Flurin Leugger

Last Name

Leugger

First Name

Flurin

ORCID

0000-0001-9027-6892

Show all metadata

Search Results

Publications 1 - 8 of 8

An integrated high-resolution mapping shows congruent biodiversity patterns of Fagales and Pinales
Lyu, Lisha; Leugger, Flurin; Hagen, Oskar; et al. (2022)
Entomologia Experimentalis et Applicata
The documentation of biodiversity distribution through species range identification is crucial for macroecology, biogeography, conservation, and restoration. However, for plants, species range maps remain scarce and often inaccurate. We present a novel approach to map species ranges at a global scale, integrating polygon mapping and species distribution modelling (SDM). We develop a polygon mapping algorithm by considering distances and nestedness of occurrences. We further apply an SDM approach considering multiple modelling algorithms, complexity levels, and pseudo-absence selections to map the species at a high spatial resolution and intersect it with the generated polygons. We use this approach to construct range maps for all 1957 species of Fagales and Pinales with data compilated from multiple sources. We construct high-resolution global species richness maps of these important plant clades, and document diversity hotspots for both clades in southern and south-western China, Central America, and Borneo. We validate the approach with two representative genera, Quercus and Pinus, using previously published coarser range maps, and find good agreement. By efficiently producing high-resolution range maps, our mapping approach offers a new tool in the field of macroecology for studying global species distribution patterns and supporting ongoing conservation efforts.
Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA
Leugger, Flurin; Schmidlin, Michel; Lüthi, Martina; et al. (2024)
Molecular Ecology Resources
More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.
Dispersal and habitat dynamics shape the genetic structure of the Northern chamois in the Alps
Leugger, Flurin; Broquet, Thomas; Karger, Dirk Nikolaus; et al. (2022)
Journal of Biogeography
Aim Understanding the drivers of species distribution ranges and population genetic structure can help predict species' responses to global change, while mitigating threats to biodiversity through effective conservation measures. Here, we combined species habitat suitability through time with process-based models and genomic data to investigate the role of landscape features and functional connectivity in shaping the population genetic structure of Northern chamois. Location European Alps. Taxon Northern chamois (Rupicapra rupicapra). Methods Using a model that simulates dispersal and tracks the functional connectivity of populations over dynamic landscapes, we modelled the response of the chamois to climate change from the last glaciation (20,000 years ago) to the present. We reconstructed species habitat suitability and landscape connectivity over time and simulated cumulative divergence of populations as a proxy for genetic differentiation. We then compared simulated divergence with the actual population structure of 449 chamois (with >20 k SNPs) sampled across the Alps. Results We found that Alpine populations of chamois are structured into two main clades, located in the south-western and the eastern Alps. The contact zone between the two lineages is located near the Rhone valley in Switzerland. Simulations reproduced the geographic differentiation of populations observed in the genomic data, and limited dispersal ability and landscape connectivity co-determined the fit of the simulations to data. Main conclusions The contemporary genetic structure of the chamois across the Alps is explained by limited functional connectivity in combination with large rivers or valleys acting as dispersal barriers. The results of our analysis combining simulations with population genomics highlight how biological characteristics, habitat preference and landscapes shape population genetic structure over time and in responses to climate change. We conclude that spatial simulations could be used to improve our understanding of how landscape dynamics, shaped by geological or climatic forces, impact intra- and interspecific diversity.
Rapid field-based detection of a threatened and elusive species with environmental DNA and CRISPR-Dx
Leugger, Flurin; Lüthi, Martina; Schmidlin, Michel; et al. (2025)
Global Ecology and Conservation
With accelerating biodiversity erosion, it is critical for species conservation to use rapid and scalable monitoring methods. One powerful biodiversity monitoring method that has emerged recently is environmental DNA (eDNA). eDNA analyses currently require lengthy protocols in well-equipped laboratories, slowing down the analyses and limiting applications across broad scales. Here, we developed a protocol for eDNA analyses, leveraging CRISPR-based diagnostic systems (Dx) with lateral flow tests to rapidly process and analyze eDNA samples on site. To test the versatility of the field-based protocol, we designed a CRISPR-Dx assay specific to the threatened and elusive African manatee (Trichechus senegalensis). We sampled water across ten locations in a national park in the Republic of Congo and detected manatee DNA directly on site in almost half of the sites. We later confirmed these detections with a high-sensitivity protocol in a well-equipped laboratory. The CRISPR-Dx detections were mainly confirmed with a previously reported quantitative PCR (qPCR) assay. Despite the lower sensitivity of the field-based protocol, our analysis shows that its speed and ease of application provide advantages over slower and more expensive methods to detect threatened and elusive species, in particular if the protocol is improved in the future. Our methodology will increase the accessibility to and speed of eDNA analyses, enhancing biodiversity monitoring efforts and species conservation initiatives.
