Topic 18: Using eDNA to determine stocking histories, pollinators and glacial bacterial communities Flashcards
What is eDNA?
Genetic material present in samples such as sediment, water, air, other organisms in a larger organism
Can be from whole cells, extracellular DNA or whole organisms in environmental samples left behind from animal material
How is eDNA identified from DNA sequences? 4 steps
It can be preserved, extracted, amplified and sequenced (or detected by qPCR), and then identified from DNA sequences
Detection of eDNA may vary based on biomass, physiology, life history, space use, age and quality of DNA
What are 4 reasons to study eDNA?
Higher chance of detecting species
Cost effective (collection is simpler, less time and expertise required)
Accurate (new species identified without error, point of much debate)
Non-invasive (causes less disturbance or organisms and sensitive habitat)
What are the differences between traditional DNA barcoding and eDNA barcoding?
Traditional: method of specimen identification using a standardized short segment of DNA, universal primers used to amplify region of mtDNA that is taxon specific
Taxon identified by Sanger sequencing
eDNA: taxon specific primers used to amplify a specific region PCR product from a mixed environmental DNA sample
Taxon is identified by qPCR or band detection
What is eDNA metabarcoding?
Multi-taxon identification using a standardized very short segment of DNA, taxonomic group universal primers are used to amplify a region of mitochondrial DNA
Taxa are identified by next generation DNA sequencing
What are drawbacks of eDNA barcoding?
No information on life tables, demographics, health of population
Little correlation between abundance of eDNA and species abundance
False positive and false negatives
Lack of connection to conservation
Can eDNA be used to detect plant animal interactions verified with conventional pollinator visual surveys?
Wanted to know if we could use eDNA metabarcoding to detect both insect and vertebrate visits from multiple flowering plants species simultaneously.
Found that eDNA identified many pollinator species that were not observed by traditional field observation, and also has some false negatives (species observed in field observation and not eDNA)
Some species identified that were likely not present (false positives), likely not pollinators, or plants were amplified by bird primers
Can sedDNA from lakes be used to reveal historical events of human-mediated trout introductions, and to reconstruct unknown history of westslope cutthroat trout?
Combined high throughput sequencing technologies with standard paleolimnological sampling techniques
Genomic regions containing species specific SNPS were amplified from the sedDNA and sequenced to detect historical presence of two common WSCTT
Results:
Mystic lake had WSCTT before human mediated introductions
Marvel lake showed the same thing
From the WSCTT experiment, what were four things that were determined about lake sedDNA?
It can be used to determine:
- the colonization history of freshwater fishes
- identification of native ranges
- novel native diversity
- introductions of non-native species
What techniques were used in the bacterial communities in glaciers study?
Taxa determined by terminal restriction fragment length polymorphism (tRFLP)
Concentration of nitrate may indicate different bacterial communities (nitrate reducing activity), and bacterial communities differ by site and type
