Prof. Dr. Loïc Pellissier

Tropical reef fishes exhibit a large disparity of organismal morphologies contributing to their astonishing biodiversity. Morphological disparity, scaling from differences among individuals within populations to differences among species, is governed by ecological and evolutionary processes. Here, we examined the relationship between intra- and interspecific disparity in 1111 individuals from 17 tropical reef fish species, representing 10 families with different dispersal abilities, across four Indian Ocean regions. We compared intraspecific measurements with species-level measures from a database of 1061 reef fish species. Species with high morphological disparity among individuals from distinct regions are found to be nested in families that display a high disparity among their genera. We show an association between the morphological disparity at the intra- and interspecific levels for several morphological ratios such as the caudal peduncle elongation. We evaluated the link between morphological disparity and genetic diversity with species dispersal ability. A structural equation model indicates that dispersal ability correlates positively with species genetic diversity, which is associated with morphological disparity. Our results suggest that traits associated with dispersal may foster gene flow and morphological evolution. Future works combining genomic, morphological and environmental data across more species is necessary to generalize these findings to other regions.

Coastal ecosystems provide a range of services including erosion prevention, clean water provision and carbon sequestration. With climate change, the rapid change in frequency and intensity of tropical cyclones may alter the composition of the ecosystems themselves potentially degrading the services they provide. Here we classify global ecoregions into dependent, resilient and vulnerable and show that a combined 9.4% of the surface of all terrestrial ecosystems is susceptible to transformation due to cyclone pattern changes between 1980–2017 and 2015–2050 under climate scenario SSP5-8.5 using the STORM model. Even for the most resilient ecosystems already experiencing winds >60 m s⁻¹ regularly, the average interval between two storms is projected to decrease from 19 to 12 years which is potentially close to their recovery time. Our study advocates for a shift in the consideration of the tropical cyclone impact from immediate damage to effects on long-term natural recovery cycles.

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.

The biodiversity crisis driven by anthropogenic pressures significantly threatens marine ecosystems. The rate of climate change and anthropogenic impacts outpace our traditional observation tools' capabilities, underscoring the urgency for new assessment methods. Environmental DNA (eDNA; DNA traces released by organisms) metabarcoding, a non-invasive method widely developed over the last decade, represents a promising biomonitoring tool thanks to a large spatio-temporal coverage, high detection of rare species and its time and cost-effectiveness. However, capturing fish diversity using eDNA requires genetic reference databases, currently lacking. Improving reference databases relies on opportunistic sampling enabling the reporting of sequences for new species. The data provided here consists of barcoding 86 species of fishes over the 12S mitochondrial DNA gene. We generated 156 sequences of the mitochondrial 12S gene adapted to the “Teleo” barcodes from fishes sampled in the Bay of Biscay (BoB; Northeast Atlantic, France) between 2017 and 2019. In addition, we provided each individual the barcode details (Genbank accession number, chromatograms), a photograph, 5 ecomorphological measures and 11 life-history traits documenting ecological functions (e.g., dispersion, habitat use, diet). Furthermore, we provided the sampling metadata (e.g., date, time, gear, coordinates, depth) and environmental variables measured in situ (e.g., conductivity, water/air temperature). This data set is valuable to improve the Northeast Atlantic eDNA genetic database, thus helping to better understand the effects of environmental forcing in the BoB, a transition zone housing mixed assemblages of boreal, temperate, and subtropical fish species susceptible to display variability in functional traits to adapt to changing conditions. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at https://jalter.diasjp.net/data/ERDP-2024-09.

While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non-invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere-length-based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10–24 days post-hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third-generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification-free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross-validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.

