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    Global warming responses within the New Zealand alpine radiation of acridid grasshoppers : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Manawatu, New Zealand
    (Massey University, 2024-07-20) Meza-Joya, Fabio Leonardo
    We are living in the Anthropocene, where humans are directly and indirectly altering climatic regimes, leading to warmer conditions with multifarious effects on the biosphere. Well-documented ecological responses to planetary heating include distributional, phenological, and/or phenotypical shifts. Anthropogenic global warming is predicted to significantly impact alpine ecosystems, yet our current understanding of alpine species responses to both ongoing and future global warming is limited. My thesis bridges this gap by investigating the influence of past and future climates on New Zealand’s endemic alpine short-horn grasshoppers (Orthoptera: Acrididae), as representatives of New Zealand’s alpine fauna. As one of the most ubiquitous herbivores in alpine areas worldwide, grasshoppers provide a marvellous lens to examine responses of native systems to increasing temperatures and explore the mechanisms behind such responses. For this, I used an integrative approach combining phylogeographic tools, demographic statistics, phenotypic data (size and shape), niche models and niche metrics, and genotype–phenotype–environment associations. My findings indicate that (1) distinct climatic, biological, and geophysical factors controlled population structuring of grasshopper species during the Pleistocene with a legacy of spatially separate intraspecific lineages; (2) departures from current climatic conditions are projected to vary with geography, and so species exposure and vulnerability to climate change will vary; (3) habitat loss predicted over the next 50 years of warming will lead to smaller and more-fragmented populations with reduced adaptive potential; (4) differences in niche features between diverging intraspecific lineages may lead to lineage-specific responses; (5) distinct climatic factors influence body size clines, and this might strongly influence potential phenotypic responses. An unexpected and important result is that closely related species are predicted to respond in different ways to climate change, suggesting such responses are more evolutionarily labile than conserved. Collectively, this body of research offers valuable insights into the eco-evolutionary responses of alpine organisms to global warming with broad implications for alpine biota everywhere in the world. The thermal environment is a powerful abiotic driver of evolution, and as we face unparalleled rates of warming, understanding how temperature hinder or foster evolution is critical for assisting management decisions that embrace evolutionary resilience.
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    Phylogenomics and evolution of polyploid Azorella (Apiaceae) in New Zealand : 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, 2023) Ning, Weixuan
    Polyploid plants have more than the usual two sets of chromosomes in every cell. Analysing the macroevolutionary patterns of polyploid plants can provide further insight into the mechanisms of polyploidization or whole genome duplication (WGD) in driving species diversification. The polyploid-rich lineage, Azorella, in New Zealand (NZ) has two sections, Schizeilema and Stilbocarpa, with a total of 17 described polyploid taxa (species, subspecies, or varieties) in three known ploidy levels (4x, 6x and 10x). The divergent leaf morphologies and distinct distribution range of polyploid taxa in NZ Azorella makes this lineage an ideal system to investigate the macroevolutionary outcomes of WGD in a polyploid-rich lineage. This thesis aimed to 1) resolve the origins and species relationships of NZ Azorella using phylogenetic inference, and 2) compare the polyploidy-associated genomic, morphological, and ecological traits to understand the post-WGD diversification of Azorella polyploids. In this thesis (Chapter 1), I first reviewed the current phylogenomic approaches for resolving species relationships in groups that have complex evolutionary histories, including polyploidization and reticulation. To resolve the NZ Azorella phylogenetic relationships (Chapter 2), I applied Hyb-Seq of the Angiosperms353 bait set via Illumina sequencing to amplify 353 target-enriched single copy nuclear genes. Additionally, nrDNA and whole chloroplast DNA were recovered via genome-skimming reads to represent high copy genes/regions that are traditionally used in phylogenetics. Hyb-Seq of Angiosperms353 loci was combined with a PacBio sequencing run to improve homeologous gene extraction (Chapter 3). Finally, NZ Azorella post-polyploidization diversification patterns (Chapter 3) were assessed using the variation in genome sizes (via flow cytometry), stomatal guard cell length (using scanning electron microscopy), and ecological niches (using the R package ENMTools). Overall, from biogeographical analyses, I found two independent dispersal events of species in New Zealand Azorella sections Stilbocarpa and Schizeilema, respectively. Using the concordance factors among gene trees and single nucleotide polymorphisms from Hyb-Seq data, as well as the topological incongruence between single copy and high copy gene trees, the results indicated hybrid origins of several hexaploid (6x) species, reticulate relationships among tetraploids, and an allopolyploid origin of the 10x species A. colensoi. Furthermore, different post-polyploidization diversification patterns were compared among Azorella taxa in different ploidy levels, which showed that phylogenetic relationships (i.e., genome content), reticulate evolutionary histories, genomic modification processes (i.e., expansion or contraction), niche shifts, and the age of the polyploid species are all important factors to predict the macroevolutionary patterns of polyploid species.