An integrated high-resolution mapping shows congruent biodiversity patterns of Fagales and Pinales
Lyu, Lisha; Leugger, Flurin; Hagen, Oskar; et al. (2022)
New Phytologist
The documentation of biodiversity distribution through species range identification is crucial for macroecology, biogeography, conservation, and restoration. However, for plants, species range maps remain scarce and often inaccurate. We present a novel approach to map species ranges at a global scale, integrating polygon mapping and species distribution modelling (SDM). We develop a polygon mapping algorithm by considering distances and nestedness of occurrences. We further apply an SDM approach considering multiple modelling algorithms, complexity levels, and pseudo-absence selections to map the species at a high spatial resolution and intersect it with the generated polygons. We use this approach to construct range maps for all 1957 species of Fagales and Pinales with data compilated from multiple sources. We construct high-resolution global species richness maps of these important plant clades, and document diversity hotspots for both clades in southern and south-western China, Central America, and Borneo. We validate the approach with two representative genera, Quercus and Pinus, using previously published coarser range maps, and find good agreement. By efficiently producing high-resolution range maps, our mapping approach offers a new tool in the field of macroecology for studying global species distribution patterns and supporting ongoing conservation efforts.
Advancing biodiversity monitoring through eDNA from singlespecies detections to ecosystem state assessments
Leugger, Flurin (2025)
To tackle the current biodiversity crisis, scalable biodiversity monitoring methods are needed to trackvbiodiversity changes and inform conservation measures across the globe. With the advancement of molecular tools over the past decades, environmental DNA (eDNA) has developed into a promising method for biodiversity monitoring. Spectacular case studies have revealed the high sensitivity of eDNA and its potential for large-scale biodiversity monitoring. The methods currently available for eDNA analysis focus either on single species (mainly with quantitative PCR [qPCR]) or community analysis with metabarcoding. As soon as multiple species are of interest, metabarcoding is the method of choice. Yet, the analysis with metabarcoding, and to some extent also with qPCR, require fully equipped laboratories and well-trained personnel, limiting the large-scale application of eDNA analysis. Thereby, existing bias in biodiversity monitoring is reinforced, as most studies focus on well-developed countries. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based diagnostic systems (Dx) were recently developed to detect nucleic acids in resource-limited settings for diagnostics and first applied on eDNA in 2019. However, they have been employed with speciesspecific primers, which makes their use for multispecies detections inconvenient and restricts their use for biodiversity monitoring. In this thesis, I introduce the concept of ‘ampliscanning’ – combining multispecies primer pairs with CRISPRDx to detect multiple taxa of interest – to close the gap between single-species assays with qPCR and metabarcoding. Additionally, I develop a field-based protocol of ampliscanning to rapidly perform eDNA analysis in the field with very limited infrastructure. By circumventing the limitations associated with metabarcoding and lab-based qPCR assays, field-based ampliscanning democratizes access to eDNA analysis. Ampliscanning is highly sensitive and very efficient to detect elusive and endangered species, such as the great crested newt (Triturus cristatus) (chapter 1). Compared to traditional monitoring, eDNA and ampliscanning detected more target amphibian species per site. Additionally, ampliscanning performs similarly to metabarcoding when using the same multispecies primer pair, highlighting its potential for multispecies assessments (chapter 2). By integrating biodiversity information from the entire catchment, even terrestrial mammals can be monitored with catchment-based sampling of river water. This allows large-scale biodiversity monitoring to be performed, for example in areas that are difficult to access. The field-based ampliscanning protocol successfully detected the threatened African manatee (Trichechus senegalensis) in a national park in the Republic of Congo (chapter 3). Moving beyond the monitoring of specific target