DNA barcoding reveals hidden species diversity

The Earth is an almost unimaginably diverse planet in terms of species. Researchers have identified between two and three million species, but there are many more that we know nothing about.

The unknown species are called ‘biological dark matter’, borrowing a term from astrophysics. 

We want to demonstrate how we can gain a better overview of biological dark matter by using DNA barcoding.”

Emily Hartop, Associate Professor 

DNA barcoding, in this case so-called ‘megabarcoding’, might sound mysterious, but it isn’t really. We will come back to that later. First, let us take a look at why we don’t know enough yet.

Why some species remain unknown

Hartop works at the Department of Natural History, which is part of the Norwegian University of Sience and Technology (NTNU) University Museum. At the department, she is surrounded by colleagues who are also used to discovering new species, and they are unlikely to run out of new tasks anytime soon.

“Biological dark matter often exists in groups consisting of very multiple species which we have not yet studied in any great depth,” said Hartop.

There are many reasons why we do not know more than we do, and some of them are purely of a practical nature.

Many of these unidentified species are found in the ocean or in other parts of the world that are difficult for researchers to access. Not all of these species are found in great numbers either, so it is not always that easy to find them.

And that is not the whole explanation: even in parts of the world where there have been dedicated researchers for hundreds of years, such as Europe and North America, we are still far from getting a complete overview.

“These unknown species can be found everywhere,” said Hartop.

A huge task and not enough experts

A lack of researchers trained within this field of expertise is undoubtedly a problem. The task is simply so large that there are not enough experts in relation to the workload.

A common estimate is that there are nearly nine million species on our planet, but we do not know for sure, and figure this does not include bacteria and other single-celled organisms. In any case, there is still much more left to discover than what we already know.

Identifying a species is not something just anyone can do. There are many species out there that most people would think look identical.

New method making the job easier

Fortunately, the biologists have started using an efficient new method in recent years: DNA barcoding.

“In DNA barcoding, you only need a tiny bit of DNA to identify a species,” Hartop explained.

This small sequence of DNA can then be compared against a database of DNA from species that have already been described and recorded. To be certain that a species is new, the DNA database must be complete with known species from the group you are comparing it to. The work to fill the reference library is continuously being carried out through national and international projects.

Large numbers of unknown insects found

The researchers in this study concentrated on insects in Sweden. They collected flies from a total of 37 habitats at four different times of year. They ended up with 31,800 DNA samples to analyse and achieved very good results.

“For example, we found a total of 549 different potential species of scuttle fly. This is a surprisingly high density and diversity,” said Hartop.

Previously, only 374 of these species of scuttle fly (Phoridae) were known, meaning that 175 species were new to Sweden.

Environmental variations affect species composition

The source data also give researchers an opportunity to find out how different environmental variations affect the composition of species in an area.

“With regard to scuttle flies, we see that the prevalence of the different species is influenced by climate factors. For example, it appears that 29 per cent of the species respond positively to an increase in average temperature, while 18 per cent respond negatively,” said Hartop.

Important to quickly establish an overview

“It is important to gain an overview of the biodiversity around us. This means that we must study the inconspicuous, but species-rich groups. We live in a time where biodiversity is under threat, including the unknown species,” said the associate professor.

According to the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the greatest threat to biodiversity is the loss of habitat, for example due to developments or the drainage of wetlands. The second biggest threat is the exploitation of species, such as hunting for bush meat, logging or overfishing. Then comes climate change, pollution and the spread of species to areas where they don’t belong.

At the root of all this is an ever-growing human population with ever-growing needs. It is essential to identify which species actually exist, and that is where DNA barcoding will play a very important role.

“We see that this method can help us to quickly and efficiently gain an overview of the species. The time is ripe to explore the biological dark matter,” concluded Hartop.