www.gov.uk/natural-england Using DNA based methods for monitoring Andy Nisbet
www.gov.uk/natural-england
Using DNA based methods for monitoring
Andy Nisbet
Why use DNA based methods for biological monitoring?
Which species? IdentificationWhere? Location/distributionHow much? Abundance
Sampling bottleneck and low detection rate
Why use DNA based methods for biological monitoring?
Which species? IdentificationWhere? Location/distributionHow much? Abundance
Identification bottleneck and taxonomic inconsistency
Why use DNA based methods?
Why use DNA based methods
DNA based methods
DNA barcoding or targeted assays• What species is this?
• Is species X present?
PCR/qPCRSingle or few targets
Presence absence or semi-quantification of genes (qPCR)
High throughput, low/medium cost
DNA barcodes = short regions of a genome, usually mitochondrial egCytochrome Oxidase 1 (CO1)
DNA based methods
DNA metabarcoding = high throughput, can analyse mixed samples• What species are here?
High throughput sequencing Many targetsRelative quantification (possibly)High throughputMedium/high costs
• Linked to reference database to identify organism (eg Barcode of Life Database (BOLD))
DNA based methods
Environmental (eDNA)
Community
Targeted assays for Protected and Invasive species
Great Crested Newt (Triturus cristatus)Annexes II and IVStandard qPCR technique in UK
Targeted assays for Protected and Invasive species
Native white clawed crayfish (Austropotamobius pallipes) – Annexes II and IV
Invasive signal crayfish(Pacifastacus leniusculus)
A metabarcoding approach for Protected Species
Nene Washes SPA and SACAnnex II species – Spined Loach, Cobitis Taenia
Spined loach in the Nene Washes
Metabarcoding invertebrate communities
Vane trapping2 sites in Lincolnshire and Staffordshire
Riparian pitfall trapsRiver Frome, Dorset
Metabarcoding invertebrate communities –River Frome by family
Using DNA based methods
Pros• Does not rely on limited number of taxonomic specialists• Can be automated and standardized• Scalable to 1000s of samples• Can identify cryptic species, species that are difficult to detect (including at
different stages in life cycle)• Less prone to error?
Cons• Costs and protocols still in flux, including field sampling• Less cost effective for small sample• Reference databases need to be improved• Need to understand transport and persistence in water and sediment• Limited information on abundance
Where are we now?
• Use for vertebrates is well developed. eDNA is very effective for surveying fish and standard protocols are being developed for fish in lakes.
• Targeted assays are being developed for Protected and Invasive species.• DNAquanet are working to standardise approaches across Europe to using
eDNA for Water Framework Directive monitoring.• Metabarcoding can be used to characterising trap caught terrestrial
invertebrate samples (but understand the limitations).• More work is needed on using metabarcoding of invertebrates from water
and sediment samples.• Huge potential – protected species, characterising communities, INNS,
pests and pathogens.• Takes time and resources to move from proof of concept to routine
operational use.• Will still need ecologists to interpret results.