Finding patterns through Phylogenetic Ecology

Dr. Jonathan Davies and the Phyloecology Lab examine the interface between ecology and evolutionary biology, and how the evolutionary history of species is used to inform our understanding of their present-day ecologies. Research projects in the Phyloecology Lab include identifying hotspots of parasite diversity and future host-shifts, integrating phylogenetic diversity metrics into conservation thinking, and understanding the connections between biodiversity, disease, and climate change. Current research in the lab is focused on pests and pathogens of forest trees, exploring how pests move between their hosts, how the phylogenetic diversity of forest trees can dilute pest prevalence, and generating ecological forecasts of climate-induced shifts in pest and pathogen pressure across forest ecosystems.

Research Strength: Phylogenetic comparative methods in ecology. Ecological forecasting.

Collaboration Interest: Merging theory and models of disease epidemiology with empirical data on the diversity and prevalence of multi-host pests and pathogens of wildlife. Predicting probability of host shifts and disease spillover. One Health.

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Evolution of emerging and established pathogens

Dr. Joy uses and develops evolutionary genetic methods to study and understand evolutionary processes in the context of molecular epidemiology, pathogen evolution, and macroevolution. His laboratory integrates evolutionary theory and computational methods with genomic, clinical and socio-demographic attribute data to make inferences relevant to public health and clinical practice, as well as for the fields of evolutionary biology and molecular epidemiology more generally.

Research Strength: His laboratory’s work is currently focused on pathogen emergence (e.g. SARS-CoV-2 and Lassa virus), the dynamics of viral epidemics such as HIV and HCV, within-host evolution, and development of novel methods for understanding epidemic dynamics based on sequence data.

Collaboration Interest: We welcome opportunities to partner on projects in molecular epidemiology, evolutionary genetics, and public health. Collaborations may take many forms, including joint analyses, co-supervision of trainees, or the development of new methods and datasets, with colleagues in Canada and Internationally.

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Evolution and the diversity of life

The Otto Lab combines mathematical models, statistical tools and evolutionary experiments with yeast to understand the evolutionary processes that have produced the incredible diversity of life. Dr. Sally Otto's current work focuses on the extent to which organisms can adapt to a changing world and why they might fail to do so.

Research Strength: Mathematical modelling, yeast experimental evolution, evolutionary rescue experiments

Collaboration Interest: Broad interests in collaborating on modelling/empirical projects

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Mathematical modeling of host and pathogen evolution

Dr. Ben Ashby's lab uses mathematical models to understand the epidemiology and evolution of pathogens and their hosts. His group is especially interested in the fundamental mechanisms and processes that drive pathogen adaptation in key disease traits such as virulence and infectivity.

Research Strength: Mathematical modelling, epidemiological and evolutionary theory, within- and between-host dynamics, and interventions. 

Collaboration Interest: Other theoreticians and empiricists who wish to use models to get a deeper insight into the mechanisms at play in their study systems.

Dr. Ashby is also the Scientific Director of the Pacific Institute on Pathogens, Pandemics and Society (PIPPS), which is looking for new affiliate members to join our community to share research and network across disciplines.

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Viral Sociality

The Leek's Lab studies social evolution in viruses. Viral lifecycles are intrinsically social: viruses depend upon shared proteins to build the molecular machinery required for both reproduction (replicase enzymes) and survival (capsid proteins). As a result, viral populations exist within a state of evolutionary tension: viruses depend upon cooperative interactions to complete their lifecycles, but each infected cell also holds the potential for the tragedy of the commons, through the emergence of viral ‘cheat’ mutants that act as molecular parasites of full-length viruses. As a result, every aspect of the viral lifecycle can be influenced by social interactions, from replication within a cell to transmission between hosts. Viral sociality raises new questions for evolutionary theory, providing the opportunity to challenge and expand our view of how social interactions evolve. At the same time, understanding viral sociality would open a new window into the biology of Earth's most prolific parasites.

