Barcoding Biodiversity: DNA Barcodes and Environmental DNA (eDNA)
Definition
DNA Barcodes
DNA barcodes are short, standardized DNA sequences unique to each species, much like product barcodes in a store. These genetic "fingerprints" enable species identification, even from small or incomplete samples.
- Traditional identification of species often depends on morphological features (e.g., flower shape, body markings).
- Many organisms are hard to identify: plants without flowers, insect larvae, or rare animals that leave only traces behind.
- DNA barcoding and environmental DNA (eDNA) provide a modern method for rapid and accurate species identification.
- A feather found in a forest can be analyzed for its DNA.
- By amplifying the CO1 gene using polymerase chain reaction (PCR) and comparing it to a reference database, scientists can identify the bird species, regardless of visual evidence.
Environmental DNA (eDNA)
Definition
Environmental DNA (eDNA)
Environmental DNA (eDNA) refers to genetic material shed by organisms into their surroundings through skin cells, mucus, feces, or other biological materials. It enables species detection without direct observation.
How Does eDNA Work?
Imagine investigating a pond’s biodiversity:
- Sample Collection: Collect water, soil, or air samples from the environment.
- DNA Extraction: Use chemical and physical methods to isolate DNA.
- Amplification: Amplify barcoding regions using PCR to increase detectable DNA.
- Sequencing: Sequence the amplified DNA to read its genetic code.
- Comparison: Match sequences to a reference database to identify species.
- Its advantages are:
- Allowing detection of elusive, nocturnal, or rare species.
- Non-invasive, preserving species and habitats.
DNA Barcodes: The Genetic "Fingerprint"
- DNA barcodes are chosen from genes conserved across species, but which also show enough variation between species.
- Animals: Cytochrome oxidase subunit I (COI) in mitochondrial DNA is widely used.
- Plants: Chloroplast genes rbcL and matK.
- Prokaryotes: 16S ribosomal RNA genes.
Applications of DNA Barcoding and eDNA
- Rapid Biodiversity Assessments: Barcoding and eDNA enable quick surveys of biodiversity, which can inform conservation priorities.
- Monitoring Invasive Species: Early detection of invasive species prevents ecosystem disruption.
- Tracking Endangered Species: DNA-based methods confirm the presence of endangered species without disturbing them.
- Disease Surveillance: eDNA can track pathogens in the environment, providing early warnings of outbreaks.
Advantages of eDNA
- Non-invasive: eDNA can be collected without harming organisms.
- Efficient: Barcoding and eDNA allow for rapid data collection and analysis.
- Broad Scope: These methods can detect a wide range of species, including those that are rare or difficult to observe.
- Cost-Effective: Compared to traditional surveys, eDNA analysis requires fewer resources and less field time.
- One common mistake is assuming eDNA can always provide a complete picture of biodiversity.
- Factors like sampling method, environmental conditions, and database quality can all affect results.
Limitations of eDNA
- Degradation: eDNA breaks down quickly, requiring timely sample collection.
- Database Dependence: Accurate identification relies on comprehensive, up-to-date reference databases.
- False Positives/Negatives:
- Contamination may cause false positives.
- Degraded or low-quality DNA can lead to missed detections.
- Taxonomic Resolution: Barcodes may not distinguish between closely related species.
Sampling water for eDNA in a heavily polluted area could lead to degraded DNA, making species identification difficult or incomplete.
Self review- Define DNA barcoding and explain how it differs from full genome sequencing.
- What is environmental DNA and why is it especially useful in detecting rare or elusive species?
