Ancient DNA

The palaeoecology branch of Hakai’s Biodiversity Genomics scientific team features a purpose-built, state-of-the-art ancient DNA facility designed to recover and analyze ancient and highly degraded DNA from a wide range of environmental contexts and fossil materials.

Ancient DNA science requires ultra-cleanroom facilities and full body coverings to mitigate modern environmental DNA (from us and the local ecosystem) from contaminating the genetic code preserved in ancient remains.

Ancient DNA (aDNA) can be recovered from many forms of buried remains such as discrete fossils like bones, teeth, and soft tissues; mixed materials like ancient faeces or residue substances on artifacts (e.g. tools and cookware) and teeth (dental plaque), and completely disaggregated contexts like sediments, soils, and ice. Ancient environmental DNA is a particular focus here, where we study the DNA that was passively released into the environment by organisms many thousands of years ago that ended up preserving outside of tissues through chemically binding to minerals and organic compounds in the environment. These disseminated sources of aDNA allow for whole ecosystem taxonomic cataloging and multi-species genome reconstructions all from what are otherwise ordinary looking clumps of dirt.

With cutting edge methods and technology, we can routinely recover genome-scale DNA from whole ecosystems using a wide range of fossils, artifacts, and other remains that are hundreds of thousands of years old (Figure design: T.J. Murchie).

Because aDNA is highly degraded and in low abundance, we require ultra-cleanroom facilities with robust operating procedures to rigorously recover and study DNA preserved in ancient remains to ensure that the ancient strands do not become contaminated with comparatively high abundance, undamaged modern DNA. This inherent challenge means that aDNA science exists at the cutting edge of genomics, next generation sequencing, computational biology, radiometric dating, archaeometry, and forensics, among many other associated disciplines and technologies. These underpinnings enable us to recover some of the most difficult and fragmentary DNA on the planet to reconstruct long lost ecosystems of plants, animals and microbes over immense timescales, and reassemble the genomes of these long dead creatures to conduct large scale evolutionary research programs on extinct organisms. These efforts have a wide variety of applications for both understanding past biological processes, managing contemporary biodiversity, and mitigating losses to come in an ever-changing world.

SedaDNA source locations targeted by our Alliance research program from their (a) geographic setting, (b) unique depositional conditions, and (c) manner by which environmental DNA is damaged and modified as it becomes part of buried records. (Grant, D.M., DOI:10.5281/zenodo.18237018)

Ultraviolet-C (UVC) light is a high-energy, short-wavelength form of electromagnetic radiation (100–280 nm) that acts as a powerful, non-chemical sterilizer for decontaminating workspaces (hoods and entire rooms) for aDNA research.

Through close integration with Quadra’s Genomics facility, we have capabilities for multi-method aDNA extractions from nearly all possible sample types, expertise with numerous double and single stranded library preparation methods, in-house RNA bait design and synthesis for targeted capture enrichment via RNA hybridization, quality control and quantification assays through qPCR, ddPCR, QIAxcel, and many other NGS associated technologies and platforms, on site high-throughput sequencing for rapid data acquisition, and fully in-house data analysis and bioinformatic processing through Hakai run high performance computing nodes house at the University of Victoria.

aDNA starts in the cleanroom and progress through to the modern genome lab, eventually ending up as billions sequences of nucleotides (A, T, C, G) on our servers that we analyzed with high performance computing systems.

We’re actively working on aDNA projects studying ancient megafauna in northwestern North America, 100,000+ year old permafrost sediments from across the Arctic, deep marine sediment cores from the Pacific, and a range of materials from archaeological sites globally. We have expertise in metabarcoding, targeted capture, and shotgun sequencing, enabling our team to tailor our approach to the samples and research question at hand to pull incredible quantities of ancient biomolecules from highly degraded materials of all forms. These data allow us to understand deep time evolutionary processes, ecological transformations over hundreds of millennia—from the impacts of humans during the Holocene to changing hydrological cycles before humans ever existed—along with reconstructing the structure and functional interactions of whole ecological systems through time.

Here are several clickable end-product examples of aDNA findings from our research initiatives at Hakai:

We’re the co-recipient of a 2.3 million dollar NSERC Alliance grant through our partnership with Dr. Hendrik Poinar at McMaster University, helping us drive forward new ancient DNA methodologies, ecological and evolutionary insights, and to help us develop a Canadian network of ancient DNA scientists nationwide to develop standards of excellence through multi-institutional cross-training and integrated research partnerships. This initiative is helping train the next generation of palaeogenomic scientists while piecing together the deep history of ecosystems and people across Canada to unlock mysteries now only preserved in microscopic fragments of long-lost DNA.