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Evolution of cytonuclear coordination in Tragopogon (Asteraceae) allopolyploids : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatu, New Zealand
(Massey University, 2023) Hussain, Sidra
Cytonuclear coordination is an important aspect in plant evolution which involves the synchronized interactions between nuclear and organellar genomes. Allopolyploidy, resulting from interspecific hybridization and genome duplication, could result in cytonuclear incompatibilities. Therefore, to coordinate cytonuclear interactions, allopolyploids may undergo alterations in duplicated nuclear gene expression via incorporating maternally biased expression patterns. To investigate cytonuclear responses to allopolyploidy, in this study, expression patterns of duplicated nuclear genes and their organelle counterparts, implicated in cytonuclear enzyme complexes, as well as dual-targeted genes were investigated in the reciprocally formed young T. miscellus allopolyploids (90-100 years) and diploid parent species; T. dubius and T. pratensis. In addition, the effect of polyploidy on morphological traits of T. miscellus allopolyploids were examined and assessed relative to parent species. The expression data showed that T. miscellus allopolyploids are regulating expression at the homeolog level, primarily through T. pratensis bias, while maintaining the total gene expression levels as to parental levels. The morphological evaluation of allopolyploids and diploids demonstrated that both reciprocal forms of T. miscellus have significantly longer, but fewer leaves compared to the diploid parent species. These findings reflect that young T. miscellus allopolyploids are certainly undergoing homeolog expression regulation to accommodate cytonuclear interactions as well as displaying morphological responses to allopolyploidy. This study provides insights into polyploid genome evolution and contributes to further understanding of the cytonuclear coordination in allopolyploids.
Exploring the origins of multicellularity using experimental populations of Pseudomonas fluorescens SBW25 : deciphering the genetic basis of an environmentally-responsive developmental switch : a thesis presented in partial fulfillment of the requirements for the degree of Master of Natural Sciences at Massey University, Auckland, New Zealand
(Massey University, 2018) Summers, Joanna Ameila
The evolution of multicellularity was a significant evolutionary event that occurred on numerous independent occasions in the history of life. It is useful to consider this in the Darwinian population framework: a population may participate in evolution by natural selection given that it satisfies the criteria of – variation, reproduction, and heredity. The transition from unicellular to multicellular life represented the emergence of Darwinian properties at a new hierarchical level, and the shift of Darwinian individuality from the level of the individual cell to the cooperating cell collective. This required a mechanism of reproduction of the collective; best conceived with nascent multicellular life cycles, likely manifest through clonal development and single-cell bottlenecks to mediate conflict between levels of selection. For the origin of multicellularity, transitioning between phases of the life cycle was also dependent on the evolution of developmental processes that integrate the activity of the individual cells and the collective. An experiment previously conducted in the Rainey laboratory explored the origins of multicellularity using Pseudomonas fluorescens SBW25, selecting for the evolution of a developmental program to transition between the soma-like SM and germ-like WS phases of the life cycle. Derived from this experiment was the TSS-f6 genotype, that demonstrates an environmentally-responsive capacity to change phenotype – resembling a primitive multicellular organism able to transition through the life cycle under developmental regulation. Whole-genome sequencing revealed the mutational history of TSS-f6, with a substitution in the wspA gene necessary for the phenotype; the WspA chemoreceptor hypothesised to sense environmental oxygen. Suppressor analysis of the TSS-f6 phenotype revealed the underlying activation pathways: for the WS phenotype – the wsp & wss operons, and mut genes; and the SM phenotype – pflu5960, amrZ, and wspE. From this genetic dissection a simple model was proposed for the TSS-f6 developmental switch, though the role of wspE and the DNA mismatch repair system remain unexplained. The TSS-f6 genotype provided the opportunity to gain mechanistic insight into the emergence of a nascent life cycle under the control of a developmental program, and thus the origins of multicellularity and development in itself.
