Sampling of the five species was fairly successful despite a wet and cold spring and a gloomy summer.
At the beginning of April 2021, the teams of the Swiss Ornithological Institute started sampling the Yellowhammer (Emberiza citrinella). They sampled about 120 bird over a two-month period. The anticipated number of 150 samples was not reached because bird trapping was hampered by the cold and wet spring. Nevertheless, birds were sampled in 23 of the 30 planned collection quadrats.
Between early April and late July 2021, experts commissioned by the Coordination Center for the protection of Amphibians and Reptiles (karch) were able to collect a total of about 150 samples in the form of embryos or tadpoles of the natterjack toad (Epidalea calamita) in 28 of the 30 planned quadrats. It was often necessary to find replacement quadrats because the natterjack toad, as a pioneer species, often changes its habitat, causing occurrences to disappear and emerge elsewhere. In addition, it is also one of the amphibian species in Switzerland whose populations are in sharp decline.
Just over 220 false heat fritillaries (Melitaea diamina) were collected by various environmental agencies between mid-June and mid-August 2021 in 22 of the 30 planned sampling quadrats. Rainy weather and hailstorms that severely impacted vegetation in some study areas hampered the collectors’ work and limited the number of sunny days on which butterflies were flying and could be sampled.
From early June to early August 2021, environmental agencies successfully sampled 30 populations and 300 individuals of hare’s tail cottongrass (Eriophorum vaginatum). A replacement collection quadrat was needed twice because the species was either no longer present or there were too few individuals at the actual designated location.
Sampling of the Carthusian pink (Dianthus carthusianorum) by environmental agencies was also successful. 31 populations and 330 individuals were sampled between late May and early July 2021. Six replacement collection quadrats were needed, often in regions where Carthusian pink was artificially seeded.
The random stratified proportional sampling strategy proved to be efficient in the field and we covered the climatic space of each species well, as it can be seen in the figure below with the hare’s tail cottongrass as an example. The randomly sampled individuals and populations (red dots) cover the climate space of the species in Switzerland (gray dots) well. The climate space covers the range from low to high mean annual temperature (e.g. low and high elevation regions) on the X-axis, and high to low rainfall regions can be seen on the Y-axis.
The work on retrospective analyses using museum and herbarium samples is currently underway. DNA from museum and herbarium samples that are older than 40 years is highly fragmented, usually with fragments shorter than 70 base pairs. It is also more damaged compared to DNA from freshly collected samples, making it highly susceptible to contamination by new and fresh DNA from humans or other samples processed in the laboratory. These properties necessitate the use of state-of-the-art clean lab, such as those available at the Institute of Evolutionary Medicine (IEM) at the University of Zurich. This clean lab has all the necessary equipment for the various stages of ancient DNA analysis, including a positive pressure system, UV sterilization, and several isolated workstations where research personnel work in full-body protective gear. Only thanks to this careful approach, the recovery and sequencing of DNA from voucher specimens is possible in a reliable manner. Currently, about 200 voucher specimens each of the hare’s tail cottongrass and the false heat fritillaries from Swiss collections are processed in the clean lab.
The preparation of the reference genomes of the five species is well advanced and thanks to new sequencing technologies (PacBio HiFi Reads and OMNI-C Scaffolding) the quality of the reference genomes have exceeded our expectations. Most genomes were assembled almost to chromosome level. This is even true for the natterjack toad, which has the largest genome of the five species and with 3.8 billion base pairs, it is even larger than the human genome.
Great work awaits us this year as well. The DNA of the 1,120 collected samples will be extracted, sequenced and analyzed. In addition, work continues on the museum samples in the clean lab. After the extraction and sequencing of the DNA, these sequences will be analyzed and compared with the modern samples.