Environmental DNA & Barcodes
DNA barcodes
- A DNA barcode is a DNA sequence that can be used to quickly identify a species
- DNA barcodes are short sequences, usually just a few hundred base pairs in length
- The base sequences that are used for barcodes are often taken from mitochondrial DNA in eukaryotes, and ribosomal RNA in prokaryotes
Environmental DNA (eDNA)
- DNA barcodes can be used to determine which species are present in a particular habitat; this can be necessary for various reasons, e.g:
- For researchers investigating the biodiversity of different habitats
- Predicting the impact of development on an area of land
- Assessing the impact of land use change
- Using eDNA to identify species can be much quicker than observing and manually identifying organisms
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- Plants can be difficult to identify if they are not in flower, or have no leaves
- Some insect larvae may be very similar in appearance
- It may not be possible to physically capture all of the species that are present
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- The process of extracting DNA from a habitat is known as eDNA sampling
- eDNA sampling can be used to identify species present in a habitat as follows:
- Multiple eDNA samples are taken from the habitat of interest, e.g. water samples from a body of water, or soil samples from a terrestrial habitat
- Traces left by the organisms will be present in the samples, e.g:
- Cells that have brushed off an animal's skin
- Fur or feathers lost by mammals or birds
- Waste that has been released into the environment
- Leaves that have fallen to the ground and partially broken down
- Traces left by the organisms will be present in the samples, e.g:
- DNA in the samples is amplified using PCR
- The amplified DNA is sequenced to determine the order of bases present
- The specific sequence within the DNA that forms the barcode is compared to a database of known sequences
- DNA sequencing technology means that the DNA sequences of many species are now known, and are stored in easily accessible databases
- E.g. the Barcode of Life Data System (BOLD)
- A strong match with a known sequence means that researchers can confidently say that a species is present at a sample site
- A less-strong match may mean that further sampling is required
- Multiple eDNA samples are taken from the habitat of interest, e.g. water samples from a body of water, or soil samples from a terrestrial habitat
Environmental DNA sampling diagram
eDNA samples can be amplified and sequenced, and then compared to a database of known sequences to allow identification of unknown species present in an environment