Climate projections for continental Europe indicate drier summers, increased annual precipitation, and less snowy winters, which are expected to cause shifts in species' distributions. Yet, most regions/countries currently lack comprehensive climate-driven biodiversity projections across taxonomic groups, challenging effective conservation efforts. To address this gap, our study evaluated the potential effects of climate change on the biodiversity of an alpine country of Europe, Switzerland. We used a state-of-the art species distribution modeling approach and species occurrence data that covered the climatic conditions encountered across the full species' ranges to help limiting niche truncation. We quantified the relationship between baseline climate and the spatial distribution of 7291 species from 12 main taxonomic groups and projected future climate suitability for three 30-year periods and two greenhouse gas concentration scenarios (RCP4.5 and 8.5). Our results indicated important effects of projected climate changes on species' climate suitability, with responses varying by the taxonomic and conservation status group. The percentage of species facing major changes in climate suitability was higher under RCP8.5 (68%) compared to RCP4.5 (66%). By the end of the century, decreases in climate suitability were projected for 3000 species under RCP8.5 and 1758 species under RCP4.5. The most affected groups under RCP8.5 were molluscs, algae, and amphibians, while it was molluscs, birds, and vascular plants under RCP4.5. Spatially, by 2070–2099, we projected an overall decrease in climate suitability for 39% of the cells in the study area under RCP8.5 and 10% under RCP4.5, while projecting an increase for 50% of the cells under RCP8.5 and 73% under RCP4.5. The most consistent geographical shifts were upward, southward, and eastward. We found that the coverage of high climate suitability cells by protected areas was expected to increase. Our models and maps provide guidance for spatial conservation planning by pointing out future climate-suitable areas for biodiversity.

Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change.
This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. Individually, both approaches are used in ecological studies to characterize biodiversity, yet they are rarely combined. Here, we integrated high-resolution habitat suitability models with eDNA-based assessments of aquatic invertebrates in riverine networks to understand their individual and combined capacity to inform on species' occurrence. We used eDNA sampling data from 172 river sites and combined the detection of taxa from three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) with suitable habitat predictions at a subcatchment level (2 km²). Overall, we find congruence of habitat suitability and eDNA-based detections. Yet, the models predicted suitable habitats beyond the number of detections by eDNA sampling, congruent with the suitable niche being larger than the realized niche. For local mismatches, where eDNA detected a species but the habitat was not predicted suitable, we calculated the minimal distance to upstream suitable habitat patches, indicating possible sources of eDNA signals from upstream sites subsequently being transported along the water flow. We estimated a median distance of 1.06 km (range 0.2–42 km) of DNA transport based on upstream habitat suitability, and this distance was significantly smaller than expected by null model predictions. This estimated transport distance is in the range of previously reported values and allows extrapolations of transport distances across many taxa and riverine systems. Together, the combination of eDNA and habitat suitability models allows larger scale and spatially integrative inferences about biodiversity, ultimately needed for the management and protection of biodiversity.

1. Urban ecosystems are formed by pronounced socio-ecological gradients, which are distinct from other ecosystems and can simultaneously filter and promote taxa, ultimately affecting their interactions. However, the strength of the effect of filtering and facilitation across the different trophic levels could vary among biotic and abiotic factors.
2. Here, we investigate the effects of habitat amount, temperature and host-enemy biotic interactions in shaping communities of cavity-nesting bees and wasps and their natural enemies. We installed trap-nests in 80 sites distributed along urban intensity gradients in five European cities (Antwerp, Paris, Poznan, Tartu and Zurich). We quantified the species richness and abundance of hosts and their natural enemies, as well as two performance traits (survival and parasitism) and two lifehistory traits (sex ratio and number of offspring per nest for the hosts). We analysed the importance of the abiotic and biotic variables using generalised linear models and multi-model inference.
3. We found that habitat amount was the main driver of multiple host responses, with larger habitat amounts resulting in higher species richness and abundance for hosts and natural enemies, as well as a larger probability of survival and a larger number of brood cells for hosts.
4. Local resources proxies shaped both bees and wasps and indicate different uses of existing vegetation between bees and wasps. Temperature proxies had a minor role in shaping host and natural enemies.
5. Biotic interactions were a main driver of host and enemy community structure, with natural enemies being strongly affected by host availability, that is, with direct density-dependence between hosts and their natural enemies. 6. Overall, our study highlights the importance of habitat amount and temperature in shaping urban food webs, as well as on biotic interactions through direct effects on hosts responses and the subsequent consequences for their natural enemies. As cities prepare to tackle the consequences of global change, strategies that make it possible to maintain habitat and mitigate urban overheating emerge as a key urban adaptation for biodiversity conservation.

