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Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - May 2021)
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.
Trees are sessile and exposed to a plethora of pests throughout their life-span and natural history. Diversification of the specialized (secondary) metabolism is known as a key factor in the co-evolution of trees with pests. This work focuses on tissue-related gene expression, and the expression of specialized pathways of phenolics and terpenoids in relation to the evolution of biochemical defenses in the coniferous species of spruce (genus Picea). Gene expression resources were assessed for the superimposition of tissue-related expression and cross-species expression profiling. Five species of spruce, P. abies, P. glauca, P. jezoensis, P. omorika, and P. mariana, were used to infer the evolution of gene expression among representative spruce species. As gene expression also depends upon tissue, I examined three sources of tissue: needles, outer stem (bark and the attached phloem) and xylem. The overall expression of phenolics was significantly diverged in the outer stem. At the gene family level, expression was predominantly stabile among species. Significant among-species divergence of gene expression, indicative of diversifying selection, was found for eight gene families. These families were: cinnamate 4- hydroxylases (C4H), dirigent-like proteins (DIR), glycosyl transferases (GLYTR), laccases (LAC), O-methyl transferases (OMT), phenylalanine ammonia lyases (PAL), putative caffeoyl CoA O-methyl transferases (pCCoAOMT) and putative phenylcoumaran benzylic ether reductases (pPCBER). Analysis of the expression of the terpenoid pathways in the outer stem revealed that for terpene synthase gene family (TPS), expression is significantly diverged among species. In a novel approach, heritability of gene expression using parent-offspring regression was inferred for Interior spruce (P. glauca x engelmannii), and average expression for TPS genes showed substantial heritability.
Complex traits including those involved with natural adaptation are determined by the contributions of numerous genes, the environment, and their interactions. Although quantitative trait locus (QTL) mapping approaches have been successful in dissecting complex traits, few studies have adopted a comparative approach of contrasting species pairs that differ in relationship, for the purpose of dissecting evolutionary changes of QTL. Furthermore, no QTL mapping approaches have explicitly inferred QTLs along lineages in a species network. This thesis brings such a comparative approach into QTL mapping. The evolution of inbreeding in the Mimulus guttatus species complex provides an excellent system where lineage-specific QTL changes can be inferred. Three intercrossable species were chosen: M. guttatus, M. platycalyx and M. micranthus, the latter two taxa being independent derived inbreeders from the first one. Five floral characters were selected as representative traits for the evolution of inbreeding in these species. A three-species crossing design was implemented, upon which QTL analyses were conducted. As expected in QTL mapping studies, the estimated number of genetic factors varies among crosses. An important role of dominance in the evolution of selfing from outcrossing taxa is supported by the data, owing to the consistency of directional dominance towards selfing taxa. The extensiveness of epistasis identified in this study suggests that in Mimulus, genes related to floral characters are co-adapted gene complexes, where genetic interdependency evolves as species diverge. Moreover, such genetic interdependency may be a key element in the evolution of stable mixed mating systems.A model for the inference of lineage specific QTL in a three-taxon network is described, and used to infer lineage-specific changes for floral traits among the three Mimulus taxa. After mapping QTL onto lineages, one can determine if QTL at the same map position are homologous (arising in an ancestral lineage leading to two taxa) or non-homologous (arising independently in derived lineages or via convergent evolution). In Mimulus, shared negative QTLs of dominant effect that arise from convergent evolution seem to play a prominent role in the early evolution of inbreeding; then derived, independent changes fine-tune further evolutionary changes of inbreeding.
Master's Student Supervision (2010 - 2020)
Under rapid global warming, it is critical to better understand the capacity of forest trees to adapt to a changing climate. Western white pine (Pinus monticola Douglas ex D. Don) and eastern white pine (P. strobus L.) are species at higher risk to climate change, as both have fragmented ranges and have suffered declines due to harvesting, fire suppression, and the white pine blister rust. We identified and compared patterns of genetic diversity and adaptation to climate in both species using a set of 267 orthologous genes. These genes included candidates for growth, bud phenology, and resistance to biotic and abiotic stresses. Genotyping resulted in 158 and 153 successful SNPs for P. monticola and P. strobus, respectively. Each set of SNPs was genotyped on range-wide samples of 362 P. monticola individuals (61 populations) and 840 P. strobus individuals (133 populations). Analyses were conducted separately in each species. STRUCTURE analyses identified two genetic clusters in each species, corresponding to north-south genetic discontinuities, as well as weak hierarchical sub-structure within each of those groups. We found evidence of local adaptation in both species. FST outlier analyses revealed that ∼7 percent and ∼10 percent of SNPs were under selection in P. monticola and P. strobus, respectively. Environmental association methods identified that ∼38 percent of P. monticola SNPs and ∼47 percent of P. strobus SNPs were correlated with climate. Strong candidate genes for future adaptation studies were identified: 7 genes in each species were detected by at least 2 methods and 22 candidate genes were common to both species. These genes were involved in growth, bud phenology, and response to abiotic and biotic stress. The implications of these findings for the conservation of white pine populations under climate change are discussed.
In 1975, King and Wilson proposed that gene expression variation can play a role in the evolution of phenotypic variation since the variation in nature could not be explained by variation in protein coding sequences alone. When a mutation which causes a change in gene expression is introduced in to a population, either selection or neutral drift can act on it. When this mutation causes no change in fitness of the organism, it will be affected by neutral drift. The bounds for neutral drift are thought to be set by stabilizing selection. If the mutation is beneficial to the organism, it will be affected by positive selection. When different populations are located in different environmental conditions, different mutations can be beneficial in each population and divergent selection can result. We looked for these patterns of gene expression evolution among populations of Populus trichocarpa, black cottonwood,using a PST vs. FST approach.P. trichocarpa is a model tree system that allows the study of an extended suite of tree biological processes. A suite of genomic tools have been developed for black cottonwood, including a genome sequence and a 15.5K microarray. It is broadly distributed in the far west of North America and shows an ecotypic mode of genetic differentiation, with populations divided into northern and southern groups.In this study, we examined gene expression from 12 P. trichocarpa populations, 6 from the north and 6 from the south. We found evidence for divergent selection acting on the expression values of many genes, as well as stabilizing selection acting on a few. This supports the prevalence of natural selection acting on phenotypic traits, but we still found an overwhelming majority of traits which seem to be drifting neutrally. We found no evidence for different selection acting on the northern and southern groups.
White pine weevil is a pest of interior and Sitka spruce species in British Columbia. It is native to eastern Canada, and migrated to the west. To date, control of the weevil has been ineffective even with the combined use of several control methods. Current research has focused on breeding resistant trees for use in plantations to overcome attack from Pissodes strobi. Knowledge of the weevil genetic structure on a small-scale stand level is extremely important in developing strategies that decrease the possible development of tolerance in P. strobi populations to resistant trees. To understand the population structure of P. strobi 15 microsatellite markers were used to investigate local population structure. Genetic structure of local weevil populations differed over stand age in both interior and Sitka spruce plantations. The younger and older plots had more single populations associated with individual trees than did middle aged plots. Middle-aged plots had increased beetle movement regardless of the number of weevil larvae per leader, increased number of females ovipositing per tree and less weevil genetic differentiation between trees. Understanding reproductive dynamics of P. strobi will help develop strategies for planting resistant trees to decrease the development of insect tolerance and further our knowledge of the possible co-evolutionary dynamics of this system.