Modeling RNA evolution : in-silico and in-vivo : a thesis presented for the degree of Master of Science in BioMathematics at Massey University, Palmerston North, New Zealand
(Massey University, 2004) Matheson, James William
We look at two aspects of the evolution of RNA. First we look at RNA replication dynamics in an early RNA world context. Experimental evidence (Spiegelman et al. 1965, Biebricher et al. 1981) shows that under some conditions RNA evolves towards small quickly replicating molecules. We investigate what conditions are sufficient for a population of RNA molecules to evolve towards a balanced population of molecules. This is a population not completely dominated by a single length of molecule. We consider two models: A linear model in which indel rate is inversely proportional to length and a game theory model in which reproductive efficiency depends on the distribution of molecule lengths within a population (this is linked to catalytic efficiency). Models are investigated using analytic, numerical and simulation methods. The linear model is not sufficient to support a population with balanced length distribution. Simulation methods show that the game theory model may support such a population. We next look at RNA evolution in the context of RNA virus evolution. Using virus samples taken over a thirty year period we investigate the evolution of Respiratory Syncytial Virus (RSV) in New Zealand. RSV most strongly affects infants and the elderly, causing cold like symptoms in mild cases and bronchiolitis or occasionally death in severe cases. New Zealand has a higher incidence of RSV bronchiolitis per head of population than many other developed countries. We compare New Zealand strains of the virus to those isolated overseas to investigate if New Zealand may have significantly different strains. We look at the evolution of the virus within New Zealand looking for evidence of antigenic drift, as well as analysing substitution rates and selection at individual codon sites. No evidence is found to suggest that New Zealand has significantly different strains of RSV from other countries. We conclude the higher rate of severe RSV in New Zealand must be caused by factors other than virus strain. The portion of the virus analysed shows strong evidence of being under positive selective pressure. This and other analyses suggest that RSV may be undergoing antigenic drift.
The ecological genetics of Pseudomonas syringae in the kiwifruit phyllosphere : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Evolutionary Genetics, New Zealand Institute for Advanced Study at Massey University, Auckland, New Zealand
(Massey University, 2017) Straub, Christina
The impact of disease-causing bacteria on their hosts is shaped by interactions with co-occurring microbes, but such interactions are rarely studied. Pseudomonas syringae is a ubiquitous and significant plant pathogen infecting a wide range of plants, often of agricultural importance. The community context of P. syringae in infected plant hosts has been little explored. I determined the population structure and genetic diversity of Pseudomonas syringae strains collected from infected and uninfected orchards over the course of a growing season during the current outbreak of bacterial canker of kiwifruit (P. syringae pv. actinidiae, Psa) in New Zealand. A total of 148 strains comprising Phylogroups 1, 2, 3 and 5 were characterised by Multi Locus Sequence Typing (MLST). The overall population structure was clonal, but with a low level of recombination for single housekeeping genes within phylogroups. More than half of the isolates belonged to a new Phylogroup 3 clade (PG3a) that was also commonly found on kiwifruit leaves in China and previously reported from kiwifruit leaves in Japan. To understand the ecological basis of the co-occurrence of PG3a and PG1 (Psa) I looked for evidence of niche specialisation by performing reciprocal invasion from rare assays of a selected representative from each lineage both in vitro and in planta. P. syringae G33C (PG3a) demonstrates antagonistic behaviour towards Psa NZ54, whereas Psa NZ54 exhibits a beneficial effect on growth of P. syringae G33C; an effect that could not be attributed to virulence activity encoded by the Type 3 Secretion System. Given this antagonistic behaviour, I explored the virulence repertoire in these commensal strains to determine their potential in the emergence of future more virulent types of Psa. In addition, I used comparative genomics to unravel the phylogenetic resolution of the novel P. syringae clade in context with known representatives of P. syringae PG3. Together my data draw attention to the community context of disease and demonstrate the value of incorporating an ecological dimension into the study of the genetic structure of pathogen populations.
Beyond BLASTing : ribonucleoprotein evolution via structural prediction and ancestral sequence reconstruction
(Massey University, 2016) Daly, Toni K
Primary homology in DNA and protein sequence has long been used to infer a relationship between similar sequences. However gene sequence, and thus protein sequence, can change over time. In evolutionary biology that time can be millions of years and related sequences may become unrecognisable via primary homology. This is demonstrated most effectively in chapter 4a (figure 10). Conversely the number of possible folds that proteins can adopt is limited by the attractions between residues and therefore the number of possible folds is not infinite. This means that folds may arise via convergence between evolutionarily unrelated DNA sequences. This thesis aims to look at a process to will wring more information from the primary protein sequence than is usually used and finds other factors that can support or refute the placement of a protein sequence within the family in question. Two quite different proteins; the Major Vault Protein whose monomers make up the enigmatic vault particle and the argonaute family of proteins (AGO and PIWI) that appear to have a major hand in quelling parasitic nucleic acid and control of endogenous gene expression, are used to demonstrate the flexibility of the workflow. Principally the method relies on prediction of three-dimensional structure. This requires at least a partially solved crystal structure but once one exists this method should be suitable for any protein. Whole genome sequencing is now a routine practice but annotation of the resultant sequence lags behind for lack of skilled personnel. Automated pipeline data does a good job in annotating close homologs but more effort is needed for correct annotation of the exponentially growing data bank of uncharacterised (and wrongly characterised) proteins. Lastly, in deference to budding biologists the world over, I have tried to find free stable software that can be used on an ordinary personal computer and by a researcher with minimal computer literacy to help with this task.