To meet the COP15 biodiversity framework in the European Union (EU), one target is to protect 30% of its land by 2030 through a resilient transnational conservation network. The European Alps are a key hub of this network hosting some of the most extensive natural areas and biodiversity hotspots in Europe. Here we assess the robustness of the current European reserve network to safeguard the European Alps’ flora by 2080 using semi-mechanistic simulations. We first highlight that the current network needs strong readjustments as it does not capture biodiversity patterns as well as our conservation simulations. Overall, we predict a strong shift in conservation need through time along latitudes, and from lower to higher elevations as plants migrate upslope and shrink their distribution. While increasing species, trait and evolutionary diversity, migration could also threaten 70% of the resident flora. In the face of global changes, the future European reserve network will need to ensure strong elevation and latitudinal connections to complementarily protect multifaceted biodiversity beyond national borders.

Anthropogenic activities are eroding biodiversity and its contributions to nature and people worldwide. Yet, the dual imperative to protect nature and sustain human well-being raises potential trade-offs that remain to be quantified. Using standardized fish surveys across 1,237 tropical reefs worldwide, we converted the presence and abundance data of 1,024 species into 29 fish community contributions that primarily benefit either nature or people. We show that “nature-for-nature” contributions are mostly positively correlated with total fish biomass, while “nature-for-people” contributions are more independent. Trade-offs among contributions are not the rule, with some tropical fish communities simultaneously providing high levels of different contributions. High mean contributions have been found in all tropical oceans, so sustaining healthy tropical reefs while promoting human well-being seems achievable within most countries, rather than mutually exclusive. Our framework offers an opportunity to explore different management strategies and pathways on tropical reefs between the use and the sparing of nature toward more favorable and sustainable ecological and social futures.

1. Human intervention often alters the availability of habitat for biodiversity. The conservation of biodiversity therefore requires an optimized habitat management. In forests, dead wood represents one of the most important habitats and in boreal and temperate regions around 25% of forest species depend on it (= saproxylic species). Increasing the amount of dead wood in managed forests has thus become a policy objective, but there is no consensus on how to best distribute dead wood in space.
2. In a landscape experiment, we exposed freshly cut beech branches in bundles of different sizes (one, three, six and 12 branches) in the forest, representing newly created habitat patches to be colonized by saproxylic beetles. We investigated how species richness in a 'single large' branch bundle compares to that in 'several small' bundles (SLOSS debate). We further tested the effects of dead wood availability (amount and isolation) in the surrounding landscape (20–200 m) and environmental factors (temperature and light availability) on species richness, abundance and community composition.
3. The species richness of the pooled small bundles (1 + 3 + 6 = 10 branches) was as high as that of the large bundle (12 branches), despite having a smaller total surface, demonstrating the benefit of spatially dispersed habitat patches for total diversity. Also community composition differed and every bundle size yielded some unique species. Dead wood availability in the surrounding landscape had a minor effect in comparison. Our results further highlight the importance of microsite heterogeneity: species richness was related to light availability, and abundance and community composition were related to temperature.
4. Synthesis and applications: Larger amounts of dead wood harbour more saproxylic beetle species and the distribution of dead wood in patches of different sizes within the forest can promote the development of variable species communities. Combined, this results in a higher species diversity. In managed forests, where retained dead wood is often homogeneous in terms of size or tree species, increasing heterogeneity by distributing dead wood in the forest could foster higher diversity of saproxylic species.

New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce ‘novel community data’ as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.

Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate—the Northern chamois (Rupicapra rupicapra)—could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.

Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance-to-reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance-to-reef on β diversity variation using generalised linear mixed models and estimated species-specific distance-to-reef effects using a model-based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance-to-reef gradient. The analysis of β-diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance-to-reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale.

Environmental DNA (eDNA) analysis is a powerful tool for studying biodiversity in forests and tree canopies. However, collecting representative eDNA samples from these high and complex environments remains challenging. Traditional methods, such as surface swabbing or tree rolling, are labor-intensive and require significant effort to achieve adequate coverage. This study proposes a novel approach for unmanned aerial vehicles (UAVs) to collect eDNA within tree canopies by using a surface swabbing technique. The method involves lowering a probe from a hovering UAV into the canopy and collecting eDNA as it descends and ascends through branches and leaves. To achieve this, a custom-designed robotic system was developed featuring a winch and a probe for eDNA collection. The design of the probe was optimized, and a control logic for the winch was developed to reduce the risk of entanglement while ensuring sufficient interaction force to facilitate transfer of eDNA onto the probe. The effectiveness of this method was demonstrated during the XPRIZE Rainforest Semi-Finals as 10 eDNA samples were collected from the rainforest canopy, and a total of 152 molecular operational taxonomic units (MOTUs) were identified using eDNA metabarcoding. We further investigate how the number of probe interactions with vegetation, the penetration depth, and the sampling duration influence the DNA concentration and community composition of the samples.

Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.

1. Understanding how ecological assemblages vary in space and time is essential for advancing our knowledge of biodiversity dynamics and ecosystem functioning. Metabarcoding of environmental DNA (eDNA) is an efficient method for documenting biodiversity changes in both marine and terrestrial ecosystems. However, current methods fail to detect and display the biodiversity structure within and between eDNA samples limiting ecological and biogeographical interpretations.
2. We present a spatial matrix factorization method that identifies optimal eDNA sample assemblages—called pools—assuming that taxonomic unit composition is based on a fixed number of unknown sources. These sources, in turn, represent taxonomic units sharing similar habitat properties or characteristics. The method aims to reduce the multi-taxa composition structure into a low number of dimensions defined by these sources. This method is inspired by admixture analysis in population genetics. Using a marine fish eDNA survey on 263 sampling stations detecting 2888 molecular operational taxonomic units (MOTUs), we apply this method to analyse the biogeography and mixing patterns of fish assemblages at regional and large scales.
3. At large scale, our analysis reveals six primary pools of fish samples characterized by distinct biogeographic patterns, with some mixtures between these pools. We identify pools composed of unique sources, corresponding to distinct and more isolated regions such as the Mediterranean and Scotia Seas. We also identify pools composed of a greater mix of sources, corresponding to geographically connected areas, such as tropical regions. Additionally, we identify the taxa underpinning the formation of each pool. In the regional analysis of Mediterranean eDNA samples, our method successfully identifies different pools, allowing the detection of not only geographic gradients but also human-induced gradients corresponding to protection levels.
4. Spatial matrix factorization adds a new method in community ecology, where each sample is considered as a mixture of K unobserved sources, to assess the dissimilarity of ecological assemblages revealing environmental and human-induced gradients. Beyond the study of fish eDNA samples, this method has the potential to shed new light on any biodiversity survey and provide new bioindicators of global change.

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.

Madagascar is a hotspot of biodiversity and unique species, both because of its long isolation from the mainland and its high rates of speciation. Liu et al. hypothesized that landscape evolution contributed to plant diversification by creating barriers and habitat heterogeneity, providing opportunities for allopatric speciation. They tested this hypothesis by modeling topographic dynamics on Madagascar over the past 45 million years and found high plant species richness and diversification rates along the landward-shifting continental rift escarpment, with low north-south connectivity and high rates of local endemism. This work shows how relatively small-scale, transient landscape evolution can shape long-term biodiversity patterns.