The role of DNA in species discovery

MSU's blog | Created 5 years ago

To the surprise of some, most of the earth’s biodiversity remains undiscovered and undescribed. In 2011, Camilo Mora and colleagues calculated there are approximately 8.7 million eukaryotic species on earth (eukaryotes are those organisms that we normally think of, like plants, animals and fungi), and of these, 85% remain undescribed and/or unknown to science.

One of the responsibilities of researchers who work with collections is to continue to discover and describe new species. Traditionally, this was based on morphological traits (how the animal looks), and associated data about geography and ecology. However, with the advent of molecular biology, traditional approaches are being supplemented with DNA to assist in the discovery of species.

DNA is often described as a blueprint for life, and as you may expect, every species has its own unique blueprint. The fact that different species harbour unique DNA allows us to directly sequence the DNA of the specimens and compare them to existing sequences from other identified specimens (a sequence library). For many specimens, the sequence will be very similar to a known, existing sequence, allowing us to identify specimens with similar sequences as the same species. This is the basic premise for DNA barcoding, which helps link specimens of unknown species to known species. Morphological identifications (IDs) are difficult or impossible for some specimens with missing body parts, or juveniles, so DNA barcoding might be the only way to ID them. You can read more about here.

However, in some instances the DNA sequence may not closely match any known sequences…

Why use DNA if the specimen looks different to known species?

In many instances, we may not know if the specimen has morphological features that would constitute a new species. This may be because the specimen is a different sex or age class to have the diagnostic features that the species description was based on. Also, it may only be a fragment of the whole organism; the result of non-invasive sampling like hair trapping, or a damaged specimen.

The final reason we may pursue DNA methods, even when morphological characters are present, is because there isn’t time to look at every morphological detail on every specimen that is needed to make IDs using species keys. This could be because the specimens are very small and difficult to see, even under microscopes, or because existing taxonomic expertise is unavailable. It is a sad reality that taxonomic specialists are becoming increasingly rare, making the morphological identification of species in some groups a troubling proposition.

Fortunately, DNA sequencing allows us to identify the specimens that do differ from known species and focus our limited resources on them.

How different is different?

I was being intentionally optimistic above when discussing matching new DNA sequences to existing sequence libraries. Very rarely do DNA sequences match exactly for the genomic regions used for DNA barcoding and species discovery. Using a gene region like CO1, two specimens from a single species may have as many as one nucleotide different for every 9 shared, equating to a divergence level of 10%. For some groups, this may even be as high as 15%, or as low as 5%.

Unfortunately, there is no solid recommendation for this, and there is always a degree of uncertainty when considering if a newly sequenced specimen belongs to an already described species. Different taxonomic groups have different rates of mutation, so any threshold considered must be relevant to the group under study. However, when your newly sequenced specimen is found to differ from existing ‘known’ sequences in that taxonomic group, it’s time to start digging a bit deeper because you may have…

…a new species!

Of course, this is what we are looking for, but there are a lot of checks to go through.

First, it may be that your sequence library is incomplete, and you may have simply produced the first sequence for an already described species. This is one of the most difficult parts of using DNA for species discovery: the incompleteness of sequence libraries.

Second, by using morphology to place the specimen into a smaller taxonomic group, like a genus, we can quickly work out what sequences are available for described species to compare to. We can also work out what sequences are unavailable, and if possible, create those sequences ourselves from specimens in the collection, or organise field trips to recollect specimens of an unsequenced species. An improved comparison library means that the power of detection of new species increases.

Putting theory into practice

WA Museum Head of Terrestrial Zoology Dr Mark Harvey and I recently travelled to Hyden to collect specimens of Merredinia damsonoides, a species of open-holed trapdoor spider that was described in 1983 by Barbara Main. The original specimen (holotype) was unsuitable for DNA work, so we returned to the original location of that description (type locality) to recollect a new specimen, which could be sequenced for DNA. The motivation for recollecting this specimen was to add it to a sequence library with species of a closely related genus, Teyl. With this library, we wanted to confirm or deny the existence of a new species of trapdoor spider collected in the Pilbara, which appeared to belong in that group.




Merredinia damsonoides
Image copyright Mark Harvey | WA Museum 

By sequencing this needed example of Merredinia damsonoides, we worked out the species may belong to the genus Teyl. We also added a sequence of Teyl luculentus to the library, which is found in the south west of Western Australia. When comparing our putative new Pilbara species to this library we were then able to confirm its identify as a new species of Teyl. This new species seems to be restricted to the Pilbara, east of Karijini National Park. This work was funded through the WA Museum’s Net Conservation Benefits Fund, which is aimed at understanding and conserving biodiversity in the Pilbara’s marine and terrestrial environments.

We are yet to add sequences from T. harveyi, T. walker and T. yeni, the other described species from the genus. However, all three are found in Victoria, making us confident that our new species of Teyl from the Pilbara is unique.

This putative new species in the Pilbara would have been difficult to confirm without DNA, as the family to which it belongs, Nemesiidae, is made up of many undescribed species, and the genera within Nemesiidae are not well understood (for example, we found that Merredinia damsonoides should, and will become Teyl damsonoides).

To identify these particular spiders morphologically, males are often required as they possess the diagnostic characters, and unfortunately females and juveniles are more commonly found. Although males of our new Pilbara Teyl are available, we couldn’t be sure that Teyl from areas south of the Pilbara didn’t also belong to our new Pilbara Teyl. Therefore, to confirm that the new species is restricted to the Pilbara, we also sequenced specimens from other areas. This demonstrated that the new species was restricted to the Pilbara, and also uncovered other new species of Teyl in Western Australia.

In this instance DNA provided a powerful tool to assist taxonomists to discover new species.



Teyl sp. Pilbara
Image copyright Mieke Strong | WA Museum 

References - Mora, Tittensor, Adl, Simpson, and Worm (2011) How Many Species Are There on Earth and in the Ocean? PLoS Biol 9(8): e1001127.

This work is funded by the Gorgon Barrow Island Net Conservation Benefits Fund.