Microsatellite evolution and population genetics of ancient and living Adélie penguins in Antarctica : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University
(Massey University, 2001) Shepherd, Lara Dawn
Microsatellites are widely used as genetic markers for examining a variety of biological questions. Despite their widespread use, little is known about the processes by which they evolve. An accurate understanding of these processes is essential for their correct use as population genetic markers. In this study, microsatellite loci from both living and cryopreserved (AMS 14C dated at up to 6424 years BP ±80) Antarctic Adélie penguins (Pygoscelis adeliae) were examined in order to gain insights into temporal population genetics and the evolution of microsatellite loci. Firstly, ancient DNA extracted from Adélie penguin subfossil bones was found to be extremely well-preserved and readily allowed the amplification of single-copy nuclear microsatellite DNA. Genotyping six microsatellite loci in ancient and living samples from three populations of Adélie penguins in the Terra Nova Bay region allowed a comparison of genetic change over time. Although the ancient sample sizes were limiting, several statistical tests indicated that the ancient and living populations from Inexpressible Island were genetically distinct. In addition, differentiation was also inferred between the three ancient populations that were examined, which is in contrast to the lack of differentiation found between the living populations. These genetic changes may be a result of population expansion out of ice-age refugia since the Last Glacial Maximum. To study microsatellite evolution over a substantial time period, up to 500 living and 100 cryopreserved Adélie penguins were genotyped at six microsatellite loci. No novel electromorph alleles were detected in the ancient samples. Numerous alleles were sequenced from four of these loci in both Adélie penguins and several other species of penguin (Spheniscidae). Analysis of these sequences provided an insight into the mutational processes occurring at these loci. In particular, these allele sequences revealed extensive size homoplasy, both within Adélie penguins and between penguin species. At one locus, variation in the flanking region allowed discrimination between the mechanisms proposed for length change at microsatellite loci. Slippage was the most plausible mechanism for length change. In this same locus, instability was observed in the region bordering the repeat tract with a transversional bias predominating. This bias may be a caused by inaccurate DNA replication resulting from structural features of DNA.
Plastid genes across the Great Divide : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Genetics/Bioinformatics, Institute of Fundamental Sciences, Massey University, Manawatu, New Zealand
(Massey University, 2014) Cox, Simon James Lethbridge
Nearly all life that is visible to the naked eye is arguably a direct consequence of one or both endosymbiotic events that took place early in evolution and eventually resulted in the mitochondrion and the chloroplast. The timing of the mitochondrial endosymbiotic event weighs argument around the nature of LUCA (Last Universal Common Ancestor) being complex or simple and challenge the commonly taught view of bacteria being the first kingdom to emerge from the primordial state. The ancient metabolic pathways of amino acid and vitamin biosynthesis are examined and Ancestral Sequences constructed in order to discover the endosymbiotic signature within the nucleus of eukaryotes. Cyanobacterial and plant enzymes from these pathways are tracked as they cross from a prokaryotic coding environment to a eukaryotic one. If the eukaryote that took up the chloroplast ancestor was heterotrophic then it probably got some of its co-factors (vitamins) and essential amino acids from its diet. However, in order to become autotrophic it would have to be able to synthesise these amino acids and co-factors directly. The most likely source of these elements would have been the cyanobacterium; therefore cyanobacterial homologs should be found in the nuclear genome of plants. Ancestral Sequence Reconstruction (ASR) had a negligible effect on uncovering deeper endosymbiotic homologs. However ASR did confirm ancestral convergence between chloroplast and cyanobacterial homologs and between eukaryote nuclear genes and their cyanobacterial counterparts for vitamin and amino acid biosynthetic pathways. The results, all significant, show that the convergence is much stronger between organisms from the same coding environment (prokaryote [chloroplast] versus prokaryote [cyanobacteria]) than from different coding environments (eukaryote [nuclear] versus prokaryote [cyanobacteria]).
Molecular studies on the New Zealand tree ferns : a thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Palmerston North, New Zealand
(Massey University, 2001) Lewis, Robbie
Molecular phylogenetic studies have been performed on the New Zealand tree fern genera Alsophila, Dicksonia and Sphaeropteris, using DNA sequencing techniques and Amplified Fragment Length Polymorphism (AFLP). Three DNA sequence markers were used, two chloroplast: rbcL, trnL-trnF spacer, and one nuclear: 188. Using a combination of rbcL sequences obtained in this study and previously published sequences from GenBank an overall phylogeny for the tree fern clade is proposed. This phylogeny suggests that the currently recognised families may need revision. Phylogenetic analysis of molecular markers in Dicksonia suggests a three way genetic split within the genus, which corresponds, to three observed spore morphologies. AFLP studies on populations of Dicksonia lanata, which possesses two distinct growth forms, shows evidence of a weak genetic split, although probably not sufficient to warrant the separation of two species. Studies on the Cyatheaceae genera Alsophila and Sphaeropteris have confirmed observations on the evolution of the New Zealand species based on morphology, and have also suggested a heretofore unknown relationship between the South American fern genus Hymenophyllopsis and the Cyatheaceae.
