4 Using DNA sampling
A variety of techniques has now been developed to identify species, based on their chemical composition rather than their visual appearance. In particular, tiny differences in the DNA molecule can be used to distinguish between species.
There are several different techniques that can be used to distinguish between species from their DNA, one of the most common of which is DNA barcoding. This is a process by which the DNA of a tiny sample is extracted and compared with the DNA of reference samples from known species. The matching between samples is an automated process.
In most groups of organism, there are species that are difficult or impossible to tell apart using traditional techniques. For example, the three large obvious bumblebee species Bombus lucorum, B. cryptarum and B. magnus are very similar and almost impossible to distinguish morphologically (Figure 8). Bees are important pollinators and are often used in citizen science projects. But these three species have to be recorded as just ‘Bombus lucorum complex’ rather than one of the three individual species, making it very difficult to track how each of the individual species is doing (Bossert, 2015).
This problem is especially acute in identifying fungi that have visible fruiting bodies for only a short period of the year. Even microscopic examination can sometimes prove inconclusive.
The waxcap fungi (genus Hygrocybe, family Hygrophoraceae) are one of the most beautiful and easily recognised groups of fungi (Figure 9). In the UK they are also a target for conservation efforts and statutory designations, since the presence of a high diversity of this group of fungi normally indicates an unfertilised, biocide-free grassland. In 2011, a report from Defra observed the following:
… the level of species diversity within Hygrocybe is substantially greater than that presented in the current guidebooks and scientific treatments. Further research is needed, but we currently believe that at least 96 species are present in the UK (as defined by DNA sequence-based methods), compared with the 51 species (plus 8 varieties) currently accepted. This newly discovered diversity has profound implications for conservation management, and the relevant SSSI [Site of Special Scientific Interest] guidelines based on species numbers will need some reassessment. Bearing in mind the diversity we have uncovered and the knowledge that western European waxcap habitats are considered of high conservation value on a continental scale, it would not be surprising if some of the species were found to be endemic to the British Isles.
The report goes on to mention that the discovery of cryptic species (i.e. species that look the same and can be distinguished only on examination of their DNA) has implications for fieldworkers and identification books. It is also possible that such cryptic species might be identified by other diagnostic characteristics such as ecological factors or geographic distribution. The report also said that there is still a place for citizen scientists in the monitoring of waxcap habitats.
The use of DNA techniques can give a high degree of confidence in species identification, which can lead to the development of new morphological characters for identification in the field. With the Bombus lucorum complex, a variety of different morphological characters has been tried and checked using DNA methods. This means that it is possible to gauge how confident we can be in using a new identifying morphological character to distinguish between different species, so that the amount of confidence can be assigned to each of the characters.
DNA barcoding can also be used in a number of other circumstances such as identifying species in complex ecosystems, identifying cryptic life stages where morphological features are unknown, the criminal investigation of illegal trading in animals and plants, and analysing food, including determining the origins of foodstuffs intended for human consumption. DNA barcoding is also used increasingly in environmental DNA analysis, where water or some other environmental material is sampled and the organisms present can be detected from traces of their genetic material. Such analysis may also give an indication of their abundance.