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Item Origins and diversity of invasive brushtail possums (Trichosurus vulpecula) in New Zealand surveyed with mtDNA haplotype and nuclear microsatellite data(Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2025-05-07) Pattabiraman N; Morgan-Richards M; Trewick SA; Su JThe brushtail possum Trichosurus vulpecula is native to Australia where six subspecies exist in distinct regions. A composite invasive population is established in Aotearoa New Zealand, which has since been subject to localised bouts of culling. We surveyed population genetic structure across New Zealand to identify the scale of genetic diversity introduced to New Zealand and the resulting pattern of admixture. Australian brushtail possums have high mitochondrial diversity (17%) and prominent spatial structure. Thirty-eight haplotypes among 25 New Zealand population samples (n = 465) were closely related to 45 haplotypes sampled from Victoria and Tasmania in Australia (n = 120), but just one was shared. High haplotype diversity is consistent with multiple successful introductions and rapid population expansion in New Zealand. Nuclear diversity of microsatellite loci screened in 18 New Zealand population samples (n = 374) comprised five genotypic clusters (K = 5), but these groups did not correlate with geography. An overall signal of genetic partitioning within the invasive population suggests limited mixing but ongoing management towards eradication will influence patterns of population recovery, migration and evolution of traits including toxin resistance. We consider the implications of mixed ancestry of the invasive population in terms of variation in toxin tolerance detected in New Zealand.Item The influence of host receptivity and conformity pressure on the intercultural transformation of Filipino migrants in New Zealand(Elsevier B.V., 2024-12-17) Separa LAC; Croucher SM; Hodis GM; Feekery AFilipinos are the second fastest-growing Asian population working in dairy farming, healthcare, construction, and other industries in New Zealand. Like other immigrants, Filipinos experience basic and advanced intercultural transformation as they communicate and interact with people in the country. Croucher and Kramer's cultural fusion theory proposes a positive relationship between host receptivity and intercultural transformation and a negative relationship between host conformity pressure and intercultural transformation. Employing a survey of 315 Filipino migrants in New Zealand, this study addresses the extent to which host receptivity and host conformity pressure affect intercultural transformation. Regression analysis is used to assess the hypotheses and research question. Results reveal both host receptivity and host conformity pressure have positive relationships with intercultural transformation. The potential role of media and Filipino values in this study are also discussed.Item A new season for climate change science and praxis?(Walter de Gruyter GmbH, 2024-01-29) Glavovic B; Bremer S; Wardekker AI write these reflections at the end of the 27th Conference of Parties meeting of governments (COP27), held in Egypt in November 2022, at which governments sought to progress climate action. COP27 was informed by the Sixth Assessment Report (AR6) by the Intergovernmental Panel on Climate Change (IPCC). Established in 1988, the IPCC provides UN member nations with comprehensive assessments of the state of climate change science and its implications. I spent much of 2017–2022 devoted to AR6. I was a Coordinating Lead Author of the chapter on sea-level rise in the IPCC’s Special Report on the Ocean and Cryosphere in a Changing Climate (1), Lead Author of the chapter on Climate Resilient Development, and co-lead for the Cross-Chapter Paper on Cities and Settlements by the Sea, in the Working Group II report (2). How can I convey the gravitas of the climate predicament outlined in AR6? Moreover, where do we stand now – after more than three decades of intensive climate change science-policy interactions? What does this portend for climate change scientists, policy advisors and elected politicians? What does it mean for you and I? And how might answers to these questions inform our understanding about seasons; and how we might navigate impending dangerous climate change?Item Managed retreats by whom and how? Identifying and delineating governance modalities(Elsevier B.V, 2021) Hanna C; White I; Glavovic BCManaged retreat has become a compelling policy imperative as climate change exacerbates socio-natural hazard risks and imminent harm looms for exposed communities. Retreats may be initiated over different times and scales using various instruments by actors, from the state to the private sector and civil society. However, in the absence of a coherent strategic vision, guiding frameworks, and capacity to manage retreats, at-risk communities, their elected representatives, policy makers, and planners are compelled to embark on retreat governance experiments. Consequently, retreat is perceived as a ‘high regrets’ policy imperative with potentially adverse impacts for community wellbeing, as well as political and professional risks. To help translate managed retreat rhetoric into reality, this paper presents a governance framework that acknowledges the multiplicity of ‘managed retreats.’ Using examples from Aotearoa-New Zealand, we identify and delineate retreat modalities and clarify terminology, converging our framework with the international mobility literature to harness the valuable lessons from decades of human mobility practice.Item Detection of loci associated with water-soluble carbohydrate accumulation and environmental adaptation in white clover (Trifolium repens L.) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Palmerston North, New Zealand(Massey University, 2021) Pearson, SofieWhite clover (Trifolium repens L.) is an economically important forage legume in New Zealand/Aotearoa (NZ). It provides quality forage and a source of bioavailable nitrogen fixed through symbiosis with soil Rhizobium bacteria. This thesis investigated the genetic basis of two traits of significant agronomic interest in white clover. These were foliar water-soluble carbohydrate (WSC) accumulation and soil moisture deficit (SMD) tolerance. Previously generated divergent WSC lines of white clover were characterised for foliar WSC and leaf size. Significant (p < 0.05) divergence in foliar WSC content was observed between five breeding pools. Little correlation was observed between WSC and leaf size, indicating that breeding for increased WSC content could be achieved in large and small leaf size classes of white clover in as few as 2 – 3 generations. Genotyping by sequencing (GBS) data were obtained for 1,113 white clover individuals (approximately 47 individuals from each of 24 populations). Population structure was assessed using discriminant analysis of principal components (DAPC) and individuals were assigned to 11 genetic clusters. Divergent selection created a structure that differentiated high and low WSC populations. Outlier detection methodologies using PCAdapt, BayeScan and KGD-FST applied to the GBS data identified 33 SNPs in diverse gene families that discriminated high and low WSC populations. One SNP associated with the starch biosynthesis gene, glgC was identified in a genome-wide association study (GWAS) of 605 white clover individuals. Transcriptome and proteome analyses also provided evidence to suggest that high WSC levels in different breeding pools were achieved through sorting of allelic variants of carbohydrate metabolism pathway genes. Transcriptome and proteome analyses suggested 14 gene models from seven carbohydrate gene families (glgC, WAXY, glgA, glgB, BAM, AMY and ISA3) had responded to artificial selection. Patterns of SNP variation in the AMY, glgC and WAXY gene families separated low and high WSC individuals. Allelic variants in these gene families represent potential targets for assisted breeding of high WSC levels. Overall, multiple lines of evidence corroborate the importance of glgC for increasing foliar WSC accumulation in white clover. Soil moisture deficit (SMD) tolerance was investigated in naturalised populations of white clover collected from 17 sites representing contrasting SMD across the South Island/Te Waipounamu of NZ. Weak genetic differentiation of populations was detected in analyses of GBS data, with three genetic clusters identified by ADMIXTURE. Outlier detection and environmental association analyses identified 64 SNPs significantly (p < 0.05) associated with environmental variation. Mapping of these SNPs to the white clover reference genome, together with gene ontology analyses, suggested some SNPs were associated with genes involved in carbohydrate metabolism and root morphology. A common set of allelic variants in a subset of the populations from high SMD environments may also identify targets for selective breeding, but this variation needs further investigation.Item Pachycladon species evolved traits to adapt to New Zealand habitats : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatū, New Zealand(Massey University, 2021) Dong, YanniP. cheesemanii is a close relative of A. thaliana and is an allotetraploid perennial herb that is widespread in the South Island of New Zealand. It grows at altitudes of up to 1,000 m where it is subject to relatively high levels of UV-B radiation. However, to date the origin of this species and the mechanisms underlying its tolerance to its harsh living environmental conditions such as moderate–high UV-B radiation, cold and drought is unclear. To gain the first insights into how Pachycladon copes with UV-B stress, I sequenced the P. cheesemanii genome and compared the UV-B tolerance of plants from Wye Creek (~300-m altitude) and Kingston (~500-m altitude) with that of A. thaliana from Col-0 (~100-m altitude) and Kondara (1,000–1,100-m altitude). A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologues. A synteny analysis involving genomes from other species of the Brassicaceae family suggested that the two subgenomes of P. cheesemanii may have the same origin as species from Brassicaceae Lineage I and EII. While UV-B radiation caused greater growth