Richard Hamelin

Professor

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Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - Nov 2019)
Using genomic data to understand anthropogenic influences on Oomycete and Phytophthora communities, and the evolution of an alien invasive species responsible for sudden oak death, Phytophthora ramorum (2018)

Emerging Phytophthora pathogens, often introduced, represent a threat to natural ecosystems. Phytophthora species are known for rapid adaptation and hybridization, which may be facilitated by anthropogenic activities. Little is known about natural Phytophthora and oomycete populations, or mechanisms behind rapid adaptation. We surveyed oomycete and Phytophthora communities from southwest B.C. under varying anthropogenic influences (urban, interface, natural) to determine effects on diversity, introductions and migration. We used DNA meta-barcoding to address these questions on oomycetes. We then focused on Phytophthora, adding baiting and culturing methods, and further sub-dividing urban sites into agricultural or residential. Finally, we studied an alien invasive species, Phytophthora ramorum responsible for sudden oak death, and how it overcame the invasion paradox, limited to asexual reproduction and presumed reduced adaptability. Anthropogenic activities increase oomycete and Phytophthora diversity. Putative introduced species and hybrids were more frequent in urban sites. Migration is suggested by shared species between urban and interface sites, and two known invasive species found in natural and interface sites. Different anthropogenic activities influence different communities. Abundance increased for some species in either residential or agricultural sites. Two hybrids appear to be spreading in different agricultural sites. In the invasive Phytophthora ramorum, mitotic recombination drives diversification of the four lineages (NA1, NA2, EU1 and EU2), generating runs of homozygosity. One genome region, enriched in putative plant pathogenicity genes and transposons, was fixed in NA1 and present in eight EU1 individuals, but affecting the opposite alleles. Longer lesions during initial colonization in inoculated larch and Douglas fir logs suggested a fitness advantage in these EU1 individuals. Mitotic recombination breakpoints were associated with transposons and low gene density. Non-core and lineage-specific genomic regions were enriched in putative plant pathogenicity genes and transposons. Gene loss was observed in the EU2 non-core genome affecting all effectors. A two-speed genome, where regions enriched in transposons and plant pathogenicity genes evolve faster, appears to drive non-core genome divergence, and mitotic recombination resulting in population evolution. This may explain invasion success and adaptability in Phytophthora pathogens. These results highlight the importance of anthropogenic activities in the emergence of forest diseases.

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Master's Student Supervision (2010 - 2018)
Development of molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera (2017)

In order to determine if living fungi of phytosanitary concern are present in wood or to evaluate the efficacy of treatments, the method of choice is to grow microbes in petri dishes for subsequent identification. However, some fungi are difficult or impossible to grow in cultures, and thus, to validate the effectiveness of existing and emerging wood treatments, a molecular methodology that can detect living fungi and fungus-like organisms is required. RNA-based molecular diagnostic assays were developed to detect the presence of living fungi and fungi-like organisms of phytosanitary concern. Since RNA represents the transcription of genes and can therefore only be produced by living organisms, it provides a marker to determine if an organism is alive. The assays were designed to target genes that are essential to vital processes, then used to assess their presence and abundance through real-time reverse transcription polymerase chain reaction (PCR). A stability analysis was conducted by comparing the RNA to DNA ratio over treatment time. The results illustrated that for treated samples, DNA remained stable over a period of 10 days post treatment, whereas RNA could not be detected after 24 hours for Phytophthora ramorum or 96 hours for Grosmannia clavigera. Therefore, this method provides a reliable way to evaluate viability of organisms following treatments and can have profound impacts on assessing both timber and non-timber forest products of commercial value.

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Genome Characterization and Population Genetic Structure of White Pine Blister Rust, Cronartium ribicola (2015)

