Loïc Pellissier

Global plant diversity is distributed unevenly across terrestrial biomes. While the effects of environmental differences on species distributions have been well studied, how the spatial configuration of biomes structures the macroevolutionary assembly of the global flora remains unclear. Here, we introduce a biome-centred framework for elucidating global floristic assembly based on joint reconstructions of biome and geographic occupancy across 160 plant lineages comprising ~20,000 species. We demonstrate that global plant diversity is assembled predominantly through within-biome speciation (~86% of variation in biome-level plant richness) rather than biome shifts (~12%), revealing pervasive phylogenetic biome conservatism. Transitions among biomes are asymmetric and jointly governed by their biogeographic configurations and evolutionary histories: species-rich biomes with deeper evolutionary histories act as major evolutionary sources that disproportionately export lineages to other biomes, with biotic interchange increasing with biome area and declining with geographic and environmental distance. These results identify biomes as fundamental evolutionary arenas that both constrain diversification and mediate the biotic exchange of plant lineages, providing an integrative framework for understanding the spatiotemporal dynamics of global plant diversity.

The response of ecosystems to ongoing rapid climate change is dependent on individualistic species response and biotic interactions 1,2. It is therefore critical to know how realised niches shift with changing climate and changing biotic interactions among species 3,4. At present, empirical niche investigations rarely include biotic niche dimensions and are limited to short time spans 5. Sedimentary ancient DNA (sedaDNA) is revolutionising our ability to study the development and dynamics of ecosystems by enabling the simultaneous identification of plants and animals from their past living environments 6,7. Here, we develop this method by combining sedaDNA from ten lakes in northern Fennoscandia with a novel compilation of regional rock-art and bone records, as well as palaeo-topography, to reconstruct animal arrival times, changes in plant–herbivore-carnivore networks, and estimate shifts in the biotic and climatic niches for key animal species over the last 16 ka. Marine fauna and tundra plants appeared soon after deglaciation, and birds and freshwater species arrived at approximately 13 ka. However, reindeer did not appear until 5 millennia later at 11 ka, and most terrestrial mammals arrived only in the last 8 ka after vegetation had stabilised. Realised climatic and biotic niches shifted with increased herbivore niche-filling, and niche-overlap increased with ecosystem complexity build-up, implying increasing herbivore interactions. Our study provides the first long-term empirical evidence that shifts in biotic interactions may be more important than climate for shaping ecosystems, and must be considered when attempting to mitigating effect of climate change.

As agricultural intensification expands globally, there is an increasing concern about the impact of food production on global biodiversity. Biodiversity decline is problematic as species provide a wealth of benefits, including pollination, soil fertility, and protection against pests, within agrosystems. Many countries, especially across Europe, have implemented incentives for farmers to introduce biodiversity‐friendly land management practices, from building hedgerows to planting pollinator fields. Quantifying the impacts of these measures on biodiversity at the farm scale is technically challenging. Here, we developed a method involving the collection of environmental DNA (eDNA) samples with drones from crops, demonstrated in a case study on rapeseed fields under three management types: conventional, biological, and IP Suisse. We analyzed swabbed material through metabarcoding of a 16S amplicon to detect the composition of hexapod in the field. After cleaning and taxonomic assignment, we obtained a total of 75 taxa assigned to 19 families, 23 genera, and 33 species. We found that the variance in recovered diversity was significantly higher for replicates between fields than for replicates within a field, suggesting that eDNA swabbing replicates provided consistent local results. We did not detect significant differences between treatments, possibly because of a landscape effect which causes spillover of species from neighboring seminatural habitats. Our results provide a direction for developing a toolbox for biodiversity measurements in agricultural fields, highlighting the potential for expanding these methodologies to suit the needs of scientists, farmers, and other stakeholders in understanding and fostering farm‐scale biodiversity.

Provides a workflow to retrieve, filter, and analyze 'GBIF' occurrence records and to generate ecologically informed species range maps using downloaded or custom ecoregions. The package includes tools for querying the 'GBIF' backbone taxonomy with get_status(), counting or downloading occurrences with get_gbif_count() and get_gbif(), creating custom ecoregion layers with make_ecoreg(), building range maps with get_range(), and evaluating them against independent validation data with evaluate_range() and cv_range(). A disk-based batch workflow (split_gbif_by_species(), species_csvs_to_ranges(), read_range_rds()) supports large multi-species 'GBIF' exports without loading the full table into memory. Bundled ecoregion layers cover terrestrial (Olson et al. 2001 ), marine (Spalding et al. 2007 ), and freshwater (Abell et al. 2008 ) realms. The 'GBIF' API is accessed via the 'rgbif' package, and coordinate cleaning uses 'CoordinateCleaner' (Zizka et al. 2019 ). The 'GBIF' API is described at .

Conservation planning requires prioritizing particular species, habitats, or objectives and handling information gaps. Spatial prioritization analyses apply various weighting schemes, for example assigning relative importance to different biodiversity features, balancing threatened and common species, or trading off ecological objectives against socioeconomic constraints. Such value driven choices may strongly affect conservation outcomes, yet little clarity exists on where and how they are employed. To address this opacity, we developed a comprehensive decision framework that organizes weighting criteria across three dimensions, conservation objectives, socioeconomic considerations, and implementation constraints, operating at species, habitat, and landscape levels. We then confronted 71 systematically chosen spatial prioritization studies with this framework to assess how weighting was considered. Representativeness and conservation urgency were the dominant motivations for weighting. However, ecosystem services were considered in only one study despite their prominence in policy-related discourse. Seventy-two percent of the studies did not explicitly justify their weighting decisions, challenging transparent communication of the underlying rationales. In a final step, we applied the framework in three case studies considering 1,472 species in Switzerland and prioritizing across taxonomic groups, realms, and threat categories to demonstrate the fundamental impact of weighting on conservation outcomes. Our results emphasize why weighting decisions require clear justification and documentation in spatial prioritization. Our framework will help planners make explicit choices that align with their conservation objectives.