Research Strength: 

Our lab combines three main methodological approaches:

1. We build theoretical models to explain the evolution of puzzling viral social traits, often drawing on frameworks within evolutionary game theory and population genetics.

2. We conduct bioinformatic and statistical analyses of viral sequencing datasets, in particular testing for the role of viral cheats in natural or clinical datasets.

3. We experimentally evolve bacteriophages in the laboratory, currently focusing on filamentous phage M13, to test how viral social interactions evolve over long timescales.

Collaboration Interest: 

We are particularly interested in collaborating with clinicians and public health experts, in order to study the clinical impacts of virus-virus interactions.

We currently collaborate with public health agencies in the United States, and with physicians in Ontario, in order to detect ‘cheat’ viruses in clinical datasets.

If viral cheats are broadly associated with specific clinical outcomes, we would be interested in developing them into a biomarker for predicting the future severity of an infection, and in using viral cheat abundances to predict the original host species, in environmental viral samples of unknown origin.W are interested in the intersection of evolutionary and clinical questions surrounding the safety, epidemiology, and evolution of viral cheats.

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A world of pathogens

The King Lab studies the evolution, ecology, and genomics of animal-pathogen interactions. This fundamental research leverages our understanding of pathogen evolution in host species to better predict and mitigate against established and emerging pathogens.

Research Strength: Her research tests ecological and evolutionary theory on infectious diseases using a combination of experimental evolution of pathogens in the lab, genomics, field collections from animals, and comparative analyses on host-pathogen systems across the tree of life. King’s group thinks about the impacts of climate change, biodiversity loss, the microbiome, and host species jumps for pathogen evolution and infection outcomes.

Collaboration Interest: We welcome collaborators interested in uncovering signatures of evolution in pathogen genomic data. We are also keen to talk with colleagues interested incorporating experimental evolution of pathogens or wild pathogen isolates from animals into their research.

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The intersection between humans, animals and the environment

Dr. Himsworth's research and practice is focused on transdisciplinary, applied One Health approaches to health issues at the interfaces among humans, animals, and the environment. Current focus areas include understanding, monitoring, and mitigating diverse harms associated with urban rodents, avian influenza virus, and enteric pathogens.

Research Strength: Combining a variety of methodologies including field research, surveillance, quantitative and qualitative epidemiology, environmental modelling, pathology, and genomics to develop a wholistic understanding of current and emerging issues at the human-animal-environmental interface. Developing resilience-based solutions for One Health issues at local, provincial, national, and international scales.

Collaboration Interest: Dr. Himsworth is always looking for collaborators on research programs involving urban rodents, avian influenza, and enteric pathogens; however, she is also interested in helping others who are conducting applied One Health research on topics of current or future importance.

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RNA at the host-virus interface

The Sagan Lab studies RNA-RNA and protein-RNA interactions at the host-virus interface. Specifically, studying positive-sense RNA viruses of the Flaviviruses family (including hepatitis C virus, dengue and Zika viruses) as well as respiratory viruses (including respiratory syncytial virus and human coronaviruses), they aim to improve our understanding how these RNA viruses usurp the host cell, replicate their genomes, and cause disease.

Research Strength: Molecular virology, RNA viruses, viral evolution and evolutionarily-acquired polymorphisms, viral RNA replication, virion assembly, and RNA biology.

Collaboration Interest: RNA biology and therapeutics, biomolecular condensates, drug design & development, and high-throughput screening.

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One Health and knowledge mobilization

Dr. Byers leads the One Health, Human dimensions and Implementation (OH-HI) Science CoLab, where they aim to understand the complex connections between health and the collective to mitigate the impact of zoonotic disease. Dr. Byers is particularly interested in understanding how environmental change drives health impacts across species and space and delivering the research through creative forms of knowledge sharing.

Research Strength: Systems-thinking

Collaboration Interest: Multi-sectoral, interdisciplinary collaborations which centre the research priorities of communities.