species, eDNA metabarcoding sequences indicative of the ecosystem state could be identified. Few – that is eight – indicator eDNA sequences from aquatic insects successfully classified ecosystem state similar to traditional methods (chapter 4). Creating indicator CRISPR-Dx assays which can detect multiple eDNA sequences was partially successful due to non-specific behavior of some CRISPR-Dx. Thus, ampliscanning and eDNA perform well when used with species-specific CRISPR-Dx, while indicator CRISPR-Dx detecting multiple taxa simultaneously demand further development. To advance biodiversity monitoring with eDNA, this thesis introduces the concept of ampliscanning including a field-based protocol. By showcasing the potential of eDNA and ampliscanning for catchment-based eDNA monitoring and to detect elusive and threatened species, this thesis and the therein developed methods should benefit large-scale biodiversity monitoring. The field-based protocol, particularly when further optimized to increase sensitivity while decreasing handling complexity, should democratize access to eDNA analysis, enabling biodiversity monitoring in regions currently lacking monitoring. Thereby, this thesis could support the advancement of biodiversity monitoring to inform efficient conservation measures, ultimately helping to safeguard biodiversity.
CRISPR-Dx and Metabarcoding Perform Similarly for Monitoring Mammals With eDNA on the Catchment Level in High-Alpine Ecosystems
Leugger, Flurin; Lüthi, Martina; Schmidlin, Michel; et al. (2025)
Environmental DNA
Biodiversity monitoring in difficult-to-access areas, such as rugged mountain ranges, is currently challenging and thus often absent. Environmental DNA (eDNA) offers new opportunities to monitor remote or strictly protected areas, as rivers integrate the biodiversity information of entire catchments. Environmental samples can be analyzed either with metabarcoding or using species-specific assays. Species-specific assays like quantitative polymerase chain reaction assays do not require a fully-equipped laboratory and thus can be used in settings with limited resources and are especially suited to monitoring elusive or threatened species of management concern. Recently developed molecular tools, such as CRISPR-based diagnostic systems (CRISPR-Dx), provide new avenues to facilitate eDNA analysis through species-specific assays. Here, we combine multispecies primers with CRISPR-Dx to detect terrestrial mammal species in parallel with one amplification to detect multiple species with CRISPR-Dx. Given the short length of metabarcoding amplicons, designing species-specific assays within them can be challenging. We designed species-specific CRISPR-Dx for eight terrestrial mammals within a commonly used metabarcoding amplicon similar to 59 base pairs in length and tested the assays on eDNA samples collected in high-alpine catchments. Additionally, we compared the detections from CRISPR-Dx with metabarcoding results of the same samples and with catchment-based species inventories obtained through traditional monitoring. First, we show that designing species-specific CRISPR-Dx within a short amplicon allows terrestrial mammal detection in eDNA. Second, we demonstrate that CRISPR-Dx assays combined with multispecies primers are comparable in sensitivity to metabarcoding and thus can bridge a gap between species-specific assays and community analysis without requiring fully equipped laboratories. Third, we highlight that catchment-based eDNA sampling can be used to monitor terrestrial mammals in remote or protected areas. Overall, we demonstrate that eDNA and particularly CRISPR-Dx are a promising tool to monitor inaccessible and/or protected areas and to detect rare species across large spatiotemporal scales, thereby promoting biodiversity conservation.
ORDNA: Deep-learning-based ordination for raw environmental DNA samples
Sanchez, Théophile; Stalder, Steven; Lamperti, Letizia; et al. (2025)
Methods in Ecology and Evolution
1. Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring, offering non-invasive tools to assess ecosystem health. The complexity of eDNA metabarcoding data poses major challenges for conventional ordination methods in understanding assemblage similarities and assessing biodiversity patterns. 2. Here, we introduce ORDNA (ORDination via Deep Neural Algorithm), a new deep learning method tailored for eDNA sample ordination. Leveraging artificial neural networks, ORDNA processes raw sequences from eDNA samples directly, bypassing potentially biased and cumbersome expert-based bioinformatic steps. The method is trained with a contrastive self-supervised learning approach, the triplet loss, to derive a two-dimensional representation of eDNA samples based on their read composition. 3. We apply ORDNA to four distinct eDNA datasets, demonstrating its robustness and superiority over traditional ordination techniques in capturing and visualizing ecological patterns. 4. Our results underline the potential of deep learning in advancing eDNA analysis, with ORDNA serving as a promising tool for more accurate and efficient biodiversity assessments.

Publications 1 - 8 of 8

Flurin Leugger

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results