Shedding light on dark diversity – Scientists aim for a breakthrough in describing new species

Research into as yet unknown species, known as 'dark diversity', will start with insect species in the jungle that do not have a name but already have a DNA barcode.

Rapidly advancing molecular technologies allow DNA to be sequenced and separated quickly, and to produce a DNA-based species identifier, or a DNA barcode, that allows species to be identified. But unknown species also need to be named and described, and this is where the new research project aims to design, test and bring systematic and automated, efficient workflow on an unprecedented scale.

The topic has inspired researchers around the world, and the "A Genomic Blueprint for the Description of Thousands of New Species" project, which was launched in September 2024 and is funded by the Research Council of Finland, involves researchers from Finland, the USA and Canada. New researchers are currently being recruited. The Research Council of Finland, Finland's contribution to the University of Oulu's research is almost half a million euros over four years.

Species identification is important for understanding changes in nature. The 2 million species described during the last 260 years of taxonomic scrutiny represent just a fraction of the species inhabiting our planet. Current estimates of the world’s true species count vary heavily from few millions to tens of millions or even more. Utilization of traditional approaches to describing the remaining majority is becoming increasingly challenging due to multiple reasons – the high number of undescribed species, their tiny size, high morphological similarity and lack of taxonomic expertise.

"We are on the threshold of a new era. Traditional methods of species identification are too slow to address the challenges of biodiversity in the face of rapid biodiversity loss," says Professor Marko Mutanen of the University of Oulu, who is leading the international research project.

The radical approach made possible by the technological revolution is also generating critical debate among researchers when it comes to the fundamental issues in the field: What should a species description include and how should it be done?

Easier to build descriptions and classifications for unknown species

Insects serve an ideal model to develop and test the “augmented minimalistic approach”. They are one of the most species-rich animal groups, and central to many ecosystems. Insects have remained largely unknown and unclassified compared to, for example, birds. In Finland, for example, there are less than 400 known species of gall midges (Cecidomyiidae). Doctoral researcher Niina Kiljunen used DNA barcoding already in her master’s thesis to discover an estimated 1000 new species of gall midges in Finland. The number of species in Finland could be considerably higher, several thousand. A large proportion of these are probably unknown to science.

Gall midges are small delicate flies, of which some species cause galls on plants, some eat decaying plant debris among other things, but do not feed on blood of humans or animals.

Under the leadership of Professor Daniel H. Janzen, a member of the research team, nearly one million DNA barcodes of an estimated 40 000-50 000 species of Costa Rican gall midges have been read. Of these, hardly any have been given a scientific name.

Is a barcode a new species?

The systematic separation, naming and description of Costa Rican DNA barcoded gall midge species is being carried out at the University of Oulu. An important fundamental question of the research project and the new species identification is: How do we determine whether unknown DNA barcodes truly are different species?

In developing a new method of species identification, independent genetic information about species will be combined with DNA barcoding. Researchers will look at other genetic traits in the DNA barcoded samples to see if they lead to the same conclusion about species boundaries. When independent genetic traits reach the same conclusion, it is then clear that the species is distinct from other species.

"DNA-based species description will be based on DNA barcodes and other genetic markers," says Kiljunen. DNA-based descriptions can also be combined with traditional identification and classification.

The method being developed could pave the way for efficient science to discover new species and accelerate and innovate species identification.

The partner universities of the new research project are University of Guelph, University of Pennsylvania, University of Kentucky and University of Eastern Finland.

The challenges of species identification

"The challenge of species identification is similar to that of physicists: most of the material is lost," says Mutanen. Some estimates put the number of animals, plants and fungi at around 8,7 million, but that leaves out bacteria and viruses, for example. Estimating the number of species is complicated by dozens of different species definitions. According to the well-known concept of species, organisms belong to the same species if they can interbreed and produce fertile offspring. On the other hand, dogs, coyotes and wolves, for example, can interbreed but are often considered to be different species.

The identification of species is still largely based on visual assessment of the characteristics of the specimens. This takes time and becomes more difficult when differences are considered over a wide geographical area on a high number of undescribed tiny species. This difficulty is compounded, for example, by the fact that old DNA and type specimens have already decayed, some species are extinct or old descriptions are incomplete.

In addition, the principle of priority requires finding out whether a species has already been described somewhere, which is a slow, almost historian's work. "If we consider the whole historical record and do a detailed anatomical analysis of each species, we will be stuck," says Mutanen. "One proposed solution is to rapidly train large numbers of taxonomists, or species classification specialists, to classify species, but we will still face a dead end if the methods and principles of classification are not developed."

However, with new forms of species identification made possible by new technology, some scientists are concerned about the disruption of traditional methods that have been in use for a long time. For example, scientists appreciate the two-part, practical naming system of the father of taxonomy, the botanist Carl von Linné. However, at the time of Linné's major work in 1758, the number of species was thought to be only a fraction of the current estimates. "If, at that time, the number of species had been estimated at, say, 30-40 million, I believe that Linné would have wanted to reconsider the classification principles," says Kiljunen.

For example, nematodes are estimated to be present on one million square metres of Finnish forest land. "Nobody knows how to identify them at all, even though they have a very important ecological function as decomposers of dead plant matter. If we could describe nematode species, we would understand the functioning and changes in forest ecosystems in a completely different way than we do today," Mutanen dreams.

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A Genomic Blueprint for the Description of Thousands of New Species project

Research in ecology and genetics at the University of Oulu