NSERC Alliance – Canadian Sedimentary DNA

What we are doing and why it matters?

Canada’s permafrost and coastal marine sediments hold extraordinary archives of environmental DNA, preserving deep records of past ecosystems over hundreds of thousands of years. Yet most of the DNA workflows we use to study these deposits remain inefficient and variable, with the vast majority of preserved molecules never making it into sequencing libraries. This limits our ability to reconstruct how ecosystems responded to major climatic transitions and to use those long-term records to inform conservation and climate adaptation today.

Ancient DNA science has transformed our ability to reconstruct past environments and evolutionary histories. But in most ancient sediment samples, >99.9% of DNA is microbial, while the tiny fraction of target DNA is damaged, mineral-bound, and mixed with chemical inhibitors. Large portions of that already-scarce signal are lost at every step of standard workflows (desorption, purification, library prep, ligation, etc.), leaving much of the palaeoecological information in sediments effectively inaccessible.

At the same time, Canada’s high-latitude ecosystems are already experiencing rapid warming, biodiversity loss, shifting species ranges, and changes in ocean chemistry and circulation. To understand and anticipate how ecosystems will respond, we need deep time baselines that span multiple glacial–interglacial cycles and capture past episodes of warming, cooling, and ecological reorganization.

Our Alliance project tackles these challenges through two main objectives:

1. Objective 1 – Expanding sedaDNA capabilities across terrestrial and marine archives
   • Experimentally optimize sedaDNA workflows at each stage (extraction, inhibitor removal, library preparation, capture enrichment, metagenomic analysis) for Arctic permafrost and deep marine sediments.
   • Apply these improved methods to key archives, including long permafrost sequences in Yukon and marine cores from the Pacific Northwest, to reconstruct how plants, animals, fungi, and microbes responded to major environmental transitions.
2. Objective 2 – Building the Canadian Ancient DNA (Can-aDNA) Network
   • Establish a national network that connects ancient DNA labs across Canada.
   • Create regular venues (virtual seminar series, annual in-person symposia, and an online forum) for labs to share method tests, troubleshooting, and comparative results that often remain “in house” and unpublished.
   • Standardize and cross-validate workflows, accelerate method development, and move more optimization work into the peer-reviewed literature and open protocols.

The overall goal is to unlock much more of the sedaDNA signal preserved in Canadian sediments, generate robust deep-time records of ecosystem change, and support evidence-based conservation and climate adaptation.