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Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - May 2021)
Sexual and asexual organisms exhibit a wide variety of biological differences that can impact their ecological and evolutionary trajectories. One result of these differences is that closely related sexual and asexual taxa often exhibit range divergence, with asexuals typically having larger geographic ranges and being found at higher latitudes and elevations. This pattern, termed “geographical parthenogenesis”, has been documented in numerous plant and animal systems and a variety of potential mechanisms have been proposed. Hypotheses relate to differences in reproductive assurance (asexuals can reproduce without mates, while most sexuals require mates), genetic consequences of sexuality vs asexuality, selection on clonal lineages, ecological impacts of sexuality and asexuality, and demographic differences between reproductive modes. In this thesis, I explore several of these potential drivers of geographical parthenogenesis in Townsendia hookeri, a subalpine perennial flowering plant in the Asteraceae that has diploid sexual and polyploid apomictic (reproducing asexually through seed) forms with divergent but overlapping ranges. Population genomic analyses of apomicts in T. hookeri revealed largely monoclonal populations and geographically widespread clones, suggesting that apomictic range expansion may have been aided by “general-purpose genotypes” that can withstand an array of environmental conditions. Results from a large-scale, multi-year reciprocal transplant garden experiment showed that sexual populations had comparable performance when planted into the apomictic range as into their own, but that fitness of apomictic individuals generally declined in sexual regions. This provides evidence that while sexuals are likely limited by dispersal (they cannot reach suitable habitat outside of their current range), apomicts are not well adapted to the ecological conditions (biotic and/or abiotic) in the sexual range. When comparing early life history traits between sexuals and apomicts, apomicts were found to have increased germination success and improved seed dispersal traits in comparison to sexuals. These traits are expected to have given apomicts a colonization advantage, which (along with reproductive assurance) has likely contributed to their increased range size. Overall, the work presented in this thesis highlights the intricate nature of geographical parthenogenesis in Townsendia hookeri, and underscores the need to investigate complex biological phenomena using a diverse suite of approaches.
Antennaria and Symphyotrichum represent two of the most taxonomically complex genera of the family Asteraceae in North America. Extensive hybridization and polyploidy contribute to many of the taxonomic difficulties encountered within both genera, and in Antennaria these are compounded by the presence of widespread apomixis. This suite of factors has contributed to considerable taxonomic uncertainty in these genera, particularly in the Pacific Northwest where they are both diverse and understudied. This study uses a traditional, specimen-based alpha-taxonomic methodology to investigate the taxonomy of these two genera within the western Canadian province of British Columbia. It uses both a detailed review of existing herbarium collections from within the region of interest, as well as a comprehensive review of existing taxonomic and floristic literature pertaining to these genera, to provide a taxonomic framework that is better representative of these genera in British Columbia. This study provides clarification on a number of unresolved taxonomic and floristic uncertainties, including the incorrect application of nomenclature, poorly defined species limits, incomplete or erroneous morphological circumscriptions, incorrect geographic distributions, and inadequate identification criteria. Several taxa that had not previously been recognized formally in the region, both native and exotic, are documented here and provided a full accounting of their occurrence. It also provides the first comprehensive summary of putative hybrids within these genera in the Pacific Northwest. Dichotomous keys for the identification of taxa within these genera in British Columbia were developed that capture new developments that have resulted from this study. Finally, the importance of taxonomy to the biological sciences is elucidated in the context of this study, and perspectives on the Taxonomic Impediment and the relationship between academia and taxonomy are detailed and discussed.
Vaccinium corymbosum (highbush blueberry) is and economically important crop in British Columbia and suffers from inconsistent and often inadequate pollination by the managed pollinator, the honeybee. The outcrossing strategy of blueberry requires a pollen vector; however honeybees are inefficient and choosey. One goal of this research was to investigate the variable attractiveness of blueberry flowers to pollinators, specifically focusing on odour, and the possibilities for improved pollination. Highbush blueberry flowers emit a wide range of volatile compounds that show heritability in the broad-sense. However, determining which compounds are important to pollinators is a challenging task and remains poorly understood. Pollinator choice was examined through monitoring of pollinators as well as determination of pollen movement through paternity analysis. There was no agreement between the analyses, which show that the genotypes Duke and Reka appear to attract more pollinators but the most common fathers are Bluecrop and Elliott. A second goal of this research was to examine reproductive success; and the discrepancy between attraction and reproduction could be due in part to the range in fertility observed among highbush blueberry genotypes. Inbreeding depression due to the use of a narrow breeding pool to develop genotypes is a potential cause of the observed range in fertility and offspring vigour. The degree to which inbreeding will increase homozygosity depends on the inheritance pattern of the tetraploid highbush blueberry; however, the current levels of inbreeding limit an accurate description of the inheritance pattern.