Formalist features determining the tempo and mode of evolution in Pseudomonas fluorescens SBW25 : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Evolutionary Genetics at Massey University, Auckland, New Zealand
(Massey University, 2015) Farr, Andrew David
In order to explain the adaptive process, it is necessary to understand the generation of heritable phenotypic variation. For much of the history of evolutionary biology, the production of phenotypic variation was believed to be unbiased, and adaptation the primary outcome of selection acting on randomly generated variation (mutation). While true, ‘internal’ features of organisms may also play a role by increasing the rate of mutation at specific loci, or rendering certain genes better able to translate mutation into phenotypic variation. This thesis, using a bacterial model system, demonstrates how these internal features – localised mutation rates and genetic architectures – can influence the production of phenotypic variation. Previous work involving the bacterium Pseudomonas fluorescens SBW25 has shown that mutations at three loci, wsp, aws and mws, can cause the adaptive wrinkly spreader (WS) phenotype. For each locus, the causal mutations are primarily in negative regulators of di-guanylate cyclase (DGC) activity, which readily convert mutation into the WS phenotype. Mutations causing WS at other loci were predicted to arise, but to do so with less frequent types of mutation. The data presented in this thesis confirms this prediction. My work began with the identification and characterisation of a single rare WS-causing mutation: an in-frame deletion that generates a translational fusion of genes fadA and fwsR. The fusion couples a DGC (encoded by fwsR) to a membrane-spanning domain (encoded by fadA) causing relocalisation of the DGC to the cell membrane and the WS phenotype. This is one of the few examples of adaptation caused by gene fusion and protein relocation in a realtime evolution experiment. I next took an experimental evolution approach to isolate further rare WS types and characterized these, revealing a range of rarely taken mutational pathways to WS. Lastly, I describe an example of extreme molecular parallelism, in which a cell chaining phenotype is caused – without exception – by a single nucleotide substitution within the gene nlpD, despite multiple mutational pathways to this phenotype. Characterisation of different nlpD mutants suggests this molecular parallelism is caused by a high local mutation rate, possibly related to the initiation of transcription within this gene.
Polyploid genome evolution : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
(Massey University, 2014) Sehrish, Tina
Genome duplication is a major force influencing plant genome evolution. Many plant species have shown multiple rounds of whole genome duplications in the past. Duplicated genes show variable rate of retention, silencing, subfunctionalization and neofunctionalization which are pronounced outcomes of genome duplication. This thesis addresses polyploid genome evolution focusing on the genetic and epigenetic consequences of genome duplication. Tragopogon dubius, T. pratensis and T. porrifolius (diploid progenitors) and their polyploids T. miscellus and T. mirus were employed as an ideal system to examine the outcomes of polyploidy. An investigation of cytonuclear coordination in T. miscellus polyploids showed a maternal influence which was evident from the biased retention and expression of the maternally inherited homeolog of rbcS possibly to facilitate its interaction with the maternally derived rbcL in independently formed T. miscellus natural polyploids. The second study involved the genetic characterization of synthetic T. miscellus and T. mirus polyploids in the context of their relationship with each other. Results showed the presence of the same multilocus genotypes reported previously in natural T. miscellus and T. mirus and also suggested that there are certain genetic rules to the formation of polyploids; that is, only some progenitor genotypes are successful in producing polyploids. In the third study, a comparative transcriptome analysis of the reciprocally formed synthetic and natural T. miscellus polyploids was conducted. This study demonstrated additivity in the expression of progenitor orthologs of floral identity genes in reciprocally formed T. miscellus polyploids, suggesting other genetic factors are responsible for the differing inflorescence and flora morphologies in T. miscellus. The fourth study explored the epigenetic consequences of polyploidy. The DNA methylation status of homeologous loci previously reported to be silenced in T. miscellus natural polyploids was investigated. This study revealed silencing of two out of five homeologous loci by DNA methylation, suggesting other mechanisms may be responsible for silencing of the remaining three homeologous loci. In short, collectively these studies significantly contribute to our knowledge of polyploid genome evolution in Tragopogon in particular and in plants in general.

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