DNA barcoding: a better way to discover species

It’s time for a change in the way we categorise life on Earth. ஆ ன ந் த ம் / a n a n d h a m

It might surprise you to learn that the idea of a “species” is one of the more ambiguous concepts in science.

Originally, “species” (meaning “kind” or “sort” in Latin) was used to refer to organisms that looked different and, for more than 250 years, physical differences were used to differentiate between species.

But now, with the rise of a technique known as “DNA barcoding”, it’s easier than ever to determine the identity of and relationships between species.

In the 250 years since Swedish botanist Carl Linnaeus formalised the taxonomic method, there have been a number of discoveries that have necessitated a better definition of “species”.

Such discoveries include:

  • sexual dimorphism: where sexes of the same species look different (such as lions and lionesses)
  • metamorphosis: where organisms radically change in form (such as caterpillar to butterfly)
  • homoplasy: where unrelated organisms look and function similarly due to similar environmental selection pressures (such as wing development in insects, birds and bats).

A shift to the idea of sexual isolation – the concept that a species is a group of organisms that can successfully interbreed – was useful from an ecological and evolutionary point of view, but not very handy for species identification. More recently, scientists have turned to genetics.

Comparing the genetic code of organisms has made species identification much easier, but there are still strong arguments about the level of genetic difference that indicates a boundary between species.

This lack of consensus about how to define a species really means any identification is subjective. Identification through taxonomy (the physical attributes of an organism) or phylogenetics (a species’ genetic code) is a bit of a “dark art”, relying on the opinion of one or a small number of experts. Such identifications are often highly contested.

For instance, the Eucalyptus genus has been controversially revised several times since the 1930s. This has included splitting Eucalyptus from one to three genera and 13 subgenera, and adding more than 100 species (usually as a result of splitting existing species).

In The Origin of Species, Charles Darwin said:

“No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species”.

So for all of the difficulty we have in understanding and identifying species, a better question might be: does it really matter?

Sexual dimorphism is one of the reasons the definition of “species” needs to be revised. tobyjm

DNA barcoding is a recent development in genetics, in which a short DNA sequence is read from any genetic sample. This DNA sequence is recorded in a public database such as GenBank or Barcode of Life Data Systems (BOLD).

This sample can then be compared against all other samples to infer how closely related two organisms are. Rather than recording the best judgement of one scientist (or a small group) in saying that a specimen is of a particular species, DNA barcoding can provide a more objective analysis.

In a famous case study, DNA barcoding was used to demonstrate that a common butterfly from Central America was in fact a complex of at least ten species with very similar morphology (form and structure) living within the same region. This discovery exposed a wealth of hidden biodiversity.

For the first time in biology, DNA barcoding means each sample is a genuine “data point”, showing that at a certain place and a certain time, an organism with a recorded gene sequence was present. When species are reclassified or previous taxonomies are thrown into doubt, ambiguity about species boundaries are removed. All data collected are as valuable as the day they are recorded.

The availability of individual genetic data means we can transform ecology from a species-based to gene-based view. This is important, because it’s much closer to how the biological world actually works.

Ecosystems are really a dynamic system of genes with fluid boundaries between what we regard as species. While we think of “evolution” as a linear process whereby organisms become more complex, it’s really just the process whereby genes change in nature. This change is particularly fluid in the microscopic world, where bacteria can spontaneously incorporate genes from unrelated organisms into their own genetic code.

The collection of genetic information will also allow data to be processed in completely novel and complex ways, and with a level of robustness and quantification not previously possible. We can track individual genes across time and landscapes to understand the nature of evolution and how ecosystems around us are changing at the most fundamental level.

Embracing genetic technologies can transform ecology from a “soft science” – subject to the opinions and vagaries of a few scientists – to a “hard science”. Irrefutable data are collected and can be analysed in a multitude of different ways (including evolutionary relationships) shifting the way we view ecosystems.

Scientists will continue to use morphology for quick identification, and often this will be good enough. But for cutting-edge science and answering the next suite of questions in biology, we will need to improve our precision.

This isn’t to say we should completely abandon the concept of species but we can do better than to see the concept of “species” as static with rigid definitions and boundaries.