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here we present a global assessment and unified analysis of riverine fish biodiversity using environmental DNA collected from 1,818 sites across 113 river systems spanning 5 continents. We quantified species richness, functional redundancy, phylogenetic diversity and genetic sequence diversity, and related them to drainage characteristics. Our results showed that environmental DNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and different aspects of human activities in shaping biodiversity–area relationships. The accumulation of biodiversity with catchment area was consistently enhanced in warmer climates, while human activities weakened this scaling. Further, species richness, functional and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity was negatively affected by human activities, yet this effect diminished as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients and catchment characteristics. Our findings demonstrate the power of environmental-DNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

Habitat configuration governs the movement of organisms across landscapes, thereby shaping both population structure and community assembly. While theoretical and empirical studies have assessed how habitat connectivity simultaneously influences intra‐ and interspecific diversity, direct comparisons across contrasting biogeographic regions remain limited. Here, we investigate patterns of genetic and species β‐diversity in tropical reef fishes across two ocean basins with distinct spatial configurations: the Caribbean Sea and the Western Indian Ocean. Using a comparative framework based on species occurrence data from five fish families and single nucleotide polymorphism (SNP) data from 19 species, we detected significant isolation by distance at both population and community levels in the Western Indian Ocean, but only at the community level in the Caribbean Sea. Additionally, genetic and species β‐diversity were positively correlated among species in the Western Indian Ocean, but not in the Caribbean Sea. Together, these results suggest that the shorter inter‐reef distances of the Caribbean Sea promote higher connectivity, leading to a decoupling of intra‐ and interspecific β‐diversity patterns.

The functionality of global rivers has been adversely affected by environmental pollution and habitat degradation. We investigated the mechanisms through which climate variables modulate the impact of human activities on basin ecosystems. We compared the Han and Wei rivers, located on opposite sides of the Qinling Mountains, and modeled how climate modulates the effects of human activities on basin food webs. Water samples were collected from the Han and Wei Rivers, respectively, and we analyzed them using a combined environmental DNA (eDNA)‐hydrological coupling model and Empirical Dynamic Modeling. We found that the food web complexity showed a gradual decline from upstream to the outlet in the Han River, while the Wei River exhibited the opposite pattern. Food web complexity in the Han River was 67.18% higher than in the Wei River. The effects of human activities on ecological networks were associated with climate, with increased precipitation weakening the negative impact of human activities. Our results suggest that climate can modulate the effects of human activities on basin ecological networks. Additionally, basin ecosystems in arid regions demonstrate reduced resilience to withstand human activities under challenging climatic conditions.

Describing and understanding diversity patterns from populations to communities remains a fundamental challenge in ecology and evolutionary biology. The main barriers to address this challenge are linked to the difficulty of concurrently assessing diversity from intra‐ to interspecific level and of obtaining genetic data for multiple species, particularly for hyperdiverse taxa like tropical reef fishes. Here, we propose environmental DNA (eDNA) metabarcoding with level‐specific primers (the conserved 12S and the hypervariable D‐loop) as a standardized approach to bridge this gap. Using 21 eDNA samples from the Caribbean Sea, we estimated species diversity across all teleosts (378 Molecular Operational Taxonomic Units, MOTUs) and intraspecific haplotype diversity for several grunt species ( Haemulon 1149 Amplicon Sequence Variants, ASVs). Our results revealed no covariation between the haplotype diversity of Haemulon and the overall species richness detected. However, we detected isolation‐by‐distance patterns at the interspecific level and species‐dependent isolation‐by‐distance at the intraspecific level. Notably, the effect of distance led to a positive covariation between fish species dissimilarity and Haemulon plumierii haplotype dissimilarity across samples. By enabling simultaneous, standardized monitoring of biodiversity across scales, eDNA opens new perspectives on unifying biodiversity assessments and understanding the eco‐evolutionary processes that shape diversity patterns from genes to communities.

Understanding the intricate dynamics of biodiversity within and across riverine ecosystems, influenced by geological history and environmental factors, is crucial for effective conservation and management strategies. Italy, particularly the Ligurian region, harbors diverse freshwater fish communities and populations shaped by unique geological and hydrological conditions. Here, we investigated the suitability of environmental DNA (eDNA) metabarcoding to identify inter‐ and intraspecific diversity patterns of riverine fish populations in drainage basins on both sides of the main drainage divide (MDD) between the Adriatic and Ligurian river basins in Northern Italy. We collected 96 aquatic eDNA samples across 48 riverine sites, amplified them using a cytochrome b primer pair, and denoised the sequences to retrieve amplicon sequence variants (ASVs). We calculated communities' phylogenetic distance with betaMPD based on genetic distances derived from the ASVs, combined them with conductance‐based landscape metrics, and applied generalized dissimilarity models to assess spatial genetic structure. Our results reveal genetic differentiation among populations of several fish species, with some displaying clustering patterns across the main drainage divide and isolation by distance patterns. Overall, taxon richness was higher on the Adriatic side (12.82 ± 3.57; 26 unique taxa) than on the Ligurian side of the MDD (8.35 ± 3.66 SD, 25 unique taxa), but the other way around for ASV richness across all species (Ligurian side: 51.94 ± 25.79, 308 unique ASV, Adriatic side: 68.00 ± 32.97, 274 unique ASV). Our findings highlight the effectiveness of eDNA metabarcoding in uncovering various facets of diversity, shedding light on hidden genetic diversity among ASVs, and revealing significant spatial genetic structuring in freshwater fish populations across multiple species.