Research

The general theme of our research is the study of evolutionary processes at the genomic level and the use of sequence information to investigate biodiversity, ecosystems, and environmental change. The work in our group spans from molecular evolutionary biology to technology development and bioinformatics. We have partnered with collaborators ranging from Government Agencies (eg. Environment and Climate Change Canada, Canadian Food Inspection Agency), NGOs (eg. Living Lakes Canada, World Wildlife Fund Canada), industry (environmental consulting firms) and have relationships with many international research groups.

DNA Metabarcoding

Over the last two decades, taxonomic marker genes (e.g. DNA barcodes) have been sequenced from a wide range of organisms. For example, BOLD (Barcode of Life Datasystems) hosts over 14M DNA barcodes from 250,000 species. Pairing these reference DNA sequences with High Throughput Sequencing (HTS) technologies has revolutionized genomics data generation. Environmental DNA metabarcoding aims at gathering biodiversity information through the analysis of selected marker genes from bulk samples such as water, soil, and sediments. This information can be used in addressing a wide range of ecological/evolutionary questions or in applications such as environmental assessment and tracking harmful or endangered organisms. Our lab pioneered DNA metabarcoding for the analysis of benthic macroinvertebrates used widely as bioindicators of aquatic ecosystems. We further developed this approach for the analysis of tropical insects and their associated microbes collected passively through Malaise traps. We are applying these DNA metabarcoding methods at a large-scale through the STREAM project, which partners with community groups across Canada to collect benthic samples for DNA metabarcoding using standardized field and lab protocols, with the goal of exploring and assessing freshwater communities across the country. See our papers on Biomonitoring 2.0 (Baird & Hajibabaei, 2012) and STREAM (Robinson et al. 2021)

Biodiversity Transcriptomics

Comparative transcriptomics provides tremendous potential for investigating how species respond to environmental change from individual physiological scale to ecological and evolutionary scales. Given recent advances in HTS technologies, RNA sequencing has become a feasible approach for large-scale analysis of transcriptomes. Whole or targeted transcriptomics (e.g. genes involved in certain pathways) can be applied on large sample sizes across a broad phylogenetic spectrum. We are developing comparative transcriptome-based approaches mainly for non-model organisms (e.g. aquatic bioindicator species) to gain insights on evolution of transcriptomes as well as understanding molecular responses at ecological scale.

Bioinformatics

At the core of any DNA or RNA-based project is the bioinformatics, including reference database construction/quality control, processing pipelines and downstream analysis. Through different facets of bioinformatics we aim to standardize, improve, and develop workflows and analyses for use in a variety of biodiversity & One Health applications. Examples of recent advances developed in the lab include: MetaWorks (Porter & Hajibabaei, 2022), and LANDMark (Rudar, et al. 2022)