A new technology detects distinct fish populations in a single lake through their environmental DNA

A new technology detects distinct fish populations in a single lake through their environmental DNA

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credit: iScience (2023). doi: 10.1016/j.isci.2023.108669

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credit: iScience (2023). doi: 10.1016/j.isci.2023.108669

Using small bits of DNA that animals leave behind as they move through the environment gives researchers greater insight into where and how they live.

A new study has allowed scientists to not only learn what types of fish are present in the lake, but also determine how populations of those fish vary.

The development of environmental DNA (eDNA) water testing has allowed scientists and conservationists to find out which species were recently living in or moving through a particular area.

But this technology has its limitations. Typically, researchers test a type of DNA known as mitochondrial DNA. While this is useful for giving a binary yes or no for the presence or absence of certain species within a sample of lake water, for example, it is often not precise enough to give more detailed information about populations of those species.

To do this, researchers need to look for what is known as nuclear DNA. The problem here is that each nuclear genome is much larger but less abundant than mitochondrial DNA. This makes any given eDNA fragment rarer in the environment and more difficult to isolate.

But if it can be done, the potential could be huge. For example, it will allow researchers to track the complex genetic changes that occur within and between animal populations without having to see the actual species.

That’s where Dr Robert Collins, chief curator of fish at the Natural History Museum, comes in, with colleagues at the University of Bristol, the University of Cambridge and the Tanzania Fisheries Research Institute. They were able to detect nuclear DNA from two different groups of fish living within the same lake.

“I’m still amazed that it worked so well,” says Robert. “It was very much a pie-in-the-sky project.”

The results have been published in iScience.

Nature’s laboratory

The countless lakes spread across the Rift Valley in East Africa are often referred to as a natural laboratory.

This is because, in a similar way to the way the Galapagos Islands isolated groups of birds, creating new species, the lakes act like isolation islands for fish. This is especially true of a group of fish known as tilapia.

The constant geological disturbance in the area, which caused the Earth’s crust to split and form countless lakes and rivers during this time, separated the fish populations, bringing them together, while causing even more fish to disappear. This dynamic process has resulted in these lakes supporting at least 1,500 different species of tilapia, although this is likely a gross underestimate.

But not only between lakes there are differences in fish numbers. Even within lakes, there can be multiple habitats that allow fish to gradually diverge from each other and evolve into multiple species.

“We get this similar pattern in freshwater fish in the Northern Hemisphere as well,” Robert explains. “When all the ice sheets retreated and lakes formed, evolution occurred rapidly as new habitats were discovered.”

“So, it’s not something that’s specific to the tropics. It’s happening right on our doorstep, but with sharks, sticklebacks, and whitefish instead of tilapia.”

Lake Masuku in Tanzania is a great example of how this happens. A roughly circular crater lake, about 35 meters deep. Within it is a species of cichlid called Astatotilapia calliptera, which has split into two groups over the past thousand years. For fish that live in the shallow edges of the lake, males are usually yellow in color and feed on benthic invertebrates, while those that live in deeper water are dark blue and feed on floating zooplankton.

Despite living in different parts of the lake, and looking and behaving differently, the two groups are probably not genetically different enough to be considered separate species (although they may be on that path).

But this meant that the fish were an ideal subject for a study to see if genetic diversity within a species could be detected by sampling water alone.

more information:
Zhifang Liu et al., Nuclear environmental DNA resolves fine population genetic structure in aquatic habitats. iScience (2023). doi: 10.1016/j.isci.2023.108669

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