eDNA – the future of conservation and ecology?

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In a paper published last month in Molecular Ecology, scientists reported that a species of frog thought by the scientific community to have gone extinct was rediscovered in the dense Brazilian Atlantic rainforest. The species, Megaelosia bocainensis, had not been sighted for over 50 years, and was known only from one museum specimen collected in 1968. However, the ‘rediscovery’ of this species was not performed by traditional means, with a textbook team of field ecologists diligently sampling a large area, but instead through the cutting-edge collection and analysis of environmental DNA (eDNA), a relatively new ecological technique which collects and analyses DNA which is ‘shed’ by organisms. 

eDNA can allow for the ‘rediscovery’ of species previously thought to be extinct

For larger animal species such as frogs this shedding is thought to mostly take place through the excretion of cells or tissue in sources such as urine, faeces, hair or skin2. Scientists then identify sites in which the DNA from the species that they are interested in is likely to reside, which in this case was samples of water from local plants, ponds, streams and rivers (but in other studies has ranged from deep sea sediments to rockpools). The DNA recovered is then sequenced and compared against other DNA samples from known species in the large databases of sequence data available for this purpose. The technique is particularly useful for gathering data on rare or difficult to find species in densely forested regions such as the Brazilian rainforest, since researchers only require access to sites visited by the animal, rather than an extensive search for the animals themselves.

This is not the first time that eDNA techniques have been pivotal in the rediscovery of species previously thought to have gone extinct. In February this year the New York Times reported that after scientists discovered a rare yellow sally stonefly, assumed to be locally extinct across large areas of Wales, the DNA sequence of this individual was then used to test other sites, with the scientists finding that the species was also likely present in several other nearby sites. 

Invasive species are often discovered too late for effective action to be taken

However, the technique has been useful for more than just searching for rare species, and has also been applied with great utility to invasive species research, community level studies, and studies of past environments, in which DNA (which degrades over time, but often can still be useful after a long period) from extinct species can sometimes be gathered from an environment to allow scientists to study past ecosystems and species.

The application of eDNA techniques to the study of invasive species operates in a similar way to eDNA studies on rare species, in which an area is sampled with a specific invasive species in mind in order to check for its presence. This has been performed in a variety of different environments for a range of different invasive species and has often been found to be highly effective. For example, in a 2016 study published in the Journal of Applied Ecology, eDNA was used to discover the presence of an invasive crayfish in two lakes where they had previously never been sighted. This highlights the ability for eDNA technologies to identify the presence of invasive species at much lower population densities than traditional methods. This is especially useful for invasive species, as they are often only detected when they reach higher numbers and start to become a problem. eDNA methods allow the detection of invasive species at much lower population sizes, allowing for more cost-effective conservation management, since less organisms need to be exterminated or removed.

Although very promising, eDNA methodologies still have a ways to go before they can reach their full potential

Another useful application of eDNA sampling is in collecting data on whole communities of species at the same time. For example, a 2017 study published in Marine Biology used eDNA sampling to study seasonal changes in fish communities off of the coast of Denmark. This study found that it was just as effective (and obviously much less time consuming and labour intensive) to take samples from the ocean water and test for eDNA rather than the traditional method of sampling with snorkelers, with eDNA identifying some species that were not picked up by the traditional method.

However, eDNA technologies are still in their infancy, and at present have weaknesses to overcome before they can reach their full potential. One of these weaknesses is the incompleteness of some DNA databases, which are essential to properly identifying the samples obtained in the field, while another weakness is the possibility of contamination of samples while sampling at multiple sites and repeatedly using the same equipment, both in the lab and in the field. However, if these problems can be overcome, the future for eDNA technologies may be bright.

Image: Tamara Masters via Flickr

2 thoughts on “eDNA – the future of conservation and ecology?

  • Excellent article, I think that all advances in DNA techniques will always be a gain for the world, both in knowledge and prevention. – Gustavo Copelmayer.

    Reply
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