• Invasion genetics:

    The Baker and Stebbins Legacy


Inflorescence of Lythrum salicaria (purple loosestrife) (© Colautti Lab).

Change is Constant

The Colautti Lab investigates rapid evolution in a changing world

Human activity is causing rapid changes to the earth's ecosystems, benefitting some species with adverse effects on others. We investigate how human activity is changing genes, genomes and phenotypic traits of species in nature, and how this in turn affects the viability of species. Our approach combines cutting-edge advances in genomics and computational biology with experiments in controlled and natural environments. We think knowledge from these experiments can help improve human health and management of ecosystem services threatened by global change.

Main Research Projects

SARS-CoV-2 Anatomy
Anatomy of the SARS-CoV-2 virus responsible for the COVID-19 pandemic


Our lab's expertise in Data Science and Genomics have been put to use in COVID-19 research, including genome sequencing of SARS-CoV-2 genomes -- the virus responsible for the disease more commonly known as COVID-19. This work is currently ongoing with collaborators from Queen's University and Kingston Health Sciences Centre including Dr. Prameet Sheth, Dr. Calvin Sjaarda and others (see coauthors on papers linked below).

Phlogenomics of early-stage COVID-19 patients in Ontario, Canada

Our first research paper (published in Nature Scientific Reports) describes our sequencing of SARS-CoV-2 genomes using two different technologies, including a 'handheld' nanopore-based sequencer called the MinION by Oxford Nanopore. We analyzed SARS-CoV-2 genomes using evolutionary phylogenetics to identify sources of introduction and spread among the first COVID-19 cases in eastern Ontario. This work shows how portable sequencers and applied evolution can improve the public health response to emerging pandemics.

Fully reproducible code for this project is available on GitHub.

Temporal Dynamics and Evolution of SARS-CoV-2 in Ontario, Canada

Different genetic lineages (i.e. variants) have different mutations that may affect the rate of spread of COVID-19. In this study published in eSphere, we found variable infection rates in different lineages through time. Even in these early stages of the pandemic, variability in infection rates and the growing number of genetic lineages was cause for concern.

Metabolomics and Immune Response

Current projects (unpublished) track the immune response of COVID-19 patients and use chemistry of nasal swabs to identify biochemical changes in COVID-19 patients. These provide insights into the pathology of SARS-CoV-2, potential therapeutic targets, and the need for age-specific booster shots.

Dissected deer tick (Ixodes scapularis) exposing gut microbes and salivary glands (© Colautti Lab)

Ticks & tick-borne diseases

In situ detection, characterization, and risk assessment of tick-borne pathogens

Our 2021 opinion paper makes the case for a transdisciplinary research programme in vector-borne diseases, published in Trends in Parasitology

Rates of Lyme disease and other tick-borne illnesses are rapidly increasing in Canada and the United States. To better address this growing threat to human health, we are taking a multidisciplinary and integrated approach for in situ detection, characterization, and risk management of tick-borne pathogens. The objectives of this project are:

  1. Screen for known pathogens and identify environmental factors affecting disease risk.
  2. Develop and test field protocols and analytical tools for in situ microbiome analysis of tick, human and pet samples. This includes identification of known pathogens including distinct strains of Borrelia (the causative agent of Lyme disease).
  3. Build bioinformatics tools to match microbial DNA sequences between ticks and bite victims to identify candidates for new and emerging pathogens.
  4. Develop new risk assessment tools that, for medical educators, public health officials, and the affected populace, using updated models of risk of tick-borne pathogens.

Media coverage:


Tick Sequencing:
CTV | CTV (website) | National Post | Globe & Mail | CBC Radio Ottawa | Toronto Star | Kingston Whig-Standard

Tick Surveys:
Ottawa Citizen | Global Kingston | CBC Radio CTV Ottawa | CTV Ottawa Website | May 2021 Press Release


Tick Surveys:
Queen's Gazette | CTV | Global | ICI(CBC) Radio-Canada | Ottawa Sun | Whig-Standard | Kingston Herald

Hand-labelled tubes (top) and a variety of use-cases of the open-source baRcodeR package (© Colautti Lab)

Open-source for Open Science


download stats CRAN status CRAN version codecov repo status

baRcodeR is a tool for generating unique identifier strings and printable Linear or 2D (QR) barcodes. It improves repeatability of labelling biological samples and facilitates data collection, tracking and curating.