reduction in A. thaliana Col-0 and Kondara than in P. cheesemanii Wye Creek, growth was not reduced in P. cheesemanii Kingston. Homologues of the A. thaliana UV-B radiation response genes have multiple copies in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii Wye Creek and Kingston may differ from that in A. thaliana. Although the P. cheesemanii genome shows close similarity with that of A. thaliana, the uniqueness of the strongly UV-B-induced UVR8-independent pathway in P. cheesemanii may help this species to tolerate relatively high UV-B radiation. Next, to understand the different stress responses of A. thaliana and P. cheesemanii, I designed a project to build multiple-stress transcriptomes for A. thaliana and P. cheesemanii. Since plant responses to salt and drought are related and have overlapping mechanisms, and salt stress can easily be applied in the laboratory, high salinity rather than drought stress was used to stress A. thaliana and P. cheesemanii plants in this study. Transcriptomes of A. thaliana and P. cheesemanii plants in response to cold, salt and UV-B radiation stresses were created. A high-quality de novo transcriptome assembly of allopolyploid P. cheesemanii was obtained by using multiple assemblers with further downstream processing. Differential expression analysis revealed a strong bias, in terms of the number of DEGs, towards upregulation in both A. thaliana and P. cheesemanii in responding to salt stress, as well as in P. cheesemanii’s cold and UV-B treatment responses. Meanwhile, in each species, a number of DEGs was shared between stresses, although the majority were unique in responding to each stress in upregulation and downregulation, respectively. Further, GO enrichment analysis revealed that these responsive genes were involved in some biological processes shared by A. thaliana and P. cheesemanii. Immune system processes, response to stimuli, signalling, developmental processes, growth, negative regulation of biological processes, multi-organism processes, biological regulation, secondary metabolic processes, cell communication, and cellular aromatic compound metabolic processes were common in the responses of both A. thaliana and P. cheesemanii to all three stresses. In both A. thaliana and P. cheesemanii, a number of these biological processes were also stress specific. First of all, in A. thaliana, cold stress may easily affect photomorphogenesis in cold responses, while the majority of the P. cheesemanii unique cold responses occurred in root differentiation, floral whorl development and regulation of programmed cell death. Second, A. thaliana responses to salt stress affected starch metabolism and lipid modification, whereas disaccharide and polysaccharide metabolism, as well as microtubule structure, were affected by salt stress uniquely in P. cheesemanii. Finally, A. thaliana responses to UV-B radiation involved a combination of physical and biological defences, including cell wall modification defence, stomatal movement, vitamin B6 metabolic processes and oxygen metabolic processes. In contrast, seed germination biological regulation was affected in P. cheesemanii under UV-B radiation stress. Further, P. cheesemanii had a larger number of unique GO enrichments in cold responses than did A. thaliana. There was a wide range of crosstalk among the biological processes in responding to the three stresses in A. thaliana, while only one main cluster was identified in crosstalk for the three stress responses in P. cheesemanii. In this main cluster, the biosynthetic process for anthocyanins was in the centre position, and it was found that multiple stress-responsive biological processes probably involved anthocyanins in P. cheesemanii. Thus, although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies such as a highly UV-B-activated UVR8-independent pathway, allowing the plant to tolerate relatively high UV-B radiation. The stress process is highly conserved in plant species under various stresses, but species also develop a few unique characteristics that may help them adapt to their own ecological niche and survive particular environmental stresses.Item Drought stress responses of the Medicago truncatula - Ensifer meliloti symbiosis on nodule senescence and nitrogen fixation : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Science at Massey University, Palmerston North, New Zealand(Massey University, 2018) Dhanushkodi, RamadossWhile the use of nitrogen (N) fertilizer has provided many benefits to agriculture, incessant use of it can reduce soil organic matter and fertility resulting in lower crop yields. Legume plants can fix its own N2 through symbiotic nitrogen fixation (SNF) to promote plant growth by developing facultative root organs called nodules. Therefore, increasing the rate of SNF to reduce dependence on N fertilizer is a promising strategy for sustainable legume production. In legume cultivation this symbiotic process confronts two major challenges. First, SNF is suppressed by readily available N in the soil and second, the early senescence of N-fixing nodules can limit any further fixation to occur. Previous reports show that N fertilizer supresses SNF activity in many legumes and supports plant growth better than SNF. Moreover, suppression of SNF can also be induced by drought stress which causes early nodule senescence and subsequent reduced rates of plant growth. This thesis addresses the process of SNF suppression in two Medicago truncatula selected genotypes in response to external N treatment and also delivers a molecular view on the regulation of drought-induced nodule senescence processes.