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    Historical biogeography of marine ray-finned fishes (Actinopterygii) of the Southwest Pacific : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Evolutionary Ecology at Massey University, Auckland, New Zealand
    (Massey University, 2023) Samayoa, André Philippe
    Current environmental and anthropogenic pressures are driving significant biodiversity loss and range shifts in marine environments. Understanding how biodiversity is generated and how it responded to past environmental changes is fundamental to inform future management strategies for marine resources. As the largest ubiquitous taxonomic group among marine vertebrates, ray-finned fishes (Actinopterygii) represent the best model to understand the generation of biodiversity and the processes that shaped contemporary geographic patterns in the sea. In this sense, centers of marine endemism are of evolutionary value as they translate evolutionary and ecological mechanisms that drive biodiversity dynamics. In the Pacific Ocean, endemism centers for marine fishes are mainly located in remote oceanic islands at the periphery of the tropical West Pacific which harbors the highest levels of biodiversity. Biogeographic research suggests that marine fish endemism in the oceanic islands of the Central Pacific originated via multiple independent jump-dispersal colonization events, and that the islands have acted as sources of new unique biodiversity. However, as the evolutionary setting starts to be revealed for marine fish endemism in the Pacific, processes that generate and maintain biodiversity in other peripheral islands remain unknown. My thesis aims to fill this gap by studying the origin, evolution, and processes that have shaped endemism and biodiversity of marine fishes in the Southwest Pacific. I examined the historical biogeography of the region´s marine fish fauna using open-access molecular data to infer evolutionary histories, and geographic distribution information to assess spatial patterns of endemism and biodiversity. Data were analyzed across three research projects based on time-calibrated phylogenies, probabilistic biogeographic modeling, and statistical analysis of phylogenetic measures of endemism and biodiversity. My results confirm the role of the subtropical islands of the Southwest Pacific as sources of new unique biodiversity, identify mainland Australia as the major source of endemic lineages, highlight the significance of jump-dispersal and vicariance in shaping endemism patterns, and reveal that the processes shaping patterns of endemism and biodiversity differ at local scales. My thesis contributes to the understanding of unique contemporary biogeographic patterns in the marine fish fauna of the Southwest Pacific.