In this thesis, I investigate several aspects of life cycle evolution using mathematical models. (1) We expect natural selection to favour organisms that reproduce as often and as quickly as possible. However, many species delay development unless particular environments or rare disturbance events occur. I use models to ask when delayed development (e.g., seed dormancy) in long-lived species can be favoured by selection. I find that long-lived plants experience `immaturity risk': the risk of death due to a population-scale disturbance, such as a fire, before reproducing. This risk can be sufficient to favour germination in the disturbance years only. I show how demographic models can be constructed in order to estimate the contribution of this mechanism (and two other mechanisms) to the evolution of dormancy in a particular environment. (2) All sexually reproducing eukaryotes alternate between haploid and diploid phases. However, selection may not occur in both phases to the same extent. I use models to investigate the evolution of the time spent in haploid versus diploid phases. The presence of a homologous gene copy in diploids has important population genetic effects because it can mask the other gene copy from selection. A key innovation of my investigation is to allow haploids and homozygous diploids to have different fitnesses (intrinsic fitness differences). This reveals a novel hypothesis for the evolution of haploid-diploid strategies (where selection occurs in both phases), where the genetic effects of ploidy are balanced against intrinsic fitness differences. (3) Many sex chromosome systems are characterized by a lack of recombination between sex chromosome types. The predominant explanation for this phenomenon involves differences in selection between diploid sexes. I develop a model for the evolution of recombination between the sex chromosomes in which there is a period of selection among haploid genotypes in pollen or sperm. I find that a period of haploid selection can also drive the evolution of suppressed recombination between sex chromosomes, which should become enriched for genes selected in the haploid phase. This model predicts that the tempo of sex chromosome evolution can depend on the degree of competition among haploids.
Townsendia is a genus of the sunflower family (Asteraceae) flush with species that frequently specialize in marginal habitats limited by various abiotic factors (e.g., soil, temperature, precipitation), particularly in higher elevation habitats. Although species are well defined geographically and morphologically, the evolutionary relationships in the genus remain unclear. This thesis investigates the evolutionary relationships of Townsendia species through phylogenetic inference, and also uses an ecological niche modelling (ENM) approach to better understand the processes that have lead to inter- and intra-specific variation of the genus. Phylogenetic analysis of plastid DNA regions and the internal transcribed spacer (ITS) establishes the monophyly of the group, and also recovers a large core polytomy in Townsendia and two clades sister to the rest of the genus. The presence of this core polytomy suggests that the diversity in Townsendia may be the result of a recent and rapid process of adaptive radiation. Further evidence for an adaptive radiation in the genus may appear as greater rates of ecological niche divergence between related species, relative to expectations based on a process of random diversification under background environmental conditions. Looking at interspecific variation, ENMs presented varying levels of niche divergence between related species, suggesting that a combination of niche conservatism and divergence played a role in the evolutionary history of the genus. Niche modelling is also used to better understand the variation present within one species, particularly one with discrete population subsets such as diploid sexuals and polyploid asexuals. Polyploid asexual populations of T. hookeri tend to have a wider and more northerly distribution than their diploid counterparts, though the role of this pattern on the speciation of Townsendia is unclear. Such unequal distributions may arise from differences in dispersal ability, or in abiotic preferences between reproductive types. Comparisons of ENMs between these groups find evidence for intraspecific niche variation, and also predict the role of competitive exclusion, as factors that drive and maintain this distributional pattern. Overall, the combined use of phylogenetic analysis and ecological niche modelling in this thesis improves our understanding regarding the distribution patterns, evolutionary history and speciation pathways of Townsendia.
The North American Crepis (Asteraceae) agamic complex was established as an important early plant system for the systematic study of polyploid agamic complexes. Research conducted over 70 years ago determined that this western North American group consists of seven species comprising diploids and polyploids, and two species comprising only polyploids. Geographical parthenogenesis is pronounced with six of the seven diploids having restricted ranges in either central Washington or northern California. Much of the historic range of the diploids, especially that on valley bottoms, has undergone extensive land-use conversion over the past 70 years so the distribution of extant diploid populations was unknown.Identifying ploidy is of paramount importance to understanding evolutionary relationships in an agamic as well as identify, and circumscribing species. Diploids are the foundation of an agamic complex because all polyploids arise from them. A flow cytometric (FCM) method was modified to work with field-collected silica-dried leaf tissue using propidium iodide. Because of problems with cultivating seedling, obtaining ploidy information from living material was not possible in this group. This FCM breakthrough made a detailed systematic study of the group possible. Maternal relationships were determined between diploids, and between diploids and polyploids using plastid DNA (ptDNA) sequence data. Species were identified and circumscribed by synthesizing information from ploidy variation, maternal relationships, morphology, distribution, and ecology.Flow cytometry identified extant diploid populations for all seven known diploids and revealed a previously unrecognized diploid occurring on edaphic soils in northerniiCalifornia. Because this diploid is not morphologically or ecologically similar to any known diploid it was described as a new subspecies. The ptDNA sequence data indicated that the North American Crepis agamic complex is monophyletic, and sister to Crepis runcinata. There is no conclusive evidence of plastid capture among diploids.The two species comprising only polyploids have been recircumscribed, and reduce in rank to subspecies. Five of the seven species comprising diploids and polyploids have been recircumscribed by synthesizing new information from ploidy variation, maternal relationships, morphology, distribution, and ecology. A new treatment with original keys, descriptions and distribution maps has been produced to reflect these changes.
