Periodic Reporting for period 1 - BEEP (Biodiversity Erosion in European medicinal Plants)
Periodo di rendicontazione: 2020-11-01 al 2022-10-31
Europe hosts a great diversity of wild species, many of which are unique to the continent. However, human-induced environmental change rapidly erodes Europe’s biodiversity, resulting in irreversible loss of valuable resources both for ecosystem functions and for human well-being. The main drivers of this loss include land-use change, over-exploitation and climate change, contributing cumulatively to species extinction. Despite the monitoring efforts put forth by many global and European conservation bodies, we still have limited understanding of the mechanisms underlying the responses of threatened populations to anthropogenic pressure. Threat status assessments under the Red List criteria of the International Union for Conservation of Nature (IUCN) rely mainly on temporal estimations of population sizes and species geographical ranges but overlook a major evolutionary mechanism that numerous conservation experts have now argued is critical for safeguarding biodiversity, i.e. the temporal variation in genetic diversity. Although this mechanism both determines and reflects species evolutionary responses to environmental pressure, incorporating it into conservation planning has been challenging due to lack of affordable technology, lack of interdisciplinarity, and gaps in the transfer of fundamental research to end-user conservation application. BEEP addresses these gaps by combining modern and affordable sequencing technologies for quantifying the magnitude of species genomic erosion, with earth observation and climate data for assessing the degree of the corresponding environmental change. By bridging diverse technological fields and scientific principles, BEEP provides an applied conservation tool for assessing extinction risk in wild populations in response to current and future anthropogenic pressure. I am showcasing the power and importance of this approach using threatened medicinal plants of the genus Sideritis (mountain tea or Ironwort), that are of significant conservation interest with regard to the United Nations' Sustainable Development Goals on good health (Goal 3) and life on land (Goal 15).
To achieve its goals, BEEP set two main objectives: 1) assess the extent of temporal genomic erosion during the last decades in three threatened medicinal herbs of mountain tea and 2) estimate temporal environmental change and predict the associated magnitude of genomic erosion in the mountain tea populations. Each objective was designed to be fulfilled through a work package (described below) and to contribute to my scientific training in the respective field.
To achieve its goals, BEEP set two main objectives: 1) assess the extent of temporal genomic erosion during the last decades in three threatened medicinal herbs of mountain tea and 2) estimate temporal environmental change and predict the associated magnitude of genomic erosion in the mountain tea populations. Each objective was designed to be fulfilled through a work package (described below) and to contribute to my scientific training in the respective field.
I started the project by visiting the three main European herbaria that hold the largest collections of the focal Sideritis species, i.e. Copenhagen (CP), Lund (LD) and the Goulandris Natural History Museum (ATH) in Athens. In these collections, I examined more than 200 samples and obtained crucial information regarding the past distribution mountain tea in the Balkans. I additionally retrieved leaf samples for DNA extraction from 120 individuals. Using the information obtained from the visited collections, I defined field work and sampling strategy for the modern populations. The goal of the field work was to revisit the same populations for which herbarium material was already available. I then carried out extensive fieldwork during the summer of 2021 and sampled populations in a total of 16 mountains in Greece. Herbarium and modern samples were brought to Senckenberg Biodiversity and Climate Research Centre (SBiK-F) for further analyses. For developing the genome of Sideritis scardica, I obtained seeds from a commercial cultivator in Greece that grows plants of known origin, and grew several plants at climate chambers in SBiK-F. I selected a single individual from the cultivated plants and conducted three types of DNA sequencing, i.e. PacBio long-read sequencing, Illumina shotgun sequencing, and Dovetail chromosome conformation capture. The resulting high-quality draft genome of mountain tea is ~1.1Gb long and is distributed in ~600 scaffolds. Finally, we extracted DNA from 64 herbarium and 64 modern samples, resequenced these individuals using Illumina shotgun sequencing at 30x coverage, mapped resequenced samples onto the draft genome, and compared historical with contemporary genetic diversity. The final results for Work Package 1, i.e. inference of demographic history and estimation of genomic erosion in mountain tea populations are being currently compiled and are expected to be available before the end of 2022 and published within 2023.
For carrying out Work Package 2, high resolution climate and satellite data had to be compiled from various sources. To this end, I evaluated several alternative data sources and I finally obtained high-quality climate data for the last four decades using the ERA5 atmospheric reanalysis product from the European Centre for Medium-Range Weather Forecasts (ECMWF). These climate data were downscaled to match the resolution of satellite data using custom analytical pipelines developed for BEEP. Similarly, I evaluated several sources of satellite data and I chose the Landsat archive (30m spatial resolution) due to its high degree of data availability through time. I then combined climate and satellite data together with more than 900 georeferenced records that were collected during the intensive field work to estimate the extent of environmental changes through time, i.e. temperature and vegetation change, in the mountain tea habitats. I further conducted habitat suitability modelling to estimate changes in suitable habitats for the mountain tea. The results of the temporal environmental change are available and show a dramatic reduction in the suitable habitats of mountain tea as a result of global warming and mountain greening. These results are expected to be published within 2023.
The first outcomes of the BEEP projects have already been presented in international conferences and are under consideration for publication in high-profile scientific journals. I further communicated the results through teaching activities to students of all ages and levels, from primary school to international PhD courses for early career scientists.
For carrying out Work Package 2, high resolution climate and satellite data had to be compiled from various sources. To this end, I evaluated several alternative data sources and I finally obtained high-quality climate data for the last four decades using the ERA5 atmospheric reanalysis product from the European Centre for Medium-Range Weather Forecasts (ECMWF). These climate data were downscaled to match the resolution of satellite data using custom analytical pipelines developed for BEEP. Similarly, I evaluated several sources of satellite data and I chose the Landsat archive (30m spatial resolution) due to its high degree of data availability through time. I then combined climate and satellite data together with more than 900 georeferenced records that were collected during the intensive field work to estimate the extent of environmental changes through time, i.e. temperature and vegetation change, in the mountain tea habitats. I further conducted habitat suitability modelling to estimate changes in suitable habitats for the mountain tea. The results of the temporal environmental change are available and show a dramatic reduction in the suitable habitats of mountain tea as a result of global warming and mountain greening. These results are expected to be published within 2023.
The first outcomes of the BEEP projects have already been presented in international conferences and are under consideration for publication in high-profile scientific journals. I further communicated the results through teaching activities to students of all ages and levels, from primary school to international PhD courses for early career scientists.
The design and outcomes of the BEEP project are highly-relevant to biodiversity protection policy and the sustainable utilization of natural resources. Protecting the natural medicinal resources is of outmost importance for future generations. Thus, the soon to be published research framework for assessing the extinction risk of medicinal plants is expected to be directly utilized by relevant policy makers, including the European Environmental Agency, the IUCN European Regional Office, IPBES, and the Greek National Centre for the Environment and Sustainable Development. The relevance of the BEEP project for the society is exemplified by its selection and publication through EU’s Horizon magazine under the title “Saving Europe’s medicinal plants from extinction”. This societal relevance is also reflected in my selection in the SCIENCE IN SOCIETY section of Horizon magazine where together with other leading European scientists I was asked to communicate my research and make predictions for scientific breakthroughs in 2022 (see europa.eu/!QTKR8G).