--Shortened abstractItem Some adaptations of the anthocerophyte Megoceros pellucidus (Colenso) E.A.Hodgs. to extremely low light environments : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Palmerston North, New Zealand(Massey University, 2002) Watkins, Roger Lionel SloaneThe New Zealand Anthocerophyte Megaceros pellucidus (Colenso) is found in wet, cool temperate rain forest and is associated with extremely low light habitats (0.5-7 μmoles photons m−² s−¹). The light available to M. pellucidus was found to be only 0.2% of the overhead crown canopy light and was heavily attenuated after passing through many leaf canopies. This thesis shows that the photon flux density in these extremely low light habitats can be augmented by two additional light sources, sunfleck light, especially at midday, and light reflected from adjacent water surfaces, such as rivers or ponds, as the sun's incident ray path angle diminishes late or early in the day. This thesis looks at some of the strategies M. pellucidus uses to survive in its low light habitat and, in adapting to acquire such sensitivity to low light parameters, how M. pellucidus protects itself from photoinhibition if exposed to high white light of more than 140 μmoles photons m−² s−¹or blue (470 nm) light of more than 3 μmoles photons m−² s−¹. The chloroplast position in M. pellucidus, when in its normal habitat, was found to retain an expanded form situated on the periclinal cell wall proximal to the light source (an epistrophe position). When thallus tissue sections of M. pellucidus were irradiated with blue light of more than 3 μmoles photons m−² s−¹ or white light of more than 140 μmoles photons m−² s−¹ the chloroplast shrank dramatically and assumed a position on anticlinal walls (a parastrophe position). Red (662 nm) light of less than 130 μmoles photons m−² s−¹ or darkness had no obvious effect on the morphology epistrophe chloroplasts, but this treatment resulted in the chloroplasts expanding and moving back to the epistrophe position after irradiation by blue or high levels of white light. Based on the rate of volume change occasioned when the chloroplasts were irradiated with blue, white, red light or darkness it was concluded that a water flux was induced across the membranes of the various intracellular organelles that depended on the wavelength of the light and the photon flux density. Various concentrations of polyethylene glycol-20 (PEG) were used as an osmoticum and induced chloroplast shrinkage to an extent and at a rate similar that induced by blue light. Red (662 nm) light of 130 μmoles photons m−² s−¹, was observed to expand the chloroplast volume against the osmotic gradient, while darkness had no effect. A comparison of transmission electron microscope (TEM) micrographs taken of both blue / high light conditions and dark or red irradiated chloroplasts show differences in thylakoid membrane architecture, the dark-exposed samples having a loose open form with pseudograna and greater areas of stroma compared to the blue and high light samples that showed a tight compression of the thylakoids and very reduced areas of stroma. Large numbers of starch granules were apparent in all but the blue irradiated TEM micrographs. Examination of the micrographs showed there were obvious differences between the size of the starch granules (TEM, x7800, micrographs having starch granules with a dark to light ratio of 2.165) as well as in the texture and density.Item Reintroduction of North Island robins to Paengaroa Scenic Reserve : factors limiting survival, nest success, and population viability in a mainland restoration area : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University(Massey University, 2001) Raeburn, Elizabeth HelenForty North Island robins (Petroica australis longipes) were reintroduced to Paengaroa Scenic Reserve in March 1999. I monitored the survival and breeding success of this population for two years post-release. This study aims to assess survival, nest success, and population viability of robins in Paengaroa in an attempt to discover whether habitat in the reserve is likely to support a population of robins. Survival from the time of release to the start of the first breeding season was lower at Paengaroa than at two other release sites, Boundary Stream Scenic Reserve and Tiritiri Matangi Island. This may be due to higher predator levels at Paengaroa or dispersal out of the reserve. Methods of estimating nest success were compared, and Stanley's (2000) method was found to have advantages over the traditional and Mayfield methods. Daily survival rates of nests at Paengaroa depended on both the stage in