A survey of genetic diversity among native Swiss living organisms

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Biodiversity researcher Lea Bauer at work in a peat bog. (Photograph: ETH Zurich
Biodiversity researcher Lea Bauer at work in a peat bog. (Photograph: ETH Zurich / Martin C. Fischer)
Switzerland is monitoring its biological diversity as part of a global effort to understand its changes and prevent further biodiversity loss. Researchers from ETH Zurich are working on a pioneering pilot study that includes the analysis of genetic diversity of native species.

The world is not only suffering from a climate crisis but also from a biodiversity crisis. Many researchers are already talking about a mass extinction of species. One of the many causes is global warming, which is rapidly changing environmental conditions.

This has prompted many countries to launch programmes aimed at monitoring and protecting biodiversity. In 2001, Switzerland created Biodiversity Monitoring Switzerland (BDM) to survey and monitor the diversity of species and habitats in a standardised way using hundreds of observation units.

Black box genetic diversity

Through BDM, Switzerland has built up a detailed picture of the species and habitat diversity visible to the naked eye. But it’s a different story when it comes to genetic diversity within species. This is because it cannot be detected by the naked eye, which makes collecting data more complex and technically challenging.

Genetic diversity is the raw material for evolution and is needed by a species to adapt to a changing environment. Understanding changes in genetic diversity and their drivers may help ensure the long-term survival of a given species. Animal or plant populations with only a low level of genetic variability face a greater risk of extinction. This is because they often lack the resilience to withstand diseases, pathogens or extreme weather, or to adapt to environmental changes.

Researchers from ETH Zurich and the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) now want to close this knowledge gap. Scientists from ETH’s Plant Ecological Genetics group are currently carrying out a pilot study on behalf of the Swiss Federal Office for the Environment (FOEN). This study aims to explore how to establish a long-term monitoring programme of the genetic diversity of selected species native to Switzerland. This pioneering study was launched in 2020 and is expected to continue until the end of 2023.

Probing five species

In their pilot study, the researchers initially restricted their investigations to five native animal and plant species: the Natterjack toad (Epidalea calamita), Yellowhammer (Emberiza citrinella), False heath fritillary (Melitaea diamina), Carthusian pink (Dianthus carthusianorum) and Hare’s tail cottongrass (Eriophorum vaginatum). These species are representative of specific habitats of conservation relevance that include dry meadows, raised bogs, amphibian habitats, agricultural landscape, and transition zones between forests and grasslands.

Having randomly selected 30 locations per species throughout Switzerland, the researchers took samples from more than 1,200 individual specimens, from which they extracted their DNA back at the lab.

While catching and sampling the Yellowhammers and Natterjacks, the researchers were assisted by specialists from the Swiss Ornithological Institute in Sempach, the Swiss coordination centre for reptile and amphibian protection (KARCH) and species specialists from three different environmental consultancies.

Using specialised analysis equipment and high-performance computer infrastructure provided by ETH Zurich, the researchers fully sequenced - in other words decoded - the organisms’ DNA one building block at a time. This generated a vast amount of data. "Printing out the genetic information contained in a single cell of a Natterjack toad would fill more than 630,000 A4 pages. That’s a stack of paper 70 metres high," says the project’s manager, Martin C. Fischer of the Plant Ecological Genetics group at ETH Zurich.

To compare today’s genetic variability with that present around the year 1900, the researchers also looked at the DNA of samples - some of them up to 200 years old - housed at herbaria and zoological collections. In this case, they restricted their investigation to two species: the butterfly and the cottongrass.

The researchers had to examine these samples in a cleanroom laboratory to avoid contaminating what little remains of this ancient DNA. "Such museum pieces contain only fragments of DNA, similar in quality to that of a 10,000-year-old mammoth in permafrost," Fischer says. "Analysing it was enormously time-consuming and labour-intensive." The results of the DNA comparison are not yet in.

High variation in genetic diversity

The researchers are now working hard to prepare and evaluate the data they collected. They can already spot some initial trends.

For the Yellowhammer, the most mobile of the species studied, genetic diversity is still fairly even throughout Switzerland. Several populations of Natterjack toad, however, appear to be genetically impoverished. They may be suffering from a lack of contact with neighbouring populations with higher genetic diversity.

Natterjack toads live in temporary bodies of water on gravel and sand banks that form and reform in dynamic rivers. Since such habitats have become very rare in Switzerland, this species of amphibian has colonised gravel and clay pits - and even military practice areas - which are often isolated pockets within the landscape. As this puts them out of reach of other toads searching for new habitats and mates, populations are no longer mixing.

"Small, isolated populations with low genetic diversity and a high degree of inbreeding are at great risk of dying out," Fischer says. Even a chance event - like an unusually hot summer or a new kind of parasite - can bring a species to the brink of extinction in a particular area. If their genetic diversity were higher, they would be better equipped to cope with such chance events and environmental changes.

It’s a different story for the Carthusian pink, a flowering plant found in dry meadows. "We identified multiple genetically different evolutionary lineages," Fischer says. These most likely formed during one of the last ice ages, which the plant survived in various refuges outside the Alps. Once the glaciers had receded, the plant made its way back into Switzerland and across the rest of Europe.

To their surprise, the researchers discovered plants from a genetic lineage that is native to eastern Europe and was not thought to be present in Switzerland at all.

This genetic variant is indistinguishable in appearance from the Carthusian pink from Switzerland and, according to Fischer, is used in seed mixes planted either as part of ecological revegetation initiatives or in private gardens. This gives imported variants the opportunity to cross with indigenous plants, introducing genetic diversity that - because it developed elsewhere under different environmental conditions - is alien to that locale. This has the potential to weaken the population. "It’s hard to predict what the effects will be when such alien genetic lines cross with native plants. That’s why we have to monitor the situation," Fischer says. "Unfortunately, when it comes to seed mixes for revegetation or private gardens, attention is sometimes paid only to species composition and not to genetic origin."

Fischer and his team want to complete their evaluation by the end of this year. They are already planning a two-year follow-up study to prepare for long-term monitoring and to gain further experience in standardised data collection, data evaluation and archiving. Their goal is to examine the genetic diversity of 50 species every five to ten years. The researchers are particularly keen to incorporate mammals such as bats, forest and aquatic organisms, and fungi into their genetic monitoring.
Peter Regg