Rust fungi cause some of the most severe pine diseases. Cronartium ribicola (J. C. Fisch.), the causal agent of white pine blister rust, was introduced accidentally to North America from Europe in the late 1800s. Since then, it has devastated a large number of native, commercially valuable white pines, and is threatening alpine ecosystem stability by endangering high elevation white pines. In order to better understand the global epidemiology of this pathogen, we conducted a genome scan of a global collection of C. ribicola using Genotyping-by-Sequencing (GBS) to: 1) ascertain the origin and the routes of introduction of C. ribicola, and 2) uncover cryptic population structure of C. ribicola in western North America, in relation to different pine hosts, climates and landscapes. More than eight thousand single nucleotide polymorphism markers were genotyped on 192 samples of C. ribicola from three continents. The highest genetic and nucleotidic diversity were observed in Siberian samples, supporting the hypothesis that central Russia is the center of origin of C. ribicola. Diversity was reduced in all other populations and was lowest in western North America. Genetic and nucleotidic diversity were two to five times lower in western than in eastern North America. This result supports the observation of multiple introductions of the pathogen in eastern North America and contrasts with the single reported introduction in western North America. However, western populations had a larger number of rare alleles. This could represent the signature of population expansion following a bottleneck or a selective sweep. A cryptic Coast/Interior split was detected within the western cluster, most likely maintained by the scarcity of white pines in central British Columbia acting like a barrier to gene flow. Finally, western individuals with a high level of eastern admixture were discovered in two populations east of the Continental Divide. This could indicate that the eastern-western barrier to gene flow is leaky. Such information is of significance to white pine resistance breeding programs and to the monitoring of this disease.

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Comparative population genetic analysis of fungal associates of the mountain pine beetle (Dendroctonus ponderosae) (2014)

The mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, has destroyed over 18 million ha of pine forest in Canada since 1999, the largest insect epidemic in recorded history. Fungal symbionts in the Ophiostomales (Ascomycetes) play an important role in the outbreak by reducing the tree defense response following beetle colonization, making its environment more conducive to the insect development. A better understanding of the population genetics attributes of the fungal associates could be important to elucidate their role and to explain epidemic patterns. We investigated the genetic structure of one of those fungal associates, Leptographium longiclavatum, sampled from 28 locations in western North America using 11 microsatellite markers developed from the genome of its closest relative, Grosmannia clavigera, another fungal symbiont of the MPB. We found that L. longiclavatum has a distinctive genetic population structure, and by using Bayesian clustering inference, we discovered the presence of three clusters that are concordant with geographic origin of the samples. In addition, we observed an apparent North-South pattern of genetic diversity consistent with the chronology of the epidemic. Structure output showed one cluster comprised of individuals from Northern Alberta where the beetle-fungus complex has been recently established, and a second cluster composed of individuals originating along the Rocky Mountains, and a third cluster was from populations in BC. High haplotypic diversity was found throughout the range sampled, a surprising result given that sexual fruiting structures have never been observed for this fungus. Consistent with recent introduction history, the least differentiated populations were located in northern BC and Alberta. We observed a strong correlation in the genetic diversity pattern observed in L. longiclavatum, G. clavigera and D. ponderosae, as shown by a significant correlation in the genetic distance matrices amongst L. longiclavatum, G. clavigera, and D. ponderosae. This correlation and the similar north-south population structure of these interacting organisms suggest a joint population history consistent with the dependence of fungal dispersal on their bark beetle vector. These results can help clarify the roles and close relationships between the beetles and their fungal associates.

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Landscape Genetics of Cronartium ribicola (2012)

White pine blister rust, Cronartium ribicola (Basidiomycota, Pucciniales), is a macrocyclic (5 different spore types) heteroecious (requires two hosts) rust that alternates on Ribes spp. It is an exotic pathogen in North America and cause high levels of mortality of pine in the subsection Strobus (white pines). To better understand the epidemiology of the pathogen, the population structure of white pine blister rust in North America was investigated. Thirty one single nucleotide polymorphism (SNP) markers have been developed to genotype 1341 individuals from 76 populations from across North America including samples from diverse landscapes. In western Canada, sampling was structured to contrast different landscapes and pine hosts. Distance-based and Bayesian likelihood methods indicated the presence of two major genetic clusters: ‘eastern’ and ‘western’ in North America, separated by the Great Plains that act as a barrier to gene flow. The eastern cluster had greater genetic diversity than the western cluster, which confirms that multiple introductions occurred in eastern North America in contrast to a single introduction in the west. Two populations, New Mexico and Minnesota were each found to form a separate cluster in some assignment analyses and the distance-based analyses clearly placed them outside of the main clusters. Both of these populations displayed the hallmarks of a founder effect, i.e. low genetic diversity and/or inbreeding. The pathogen was discovered in New Mexico in the 1970’s, almost a century later than the populations in the two major clusters. Although white pine blister rust has been present for longer in Minnesota, the population parameters strongly suggest a founder effect and a barrier to gene flow between Minnesota and the populations within the eastern cluster. However, no landscape, host, or other patterns could be correlated with these clusters. A rare SNP was detected in Smithers, a population with high levels of inbreeding located at the northern most extent of the rust. Understanding the population structure will provide great knowledge of the rust for breeding programs and deployment of rust resistant pines.

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