the nesting cycle and stage of the breeding season, with the survival rate lowest for early nests at the incubation stage. Nest success for the first two breeding seasons after translocation was compared to that for the first two seasons after release at Tiritiri Matangi and Boundary Stream. Paengaroa had a similar nest success rate to Tiritiri Matangi (25% and 26% respectively), and both of these sites had lower nest success than Boundary Stream (47%). Survival at Paengaroa was most affected by whether a bird was recently-translocated. a juvenile, or an adult. Recently-translocated birds and juveniles suffered similarly low survival rates, suggesting that this high mortality may be due to problems faced when finding and establishing a territory. The survival of juveniles from January to September was estimated to be 29%. The annual adult survival rate was also low (59%). Fecundity and survival estimates were used in a stochastic simulation model to predict the viability of the Paengaroa population. Under current conditions, the population was predicted to have a 17% probability of surviving 10 years. However, variation of parameters to lower and upper 95% confidence limits gave survival probabilities of 0% to 100% over 10 years. When data from the first year after translocation were excluded, the population was predicted to have a 100% probability of surviving 100 years. These results demonstrate the large uncertainly associated with small sample sizes and short-term studies. To assess whether habitat quality is likely to account for the poor overall viability predicted at Paengaroa, the habitat quality at Paengaroa was compared to that at Waimarino forest, where robins still persist. Food supply and predator levels were used to assess habitat quality, as these are obvious factors that may limit viability. Data on food and predator levels provided no indication of why robins may be non-viable at Paengaroa. The power of statistical tests was low due to small sample size, but results suggest Paengaroa has more food as well as fewer rats and stoats than Waimarino. There is a need for further research to improve our understanding of why robins are present and common in some mainland areas but have disappeared from others without any obvious difference in habitat quality. Continued research is also required to reduce the uncertainty regarding population viability at Paengaroa and to determine whether improved management is needed.Item Understanding bacterial adaptation to aerobic and anaerobic environments through experimental evolution and whole genome analysis : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Palmerston North, New Zealand(Massey University, 2014) Finn, ThomasFacultative anaerobic organisms have the metabolic versatility to grow in both aerobic and anaerobic environments. However, molecular mechanisms that underpin adaptation to anaerobic environments are not well understood. This study aims to understand how the facultative anaerobe, Escherichia coli, adapts to environments that vary in oxygen content. An experimental evolution experiment was conducted in which replicate lineages were established from a preevolved clonal culture of E. coli REL4536. Lineages were serially sub-cultured for 4,000 generations within strict aerobic and strict anaerobic environments, and a treatment that fluctuated between the two environments. Significant increases in the relative fitness of lineages exposed to anaerobic conditions were observed, whereas the relative fitness of lineages in aerobic conditions did not increase, likely as the ancestor had been pre-adapted to aerobic growth. Mutations that arose during evolution were identified by genome sequencing randomly-selected clones from each lineage at 2,000 and 4,000 generations. Traits that contributed to adaptation were predicted via the occurrence of independent mutations affecting common traits among lineages. Adaptation to the anaerobic environment was facilitated by modifications to anaerobic fermentation and the inactivation of virulence genes, whereas in the aerobic environment, mutations predicted to confer a growth advantage in stationary phase were observed. The evolution of generalists involved traits that were similar to those found in both aerobic and anaerobically evolved lineages, as well as the deletion of cryptic prophages from the genome and modifications to amino acid transport. Phenotypically distinct small colony morphotypes (SCM) arose within anaerobic lineages and two separate adaptive pathways are hypothesised for this divergence. SCM1 were capable of stable coexistence with co-evolved cells of typical colony morphotype, most likely through an acetate crossfeeding mechanism. In contrast, SCM2 was able to out-compete the ancestor within 14 days, despite exhibiting a lower growth rate than the ancestor. SCM2 likely evolved the ability to inhibit the ancestral strain through a contact dependent inhibition mechanism, as evidenced by a mutation in glgC. This thesis demonstrates the complex nature of adaptation to anaerobic environments, as revealed by experimental evolution and whole genome sequencing.