly technical and economic aspects. This research is
the first to quantify integral sustainability benefits of co-product recovery of treated effluent,
biosolids, biogas and nutrient in two full-scale “Biofactory” wastewater circular economies in Chile.
Life Cycle Sustainability Assessment (LCSA) was implemented, combining Life Cycle Assessment
(LCA), Social Life Cycle Assessment (SLCA) and Life Cycle Costing (LCC) with a Multi-criteria
Decision Making (MCDM) model to quantify integral environmental, socio-cultural, and economic
sustainability impacts of two Plants, A and B. Three scenarios for each plant were considered,
discharge of wastewater without treatment, conventional wastewater treatment with no resource
recovery, and biofactory wastewater circular economy configurations, to determine if each plant
decrease impacts and determine which had better performance. LCA results showed Plant A
decreased overall environmental impact by -37 % compared to baseline conventional scenarios,
while Plant B -31 %. SLCA results showed Plant A decreased social impacts – 56 %, while Plant B
– 18 %, therefore, Plant A had better overall environmental and social performance. However, Plant
B decreased economic impacts by -48 % compared to an increase of 20 % in Plant A. Therefore,
when combining scores using a MCDM model, Plant A decreased total sustainability impacts
by -30 % and Plant B by -58 %, therefore, the resource recovery systems implemented in Plant B
had better overall sustainability performance. These results were discussed across process
contributions to environmental, social, and economic benefits. Model limitations were discussed,
and recommendations were made for future applications of this research. The investigation
demonstrated that the transition to WW-CEs improved integral sustainability according to the LCSAMCDM model implemented in both Plants. The urgent need to adopt sustainable decision-making
models was highlighted and discussed, to not only improve sanitation coverage, but also improve
sustainability performance of the sanitation industry across the globe.
Does a dimensionally-gated reselection process restrict the entry of visual features into working memory?
(2023) Williamson, Kieran James
Visual working memory (VWM) is a limited-capacity cognitive system that allows us to
maintain and manipulate visual information over a brief period of time. It plays a critical
role in many cognitive functions, including visual search, problem-solving, and decisionmaking. While the importance of VWM is not disputed, a critical issue addressed in
research is whether visual objects bind all their component features during VWM entry
or if task-relevant features are prioritised for representation. In a recent study,
Zhu et al. (2022) proposed that attended sensory information does not automatically
enter VWM, but instead is subject to an additional reselection process that determines
whether items are selected for VWM entry. Furthermore, they suggested that
reselection operates using a dimensional memory filter, such that when an individual
feature value (e.g., red) is selected for entry into VWM, all attended feature values
within the same feature dimension (e.g., all colours) automatically enter VWM. Across
three experiments, we systematically investigated these hypotheses by conceptually
replicating two of Zhu et al.’s experiments, while incorporating modifications to address
our concerns about their methodology. In Experiment 1, we investigated Zhu et al.’s
proposal that a reselection process operates to restrict the entry of features into VWM.
We assessed whether the irrelevant colour of a target object captured more attention
than a new colour when it appeared as a distractor singleton in an orthogonal visual
search task. We found that this was the case, indicating that the irrelevant colour of the
target object was held in VWM, contrary to the key result that Zhu et al. cited to support
reselection. In Experiments 2 and 3, we investigated Zhu et al.’s claim that VWM
consolidation operates via a dimensional memory filter. Specifically, we assessed
whether memorising the colour of a fixation cross would cause the task-irrelevant
colour of a target object to enter VWM. To determine whether this colour entered VWM,
we measured its interference in an orthogonal shape change detection task. Experiment
2 used a 700 ms ISI, while in Experiment 3, we reduced the ISI to 100 ms. Unlike Zhu et
al., who only reported trials where shape was consistent between displays, we included
trials where shape changed between displays in our analysis and included trials in
which the shape probe matched the memorised fixation colour. In Experiments 2 and 3,
we found evidence that the target colour had entered VWM, consistent with a
dimensional memory filter. However, we also found that the fixation colour had a
stronger impact on shape change detection than the target colour, a finding that was not
explicitly predicted by Zhu et al. Overall, our results align more closely with predictions
from object-file theory (Kahneman et al., 1992) and event-file theory (Hommel, 1998,
2004), which propose object-specific binding occurs during encoding, and objectspecific benefits and costs emerge during object retrieval and review. The facilitation
we observed when features were consistent between displays could reflect objectspecific repetition benefits, while the interference we observed when features partially
changed between displays may indicate partial repetition costs.