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Cryptic Clues: Spot the Difference with DNA

By Angela Lush

Scientists at the South Australian Museum are using molecular techniques to unlock one of nature's secrets – cryptic species.

Cryptic species appear almost identical and you can't reliably tell them apart based on their physical features. Despite their similar looks, cryptic species are genetically very different and can't interbreed.

In recent years, large-scale DNA sequencing technology has become more efficient and affordable and is increasingly being used to more accurately identify species. The technology is a valuable tool that is enabling researchers to reclassify many of the world's species, more reliably identify existing species, and uncover many new ones.

A study of Australian freshwater crustaceans (amphipods) by Dr Remko Leijs and Dr Rachael King has confirmed the existence of two species using DNA analyses. The two species had previously been classified based on slight physical differences and poorly understood geographical distributions. This made identifications quite haphazard and controversial.

"Identification of the two most common amphipods has been difficult and unreliable. While we thought there may be two separate species, we couldn't be sure," said Dr Leijs.

Dr King, a specialist in crustacean systematics, said that DNA analysis helped make identification based on physical characteristics (morphology) more accurate.

"The DNA analyses have helped us understand more about the group's morphology. They gave us strong clues to the physical characteristics that are variable within species and those that could be used to reliably define the different species," said Dr King.

Amphipods are a type of macroinvertebrate – animals without a backbone – that are large enough to be seen without the aid of a microscope. These freshwater crustaceans are commonly known as side swimmers or scuds and resemble short, fat prawns. Macroinvertebrates like amphipods are a critical component of healthy water systems. They are central to food webs; eating algae, living plants and the debris of dead plants as well as being eaten by fish, frogs, turtles and each other.

In a comprehensive and multi-year program, the researchers sampled amphipods from river systems throughout South Australia, Victoria and Tasmania and used molecular techniques to identify species.

"We uncovered two cryptic species in Tasmania and our DNA results showed that these Tasmanian species are sister species to the more common amphipods from South Australia and Victoria," Dr Leijs said.

The amphipod species discovered using molecular techniques also appeared to be specific to certain catchments or water sources. Female amphipods brood their young – they are not released from their mother until they are juveniles which is likely to limit their ability to disperse.

Around the world, similar molecular techniques have helped other researchers reveal cryptic species in populations of elephants, mosquitoes, birds and bats. Uncovering cryptic species is critical for conservation of species, particularly breeding programs, as well as effective management of pest species like mosquitoes.

Many water systems around Australia have yet to be sampled or have not been re-sampled since molecular techniques have become more accessible. This means that there is huge potential for discovering or more reliably identifying many more species hidden in Australia's rivers, ponds, billabongs and underground aquifers.

"We're now working on the amphipods of Kangaroo Island. There are four species there that evolved separately over half a million years ago," Dr Leijs said.

Excitingly, many of the species being uncovered are also new to science. It's a chance to reclassify species with far-reaching implications for effective conservation and protection of our natural environment.

Written by Angela Lush, lush logic.

South Australian Museum