Master's Student Supervision (2010 - 2020)
If we hope to mitigate the effects of the climate crisis, it is critical that we accurately represent the contributions of plants in global models and predictions. The need to link global cycles to biological processes that feed into these cycles involves making scaling assumptions. In the case of photosynthesis, most global models use parameters extrapolated from a handful of species. However, the variation in leaf form and function that we observe both within and across species makes one question the biological accuracy of this assumption. Despite advances in quantifying the differences between deeply divergent lineages, there is still a substantial gap in what we know about how C3 photosynthesis evolves both at very deep and very shallow evolutionary timescales. Filling this gap will allow us to better infer and incorporate photosynthetic behaviour in global models. Here we address two specific gaps: i) we assess the evolution of photosynthetic trait variation and ii) we evaluate the relationship between photosynthetic traits and a set of plant functional traits. These latter traits are often used as proxies for metabolic variation even though we don’t know how metabolic and morphological features are coupled through their evolutionary trajectories. We collected data for a phylogenetically structured sample of 106 species growing in a common environment, sampling metabolic and functional traits from the same individuals. Using estimates of phylogenetic half-life, we find significant phylogenetic structure in both metabolic and morphological traits, but the evolution of metabolic traits is much more constrained than that of morphology. We also ask whether changes across traits are coupled, and find that even when there are present day trait correlations, most traits do not seem to share correlated evolutionary history. Our finding of substantial interspecific variation in photosynthetic traits is not captured in current global ecosystem models; further, using functional trait variation as a proxy does not adequately represent this variation. Future work would benefit from using some element of evolutionary history or species identity in modeling photosynthetic behaviour.
Mushrooms of some Galerina species equal the most poisonous Amanita species in their concentrations of deadly amanitin toxins. Although individual Galerina mushrooms are small, eating about ten would risk delivering a lethal dose of amanitins to a child. Understanding which species of Galerina pose an acute poisoning risk requires a better understanding of species boundaries within the genus, as well broad sampling for the presence of amatoxins. I analyzed 61 Galerina and eight outgroup specimens for the presence of amatoxins using HPLC/LC-MS. I then used multi-locus DNA data (ITS, LSU and RPB2) from a broad sampling of Galerina and outgroup taxa to generate a constraint tree, to which 322 Galerina ITS sequences from herbarium specimens at UBC, from A.H. Smith’s type material (University of Michigan) and from Genbank were added. I mapped toxin analysis data onto the resulting phylogeny, which indicated that amatoxin-production in BC Galerina is restricted to two species, G. venenata and G. castaneipes. These two species, along with two other reportedly toxic species (G. aff. marginata and G. sulciceps) and seven other species whose toxin production status remains unknown form a broad clade referred to as the G. marginata complex. Phylogenetic and toxin data suggest that the sister clade to the G. marginata complex (G. badipes) does not produce toxins, implying that the origin of amatoxin production in Galerina is somewhere within the G. marginata complex. Additionally, phylogenetic data also supports past evidence that members of the genus Gymnopilus are nested within the ‘Mycenopsis’ lineage of Galerina. The results provide the first comprehensive look at toxin production in Galerina, as well as the first report of additional toxin-producing species in North America. Using the molecular data from this study to update specimen names in herbarium collections and online databases will reduce downstream confusion resulting from inaccurate identifications or misapplied names. Doing so will contribute to ongoing efforts to update of field guides and other resources that list poisonous and edible mushrooms, allowing amateur mycologists, foragers and healthcare professionals to gain a better understanding of which Galerina pose a poisoning risk.
