City : Hamilton

Category : Other

Industry : Education

Employer : McMaster University

Project overview

Our program aims to:

- Experimentally improve/optimize sedaDNA workflows (extraction/purification, library preparation, capture enrichment, and metagenomic analysis) for terrestrial permafrost and marine sediments.

- Use these improved methods to reconstruct long-term terrestrial and marine ecosystem dynamics across the Quaternary, focusing on Canadian relic permafrost deposits and Pacific marine cores around Vancouver Island and the Canadian Arctic.

- Build the Canadian Ancient DNA (Can-aDNA) Network, a national platform for methodological sharing, training, and coordinated method comparisons/validation across Canadian ancient DNA labs.

Focus: Cross-cutting analytics and method development across permafrost and marine components, with an emphasis on metagenomics, de novo assembly, classification accuracy, and reproducible and sensitive pipelines. Develop AI or machine learning classification tools for low read abundance data and model accuracy and robustness of palaeoecological reconstructions (using serially sampled temporally discrete isolates).

Example activities:

- Test and optimize pipelines for shotgun, capture-enriched, and metabarcoding sedaDNA data, including quality control, taxonomic assignment, phylogenetics, and community analyses.

- Evaluate and compare metagenomic classifiers using simulated and empirical data to quantify false-positive and false-negative rates.

- Explore machine-learning approaches for improved sedaDNA identification and ecological dynamics reconstructions.

- Work with McMaster and Hakai’s in-house high-performance computing infrastructure systems and bioinformatics teams to support the project’s analytical needs.

Responsibilities

- Lead an independent but collaborative research program within your thematic area (bioinformatics), including experimental design, data generation, analysis, and manuscript preparation.

- Mentor and collaborate with PhD candidates and other trainees working on related sedaDNA projects (with 1-2 PhD and/or MSc students).

- Contribute to the Can-aDNA Network, including organizing and moderating online seminars, helping coordinate annual symposia, and engaging with the national community through the online forum.

- Spend time at both the Hakai Institute Biodiversity Genomics facilities on Quadra Island, BC (near the city of Campbell River on Vancouver Island) and McMaster University (Hamilton, Ontario), and other collaborating institutions as needed.

- Present research at national and international conferences and contribute to open, reproducible data and method sharing.

Qualifications

Required:

- PhD (completed or near completion) in a relevant field such as ancient DNA, molecular ecology, biomolecular archaeology, evolutionary genomics, bioinformatics, marine science, Quaternary science, or a related discipline.

- Demonstrated experience with ancient or environmental DNA and/or high-throughput sequencing data, with contamination control for the wet-lab-heavy roles, or with large-scale sequence data analysis and pipelines for the bioinformatics role.

- Strong quantitative, analytical, and writing skills, with evidence of peer-reviewed publications commensurate with career stage.

- Ability to work collaboratively within a multi-institution, interdisciplinary team and to mentor junior trainees.

Preferred:

- Strong skills in programming (e.g., Python, R, Bash, Machine Learning), high-performance computing, and metagenomic analysis; prior work with classifier benchmarking or machine-learning approaches is an advantage.

Terms and compensation

- Appointment length: 2 years (with the possibility of extension subject to funding.)

- Annual salary: CAD $70,000 plus benefits (provided in accordance with McMaster University guidelines.)

- Postdoctoral fellows will be employees of McMaster University, working closely with and spending time at the Hakai Institute.

- normal hours of work are 35 hours per week.