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    Convergent evolution of flightlessness in rails (Aves: Rallidae) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Ecology at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Gaspar, Julien
    Different species can independently evolve similar phenotypic traits in response to the same environmental challenges. The resulting convergence of traits shows how environmental circumstances that apply selective pressure on the genomes of different lineages can result in analogous adaptations. A remarkable example of this evolutionary process is the secondary loss of flight in birds which repeatedly occurs in avian diversification. Flightlessness in bird species have been encountered on many oceanic islands and is interpreted as an effect of the insular condition that often provides a habitat with few or no predators, reduced competition for resources, and the opportunity to forage without flying. The rails or Rallidae are an exceptional avian family to study the evolution of flightlessness as among the 130 extant species, 30 have independently lost the ability to fly. In this research, genomic and morphological data were integrated to compare traits of volant and flightless species in a phylogenetic context and to investigate the evolutionary processes involved in the loss of flight. First, morphological and phylogenetic data were used to compare species with and without the ability to fly in order to determine whether major phenotypic effects of the transition from volant to flightless are shared among lineages. Second, genome assemblies were generated for representatives of four rails: two volant and two flightless species. Then, a genome-wide comparison of coding regions from volant and flightless rails was performed to detect genetic regions associated with the flightless trait. The newly assembled and annotated genomes showed differences in heterozygosity between flightless and volant species with lower heterozygosity in flightless species that probably reflects their relatively small populations. I found statistical support for similar morphological responses among unrelated flightless lineages, characterised by a shift in energy allocation from the forelimbs to the hindlimbs. Flightless birds exhibited smaller sterna and wings than volant taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests showed that those differences were independent of phylogeny and instead demonstrated convergent morphological adaptation associated with a walking ecology. Evidence of different selective pressures between species with and without the ability to fly was detected in hundreds of genes. This included relaxed, intensified, and positive selection in flightless species as well as evolutionary rate differences of genes in volant and flightless taxa and proteins carrying function-altering amino acid changes in the flightless rails. Genes associated with flightlessness were enriched in biological functions that aligned well with the ability to fly such as muscle, bone, limb, and heart development. However, other enriched functions were not directly linked to flying and may result from the ecological consequences of flightlessness; these included the immune system, renal functions, lipid metabolic system, cognition, and the sensory system. Finally, many genes under selective pressures in flightless species were involved in gene regulation and post-translational modification. This suggests that genetic adaptations to flightlessness are not only found in important developmental genes but also in patterns of gene expression and protein modifications. This study presents reliable methods to generate genomic data and to use it to assess the selective pressures involved in a convergent phenotype.
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    Chloroplast genome evolution in New Zealand mycoheterotrophic Orchidaceae : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Manawatu, New Zealand
    (Massey University, 2019) Murray, Katherine Jane Hope
    The plastid genomes, or plastomes, of most photosynthetic land plants are highly similar. In contrast, those of non-photosynthetic, heterotrophic land plants are often reduced in both size and gene content. The apparent degradation of mycoheterotrophic plant plastomes has been attributed to a functionally-driven stepwise pattern of loss. However, the number of complete plastome sequences available for mycoheterotrophic plants is small and taxonomic coverage is biased. In this thesis, the plastomes of two mycoheterotrophic orchid species endemic to New Zealand, Corybas cryptanthus Hatch (Diurideae) and Danhatchia australis Garay & Christenson (Goodyerinae), as well as those of an albino and several photosynthetic representatives of Corybas are reported. Beyond increasing the number of mycoheterotrophic plastomes available for evaluating broad hypotheses about plastome evolution in non-photosynthetic plants, these data also provide insights into two little studied aspects of plastome evolution in mycoheterotrophs; intraspecific variation in the plastomes of mycoheterotrophs and the differences between mycoheterotrophs and their closest photosynthetic relatives. The plastomes of C. cryptanthus and D. australis differ in the extent to which they are degraded. Perhaps unexpectedly, the plastome of C. cryptanthus, which has close photosynthetic relatives and therefore is likely to have arisen more recently than the taxonomically isolated D. australis, is more reduced. Specifically, the plastomes of C. cryptanthus are approximately half the size and have half the gene content of the other Corybas sequenced whereas the plastome of D. australis is similar to those available for photosynthetic relatives. This contrast may reflect underlying differences between the two genera; the photosynthetic relatives of D. australis have plastomes containing NADH dehydrogenase (ndh) genes whereas those of photosynthetic Corybas have lost their ndh genes and their small single copy regions are highly reduced. These features may have predisposed the ancestor of C. cryptanthus to rapid genome degradation. Finally, observations on these results strongly suggest that plastome degradation follows, rather than precedes, the shift to mycoheterotrophy.