Much is known about plant-environment associations, but we are far from able to predict community species composition under a given set of environmental conditions. Recent research using functional traits suggests niche-based processes are vital in structuring communities, though the generality of results across different ecosystems is unknown. I investigated community trait distribution along environmental gradients in sub-Arctic roadsides-- communities which represent novel ecosystems in which to apply trait-based analysis, and which allow for the comparison of ecological strategies and trait distribution of native and exotic species. While these environments have features specific to northern latitudes, they also broadly represent global roadside environments and their important role in the establishment and spread of exotic species. Invasive exotic species present a pervasive threat to global diversity, and understanding mechanisms of assembly, coexistence and strategies of native and exotic roadside communities can improve our ability to predict invasive species' behaviour. I measured species abundance and three functional traits in 42 roadside plots in the Yukon Territory and compared community traits across elevation, latitude and age of road. Across all species, abundance-weighted community height was negatively correlated with elevation and positively correlated with latitude. Native and exotic species tracked environment differently, however, and exotic species showed correlations between height and road age and between specific leaf area (SLA) and latitude that were not present among native species. A comparison of mean trait values of native and exotic species irrespective of environment revealed specific leaf area (SLA) was greater in exotic species than native species. In addition, I used three null models to test for habitat filtering and competitive exclusion, two important niche-based assembly processes. Ranges of trait values across plots were smaller than expected and trait values more evenly spaced compared to random samples from the regional species pool, suggesting both habitat filtering and competitive exclusion (limiting similarity) shape these disturbance communities. Both processes were found to also affect both presence/absence and abundance of species. Understanding mechanisms of community assembly along roadsides and the characterization of native and exotic community constituents will have important implications for development of conservation management strategies.
Townsendia hookeri (Asteraceae) plants can reproduce sexually or via apomixis (i.e. asexual reproduction through seeds), and the breeding system is tightly linked with ploidy level, so that sexual outcrossers are exclusively diploid while apomictic plants are polyploid. The species grows from central Colorado to British Columbia, with a disjunct distribution in Yukon Territory. Outside Yukon, sexual populations are restricted to the southernmost portion of the range (Colorado and southern Wyoming) and apomictic populations occur from Wyoming to Canada, a pattern consistent with geographical parthenogenesis. The major objective of this study was to expand our understanding of the factors that have shaped and maintain this distribution, conferring an apparent advantage to apomictic lineages over their sexual progenitors. Having documented that polyploid plants retain the ability to produce some functional pollen, I hypothesized that if sexual forms spread into an apomictic population, and thus receive mostly heterospecific pollen, they would have reduced reproductive success, because the progeny sired in sexual-asexual crosses are predicted to be weak or inviable, and to include hybrid apomicts. This asymmetric reproductive interference could help explain why diploids have failed to spread into the territory dominated by apomicts. To test this hypothesis I performed a cross-pollination experiment in the field. I showed that diploid and polyploid cytotypes have comparable reproductive success (at least, in the area where the experiment was conducted), and I also confirmed that diploids are outcrossers while polyploids are apomictic. The crossing experiment indicates that, despite its low viability, pollen produced by apomicts can fertilize and negatively affect diploid seed parents. As predicted, when sexual plants received heterospecific rather than conspecific pollen, seed set and germination rate were reduced, and seedlings had a lower survival rate. Flow cytometric analysis of offspring from sexual-asexual crosses revealed the presence of putative euploid (diploid, triploid and tetraploid) as well as aneuploid cytotypes. Based on ploidy level it is reasonable to expect that polyploid hybrids inherited apomictic genes and that at least some of them might be fully apomictic.
Despite the classic place that the North American Crepis (Asteraceae) agamic complex holds in evolutionary literature, few of the hypotheses about the group presented by Babcock and Stebbins 1938 monograph have been tested. In particular, they hypothesized that the seven sexual diploids had strong interfertility barriers that prevented the formation of diploid hybrids. Here I present an analysis of two previously unrecognized diploid morphotypes, which belong to an unresolved clade with Crepis pleurocarpa and Crepis occidentalis based on plastid DNA variation. Morphological traits suggest that both morphotypes may be the product of diploid x diploid hybridization. I gathered nuclear SNP markers using genotyping by sequencing to assess the origins of these two lineages. I constructed a de novo assembly of the nuclear genome of Crepis monticola to serve as a reference for SNP discovery. Analysis of contig length,number, and coverage indicate that the nuclear genome of Crepis is highly repetitive and shares features in common with other plant genomes that make angiosperm genomes challenging to work with. This complexity, as well as technical challenges likely due to partial enzymatic digestion of genomic DNA during GBS library preparation, resulted in only 19 SNPs passing the quality filters. Nonetheless, these 19 markers were used to provide a preliminary assessment of the origins of novel morphotypes. A signal of mixed ancestry was found for one of these morphotypes with the majority of their genome being distinct from both C. occidentalis subsp. occidentalis and C. pleurocarpa. The second morphotype is of non-mixed ancestry most closely resembling Crepis occidentalis. In a separate study, I provide a draft assembly of the Crepis monticola chloroplast genome. I show that gene order and content are unchanged from other members of Asteraceae with the exception of the rpl16 gene, which retains an intron that is reported as lost multiple times in Asteraceae. Results of a preliminary data analysis detailing the presence or absence of the first exon of rpl16 in published Asteraceae plastome sequences indicates that most of these supposed losses are errors, pointing to the need for careful examination of plastome assemblies gathered from databases.