Available for R and on the web


  1. Graphical interface (R Studio) and command line options : install.packates(baRcodeR) in R
  2. Generate simple ID codes (Ex001, Ex002, Ex003,…)
  3. Generate hierarchical (i.e. nested) ID codes (Pop01-Trt01-01:00, Pop01-Trt01-02:45, Pop01-Trt02-01:00, Pop01-Trt-02-02:45, Pop02-Trt01-01:00,…)
  4. Generate printable PDF files of paired ID codes and QR barcodes
  5. Customize the PDF layout for any type of printable format (e.g, vinyl stickers, waterproof paper)
  6. Generate reproducible code for archival purposes (e.g. in publications or online repositories)
  7. Create CSV files to link unique IDs and sampling hierarchy with downstream data collection workflows.
  8. Integration with the PyTrackDat pipeline to set up a web-based data collection platform: PyTrackDat
baRcodeR links:
2pg Cheat Sheet | Quick-start guide | RStudio GUI instructions
GitHub | CRAN

Overhead view of ~4,000 Lythrum salicaria (purple loosestrife) plants growing in a common garden study at Queen's University Biological Station (QUBS) (© Colautti Lab)

Invasive Species and Evolution: Establishment and Spread

Rapid evolution facilitates invasion of invasive purple loosestrife

Climate and biotic interactions (e.g. herbivores, pollinators) can dramatically affect survival and reproduction in plants. We are combining genome and transcriptome sequencing with a large field experiment at the Queen’s University Biological Station (QUBS) to understand ecological and genetic factors that promote or constrain rapid adaptation in invasive Lythrum salicaria (purple loosestrife). This research helps to understand the role that evolution plays in the spread of invasive species.

Media coverage:

CBC | Popular Science | io9

Garlic mustard (Alliaria petiolata) growing in a common garden experiment at the Queen's University Biological Station (QUBS) (© Colautti Lab)

Invasive Species and Evolution: Impact

Do ecological impacts of garlic mustard evolve?

The invasive plant Alliaria petiolata (garlic mustard) engages in a natural form of biochemical warfare, secreting chemicals that can harm native plants directly and also indirectly by changing soil microbial communities. We are using genomic tools and field experiments at QUBS to investigate the effects of different garlic mustard genotypes on soil microbial communities. In short, we are examining how evolution affects the impact of invasive species.

Collecting seeds from native plants in the Northwest Territories (© Pippa Seccombe-Hett)

P-PLANTs Project

Predicting Plant Local Adaptation in the Northwest Territories

A major challenge for resource extraction and industrial development in Northern Canada is lack of access to biological resources for restoring disturbed habitats to near-pristine states.

The P-PLANTs project is a collaboration with the Aurora Research Institute in the Northwest Territories. We are applying genomic tools and field studies to characterize population genetic structure in native species used in restoration and reclamation projects. Many of these species can be difficult to distinguish based on morphological characteristics, and the extent to which populations are differentiated and adapted to local conditions is largely unknown. Our research will help restoration projects maintain the integrity of locally adapted populations.

Research Methods

Clockwise from top left: 1. Boechera retrofracta rosette in prototype imaging chamber; 2. Sequence alignment close-up; 3. Transplanting for large growth chamber experiment; 4. Illumina HiSeq Next-Generation DNA Sequencer (© Illumina)

Genetics & Bioinformatics

Decoding the Building Blocks of Life

We use high-throughput sequencing, 'big data', and bioinformatics to probe genetic variation underlying ecologically important traits and to understanding the complex relationship between genoype, phenotype, and the environment. Our ultimate goal is to understand how naturally-occurring genetic variants affect survial and reproductive rates (i.e. performance) under a variety of natural environments.

Lythrum salicaria a.k.a. purple loosestrife growing in a common garden study at the Koffler Scientific Reserve (University of Toronto). See Colautti and Barrett (2013)


Our research begins and ends in the field

Observations of organisms in natural and human-altered environments underpin our research in ecological genomics and evolutionary ecology. To investigate genes in nature we rely on field surveys and experimental manipulations at Queen's University Biological Station (QUBS) and other field sites around the world. These are complemented with the analysis of 'Big Data' characterizing aspects of the natural environment and human activity at regional to global scales.

Fitness surface from Colautti and Barrett (2010)


The Theoretical Foundation of Modern Biology

From the elegant simplicity of the Price Equation to the profound complexity of living systems, evolutionary theory provides a robust scientific foundation to develop a better understanding of the structure, function and dynamics of living systems.