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    Evolution of the spherical cell shape in bacteria : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Albany, New Zealand
    (Massey University, 2019) Yulo, Paul Richard Jesena
    Cell shape is an important feature of bacterial cells. It is involved in critical aspects of bacterial cell biology such as motility, growth, and the evasion of predators. Despite this, how cell shape has evolved in bacteria is unclear. For most rod-shaped bacteria, the maintenance of cell shape depends primarily on the bacterial actin-like protein, MreB. In this study, we show that the deletion of MreB from the rod-shaped model organism Pseudomonas fluorescens SBW25 results in the formation of aberrant spherical cells that have increased size and reduced fitness. This new MreB-null strain (ΔmreB) is susceptible to mechanical damage and grows poorly due to cell division defects. Furthermore, synthesized peptidoglycan (PG) chains were shorter and cell wall assembly was disorganised in this strain. A 1,000-generation evolution experiment comprised of multiple independent lineages produced spherical cells that have a reduced cell size and improved fitness. Mutations in the PG synthesis protein PBP1a were found across multiple lineages. Genetic reconstructions demonstrated that these mutations have a loss-of-function effect that reduced PG cross-linking and restored the ordered assembly of the cell wall, thereby reducing cell size and improving fitness in MreB-null cells. In one lineage, a five-gene deletion that included the gene coding for the outer membrane channel OprD was found to be beneficial. This deletion reduced cell size, improved fitness, and restored orderly cell wall construction. The mechanism responsible for this is unknown, but it may be related to modifications in septum localisation via the Min system. Finally, we show using phylogenetic analysis that PBP loss is a general trend in bacteria that evolved to become spherical, hinting at a plausible strategy for the evolution of the spherical cell shape from rod-shaped progenitors.
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    The dominance of the physicalist-reductionist approach to the study of consciousness and its evolution : the case for a non-physicalist paradigm : a thesis presented in partial fulfilment of the requirements for the degree of Master of Arts in Psychology at Massey University
    (Massey University, 1992) Jackson, Peter Anthony
    In this thesis it is argued that the dominant physicalist-reductionist view in psychology has hindered the study of consciousness and its evolution. The thesis begins with an overview of the physicalist-reductionist position, from a philosophical viewpoint. The weakness of this position is exposed in that matter can be viewed not as a physical substance, but as the derivative of a non-physical realm. This is argued by using the theory of David Bohm, who postulated the existence of an implicate order (hidden from the senses) and an explicate order (the sensory realm). Bohm's reasoning is explored and justified, where his theory is shown to be the way to reconciling the difficulties faced by quantum mechanics and relativity theory. Using Bohm's implicate-explicate notion as a basis, an implicate-explicate model of the evolution of consciousness is developed. This model is able to deal with biological evolutionary factors, and not simply with the evolution of consciousness. This is because the model assumes that biological forms evolved as a result of the interaction between the implicate and explicate orders. In this model, evolution is seen as the unfolding of what lies implicate, which then becomes explicate. The earliest stages of this unfolding were automatic, and led to increasingly complex physical, chemical, then biological structures. A stage was reached where biological structures gave rise to sufficiently complex neural structures which, in turn, permitted consciousness to appear. In this model, consciousness is a very high order explicate of a special region within the implicate order, which is called Mind. Thus, the evolution of consciousness is the result of the unfolding of Mind. The model shows that consciousness is an active factor in the further evolution of biological forms. The notion of consciousness is explored and a variety of theories of consciousness are reviewed and critiqued, where these are examined in the light of the implicate-explicate model. This model is then used to explore the way consciousness evolves through the infrahuman life forms to the human form. Palaeoanthropological evidence is used to justify the claim that consciousness has evolved, with a special focus on primate evolution, and on the critical phase of transition from proto-human to truly human consciousness. In this, the acquisition of speech is seen as crucial, where the implicate-explicate model offers an explanation for this acquisition. The notion of psychological paradigms is explored, and a set of paradigms delineated, where these are located along a spectrum of the relevance of consciousness to any given paradigm. The relevance spectrum is related to the implicate-explicate model as a metaparadigm. This is used to reveal the strengths and limitations of the various paradigms. The implicate-explicate model shows that present­ day humans have reached an impasse in the evolution of their consciousness. A means to overcoming this is suggested, and the next stage in the evolution of consciousness that might arise is speculated upon.
