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 CANADA RESEARCH CHAIR IN EVOLUTIONARY CELL AND SYSTEMS BIOLOGY

Overall objectives
We study diversity in the natural world as well as diversity that we create in the laboratory in order to understand how biodiversity comes about and how the natural variation that has evolved for billions of years shapes the ability of organisms to adapt today. In our four main research topics, we take a deep plunge and look inside the cell to understand the molecular basis of several aspects of evolution.

The Landry Lab 2018
From back to front and left to right: Johan, Pauline, Alexandre, François, Rohan, Angel, Philippe, Anna, Diana, Mathieu, Souhir, Hélène, Chris, Simon, Guillaume N., Lou, Emilie, Véronique, Caroline, Carla, Christian, Ugo, Guillaume C., Clara and Axelle (missing member: Isabelle).

I. Evolution of cellular networks using synthetic biology
Cellular systems are constantly perturbed by changes in their environment and by changes in their internal conditions. How cells respond to perturbations will determine their long-term success. We are particularly interested in how proteins accomplish their functions when mutations occur, how the mutations change the relationships among proteins and how these changes ultimately affect fitness. We are examining these questions using synthetic biology approaches to manipulate and engineer genomes in order to probe the effect of mutations on cellular signaling networks. We are for instance measuring the consequences of spurious interactions (Ugo Dionne, Emilie Bourgault) and how they relate to cellular performance (Rohan Dandage). We also systematically study the modification of proteins to find how and why certain changes affect fitness while others do not (Philippe Després). Finally, we are investigating how protein function diverges between species and how this functional divergence depends on the ability of the proteins to interact properly with their interaction partners (François Rouleau). For this work, our signaling networks model systems are yeast and human.

II. Evolutionary systems biology of novelties
We study how novel proteins emerge and evolve from the duplication of existing genes as well as from non-coding parts of the genome. Gene duplication can be an important force in evolution. However, it is thought to be of limited use for acquiring completely novel functions due to phylogenetic constraints, i.e. genes born from duplication have inherited several features from the ancestral copy, including biophysical constraints. We are interested in identifying these evolutionary and biophysical constraints (Angel Cisneros, Axelle Marchant, Simon Aubé). Another interesting aspect of gene duplication that we are studying is how changes in gene dosage that can result from gene duplication affect the assembly of protein complexes and in turn affect fitness (Caroline Berger, Diana Ascencio).

Although gene duplication accounts for the emergence of most new genes in the genome, genes that emerge from non-coding sequences have more degrees of freedom and could be a larger reservoir of novelties. We are therefore interested in how the properties of the non-coding parts of the genome and their mutational turnover can affect what is accessible to natural selection for the evolution of novel functions (Lou Nielly-Thibault). At the same time, we would like to know what effects a newly emerged gene has on fitness and other cellular functions and whether this could impede their evolution (Johan Hallin). Our study systems are theoretical modeling, computational simulations and experimental work with yeast.

III. Evolutionary genomics of responses to ecological and cellular interactions
The architecture and evolution of genomes is affected by natural selection that is driven by the external environment and also by internal forces that affect, for instance, mutation rate. We use yeast natural populations to examine how ecological factors shape genome diversity and function (Chris Eberlein) and to determine what is the consequence of this diversity on the formation and evolution of new species (Guillaume Charron). We also care about understanding how the impact of microbial interactions affect the fitness of organisms and how these interactions may alter how natural selection acts on genetic diversity within species (Clara Bleuven, Guillaume Nguyen). We are interested in the role of inter-species hybridization in generating adaptive diversity (Carla Bautista Rodriguez) and how hybridization affects the architecture and the rate of evolution of genomes (Souhir Marsit). Finally, we are examining the dynamics of propagation of internal cellular DNA parasites as a function of population demography and how the parasites could affect the organization of genomes and the fitness of the host organism over long-evolutionary times (Mathieu Henault, Marika Drouin). Our study systems are yeast and their associated microbes.

IV. Evolutionary genomics of pathogens and parasites
Parasites and pathogens have to evolve quickly to counteract the defense mechanisms of their hosts. We are examining how the host-pathogen and host-parasite evolutionary arms-race affects the evolution of pathogens and parasites. We use two very different systems to examine the consequences of these battles on genome evolution: one fungus and one animal. The first one is the pathogenic and dimorphic fungus Ophiostoma sp., which causes Dutch Elm Disease (Pauline Hessenauer, Anna Fijarczyk, Helene Martin) and the second, is the parasite worm Schistocephalus solidus, which has three intermediate hosts, including a model fish species, the three-spined stickleback (Helene Martin). In both cases, we are studying genomic and phenotypic diversity within pathogenic and parasitic species and among closely related species to identify how their genomes are impacted by their lifestyle.

Team and collaborators
All of the projects described above are led by students and postdoctoral fellows. They are supported by the work of research associates, Alexandre Dubé, Maria Isabel Acosta and Isabelle Gagnon-Arsenault. Most of these projects involve collaborations with other teams, including our principal collaborators Judit Villen (University of Washington), Gasper Tkacik (IST Austria), Nozomu Yachie (University of Tokyo), Marie Filteau (ULaval), Richard Hamelin (UBC), Nadia Aubin-Horth (ULaval) and Nicola Bisson (ULaval).

Visit our publication page for more details on our recent work.
Our research is supported by the Canadian Institutes of Health Research (CIHR), le Fonds de la Recherche en Santé du Québec (FRQS), the Canadian Foundation for Innovation (CFI), le Fonds de la Recherche Nature et Technologie du Québec (FRQNT) the Quebec Research Network on Protein Function, Structure and Engineering (PROTEO), the Natural Sciences and Engineering Research Council of Canada (NSERC), Genome Canada and Université Laval.