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Virus and pathogen hunter

Dr. Mark Paul Rivarez heads the Phytopathology and Virology research group within the Land and Food Systems department. His research focuses on viruses and microbes in the agricultural ecosystem, examining their ecology, evolution, and epidemiology to develop sustainable strategies for safeguarding plant health. He has a particular interest in pathogens that affect crops such as tomatoes, as well as related weed plants found in field or greenhouse settings.

Research Strength: Dr. Rivarez specializes in discovering and analyzing plant viromes with high-throughput sequencing (HTS), covering the fullviromics workflow—from sample collection, RNA sequencing, to bioinformatics for assembly and classification. He alsocharacterizes new viruses and assesses emerging plant pathogen risks. His main research areas include:

• Virology (Plant Virology, Virus Ecology and Diversity) 
• Plant Pathology (Phytobacteriology, Fungal Plant Pathology, Biological Control)
• Sequencing Technologies (Metagenomics, Viromics, Nanopore Sequencing)
• Evolutionary Analysis (Phylogenetics, Phylodynamics, Phylogeography)
• Epidemiology (Pathogen Risk Assessment, Species Distribution Modeling)

Collaboration Interest: Dr. Rivarez engages in inherently interdisciplinary research grounded in real-world applications through active collaborations with government agencies like AAFC and CFIA, as well as major industry groups such as the BC Greenhouse Growers Association, BC Wine Grape Council, and BC Cherry Association. Building on this foundation, he is eager to expand future partnerships, especially with researchers at UBC and beyond who focus on pandemic and biothreat preparedness and data-driven predictive modeling. He is actively pursuing new collaborations centered on outbreak modeling, agri-biosecurity, and developing rapid, field-deployable diagnostic platforms to strengthen Canada's biosecurity measures.

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Evolution of cross-tolerance to metals in yeast

PrePARE Member: Sally Otto                   Read

Efficient coupling of within- and between-host infectious disease dynamics

PrePARE Member: Ben Ashby                 Read

Exploiting social traits for clinical applications in bacteria and viruses

PrePARE Member: Asher Leeks              Read

Ecology and evolution of virulence

PrePARE Member: Kayla King                 Read

Warming during different life stages has distinct impacts on host resistance ecology and evolution

PrePARE Member: Kayla King                 Read

Rising temperatures favour parasite virulence and parallel molecular evolution following a host jump

PrePARE Member: Kayla King                 Read

Risk metrics vs. rat metrics: An alternative approach to measuring and managing urban rat infestations

PrePARE Member : Chelsea Himsworth & Kaylee Byers                                                        Read

Living with urban Norway and black rats (Rattus norvegicus and Rattus rattus) in high income countries (in Press)

PrePARE Member: Chelsea Himsworth & Kaylee Byers

Within-host genetic diversity of SARS-CoV-2 across animal species

PrePARE Member: Selena Sagan            Read

Inequality in Exposure and Knowledge Drives Vulnerability to Rat-Associated Leptospirosis

PrePARE Member: Kaylee Byers             Read

From vision to action: Prioritizing in One Health (in Press)

PrePARE Member: Kaylee Byers 

Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses

PrePARE Member: Mark Paul Rivarez     Read

Streamlining Global Germplasm Exchange: Integrating Scientific Rigor and Common Sense to Exclude Phantom Agents from Regulation

PrePARE Member: Mark Paul Rivarez     Read

Evolutionarily Distinct Species and Their Partners Have Fewer Links in Ecological Networks

PrePARE Member: Jonathan Davies       Read

Co-phylogenetic constraints on host breadth within an emerging fungal pathogen complex of global concern

PrePARE Member: Jonathan Davies       Read

Multi‐host pathogen transmission and the disease–diversity relationship

PrePARE Member: Jonathan Davies       Read

Impacts of Weather Anomalies and Climate on Plant Disease

PrePARE Member: Jonathan Davies       Read