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    Investigating the evolutionary changes in Crabtree-negative yeasts during a long-term evolution experiment : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Albany, New Zealand
    (Massey University, 2017) Morley, Annabel
    The Crabtree effect is a metabolic strategy that allows yeast to ferment in the presence of oxygen. This is of interest as not all yeasts display this strategy, and nearly 100 years after its discovery it is still unclear what the overall benefit is. Two key theories attempt to explain the emergence of this phenomenon, the make-accumulate-consume theory and the rate/yield trade-off theory. The aim of this thesis was to investigate whether a trade-off between rate and yield develops in Crabtree-negative yeasts over the course of 1500 generations in a high sugar environment. Chapter Two demonstrates that growth rate is more likely to increase than decrease while growth yield is more likely to decrease than increase in the isolate-derived populations of yeast. We find that species that started out relatively fast, changed little while the slower species had more significant gains in growth rate. With growth yield, the species with initially high yield lost more significantly than the already low yield species. This could suggest there is an overall optimum growth rate and growth yield, that the species are evolving towards. In Chapter Three, ethanol production was measured using colorimetric tests and no change was observed to support the development of the Crabtree effect in these populations after 1500 generations. In Chapter Four growth yield was investigated using flow cytometry and it was found that several yeast populations both increased in cell size and decreased in growth yield. This is an interesting observation that has been observed in several previous experimental evolution experiments. In Chapter Five, as cell size is often associated with ploidy changes, DNA content was measured using DAPI and SYTOX DNA stains, detected by flow cytometry. This did not provide any statistically significant conclusions but highlighted the importance of employing further techniques to analyse the DNA content of these populations. This thesis has illustrated the importance of studying the competitive behaviours of microorganisms in isolation, where selfish traits appear to thrive.
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    Evolutionary lineages and the diversity of New Zealand true whelks : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Biology at Massey University, Manawatū Campus, New Zealand
    (Massey University, 2017) Vaux, Felix
    Biological evolution fundamentally operates according to the basic principles of variation, heritability and selection, but it generates the astounding complexity of nature. One of the greatest challenges for evolutionary study is the interpretation of this diversity, and the ability to identify and communicate the underlying biological changes that are responsible. In this thesis, I consider the identification of evolutionary lineages using molecular and morphological data. I address the problem of confusing terminology regarding the evolutionary process, focussing on the concepts of anagenesis and cladogenesis, and the challenge of genetic introgression for taxonomic classification. I investigate molecular and morphological variation in New Zealand true whelks. There are many species of true whelks described, however their taxonomy is mostly restricted to the traditional examination of shell traits. Evolutionary relationships of true whelks inferred from DNA sequences indicate that neither New Zealand nor Southern Hemisphere true whelks are monophyletic, contradicting taxonomic hypotheses and expectations of geographic isolation. I focus on the siphon whelk genus Penion Fischer, 1884, a diverse genus with extant species restricted to New Zealand and Australia. All extant species are genetically sampled for phylogenetic and allelic variation analysis. A monophyletic clade is identified for New Zealand Penion. Results suggest the existence of a new species and indicate evolutionary relationships for some taxa not captured by the taxonomy. Shell shape and size are studied using geometric morphometric analyses, confirming that these traits can distinguish taxa divided by deep evolutionary splits under both informed and naïve analyses. Morphometric variation is hierarchical, with closely related taxa being grouped together within large datasets including samples from multiple evolutionary lineages. Overall, morphometric results show reasonably strong concordance with molecular evidence. Evolutionary lineages in the fossil record are investigated using morphometric analysis within the context of previous molecular and morphometric findings. Results assist with the identification of fossils from two localities and suggest that multiple extinct species of Penion are misclassified. Variation in morphometric traits through time is fitted to models of evolutionary change, and results indicate that the identification and selection of a lineage has a significant impact upon those results. Keywords anagenesis; benthic; Buccinidae; Buccinulidae; Buccinioidea; Caenogastropoda; cladogenesis; deep sea; dispersal; developmental biology; endemism; evolution; evolutionary biology; evolutionary lineage; evolutionary rate; divergence; diversity; fossil; gastropod; geometric morphometrics; high-throughput sequencing; hybridisation; introgression; lineage split; marine snail; mitochondrial DNA; mollusc; monophyly; morphology; Neogastropoda; next-generation sequencing; nuclear DNA; palaeontology; paraphyly; phylogenetics; RADseq; ribosomal DNA; sexual dimorphism; shell; siphon whelk; snail; speciation; species; systematics; taxonomy; whelk; zoology
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    Transmission and evolution of bacteria during the course of enteritis outbreaks : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy, Massey University, Palmerston North, New Zealand
    (Massey University, 2017) Bloomfield, Samuel
    Bacterial enteritis outbreaks are a worldwide problem. They are hard to investigate as the bacterial agents are often associated with multiple sources, closely-related bacteria often co-colonise these sources, highly discriminatory tests are often required to distinguish between these bacteria, and bacteria are continuously evolving, changing how they behave. In this thesis I investigated the transmission and evolution of bacteria over the course of enteritis outbreaks by integrating genomic, phenotypic and antibiotic susceptibility testing, and phylogenetic modelling in four studies. The aim of the first study was to investigate the origin, evolution and transmission of Salmonella enterica serovar Typhimurium DT160 over a 14-year long outbreak in New Zealand. Genomic analysis of 109 DT160 isolates collected over this timeframe established that the DT160 strain was introduced into New Zealand approximately a year before the first human isolate was reported; there were frequent transmissions between the source groups investigated (human, wild bird, poultry and bovine); and there was no evidence of specific selective pressures imposed on DT160. This study demonstrated how genomic analyses can be used to investigate extended outbreaks of bacterial diseases. The aim of the second study was to investigate whether two ancestral state reconstruction models (the discrete trait analysis and structured coalescent models) were applicable to salmonellosis outbreak investigations. Both models were used to estimate transmission and population parameters of simulated salmonellosis outbreaks. Comparisons between the models' estimates and the true transmission and population values for the simulations revealed that both models made assumptions that did not apply to outbreaks and prevented them from accurately predicting these parameters. This study highlighted the need for outbreak-specific phylogenetic transmission models. The aim of the third study was to investigate the relationship between two strains of Salmonella that were the predominant causes of human salmonellosis in New Zealand in the 2000s (S. Typhimurium DT160 and S. Typhimurium DT56 variant), and identify potential reasons for one strain declining (DT160) as the other emerged (DT56 variant). This study demonstrated how genomic analyses can be used to compare Salmonella strains and identify genetic elements that may influence strain behaviour. The aim of the fourth study was to investigate a patient that had presented excreting the same genotype of Campylobacter, C. jejuni ST45, on multiple occasions over a 10-year period. Genomic analyses, pheno-typic testing and antimicrobial susceptibility testing of sixteen Campylobacter isolates collected from the patient found that the patient was persistently colonised with Campylobacter over this period, and that the Campylobacter had adapted to long-term colonisation by altering its motily and developing resistance to the antibiotics the patient had been prescribed. This study demonstrated how genomic analyses can be used to investigate a patient's infection history. These studies demonstrated the applicability and limitations of genomic analyses when investigating bacterial enteritis outbreaks, how genetics and the environment influence bacterial evolution, and highlighted areas in the fields of microbiology, phylogenetics, epidemiology and public health that require further research.