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<title>bioRxiv Subject Collection: Ecology</title>
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This feed contains articles for bioRxiv Subject Collection "Ecology"
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.01.722334v1?rss=1">
<title>
<![CDATA[
Crop raiding as an emerging threat to giraffes: drivers and perceived effectiveness of countermeasures 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.01.722334v1?rss=1
</link>
<description><![CDATA[
Giraffes, unlike other large mammals, typically pose minimal risk to humans, their animals, and crops, so they are traditionally not involved in human-wildlife conflict. Tree crops, however, are expanding across Africa, resulting in crop raiding by giraffes and retaliatory snaring, poaching, and killing of giraffes in response. The dynamics of giraffe crop raiding, however, are poorly understood, making effective interventions difficult to implement. To better understand key factors for humans and giraffes that mediate crop raiding, we used a multi-method approach to estimate giraffe abundance and activity, understand farmers' perceptions and decisions, and test countermeasures around Garissa Giraffe Sanctuary in eastern Kenya. We hypothesized that 1) giraffe farm invasion would occur in dry seasons, 2) farms growing mangoes would be more likely to be invaded, 3) reducing invasion with only physical barriers would be less effective than adding behavior-based countermeasures, 4) perceptions would match giraffe activity and 5) countermeasure adoption would be driven by cost. We found that invasion and crop raiding primarily occur during the dry season and are associated with mangoes. Farmers are using many countermeasures. Effective countermeasures target giraffe behavior combined with physical barriers. Countermeasures are most effective when negative associations with humans are reinforced. Floodlights and speakers that play predator calls both reduce invasion, but only if used consistently. Overall, farmers' perceptions matched giraffe dynamics. Availability was the most important factor in farmers' willingness to try a countermeasure. Our results suggest that conflict can be reduced and there is interest from farmers in doing so, but use of countermeasures should be consistently applied and supported by making necessary equipment and instructions available.
]]></description>
<dc:creator><![CDATA[ Owino, R. O., Golding, J., Sangale, E. L., Ali, A. H., Alston, J. M. ]]></dc:creator>
<dc:date>2026-05-03</dc:date>
<dc:identifier>doi:10.64898/2026.05.01.722334</dc:identifier>
<dc:title><![CDATA[Crop raiding as an emerging threat to giraffes: drivers and perceived effectiveness of countermeasures]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-03</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.721856v1?rss=1">
<title>
<![CDATA[
Convergent gliding, divergent ecology: Environmental drivers of gliding vertebrates in Southeast Asia 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.721856v1?rss=1
</link>
<description><![CDATA[
Gliding has evolved repeatedly across vertebrates and is often regarded as a classic example of convergent evolution associated with arboreal habitats. However, it remains unclear whether convergent locomotion corresponds to shared ecological responses across taxa. In this study, we investigated the distribution patterns and environmental drivers of gliding vertebrates in Southeast Asia using occurrence records and environmental variables representing climate and forest structure. We analyzed five major groups, including flying lemurs, flying squirrels, gliding lizards, gliding snakes, and gliding frogs, using presence-background logistic regression models. Across taxa, temperature seasonality showed consistently negative effects, while canopy height showed positive effects, indicating a shared association with climatically stable environments and well-developed vertical forest structure. In contrast, other environmental variables exhibited substantial taxon-specific variation. For example, elevation showed a strong negative effect only in gliding snakes, suggesting a tendency toward lowland habitats, whereas precipitation variables had limited explanatory power for gliding frogs. These results demonstrate that, despite the convergent evolution of gliding locomotion, ecological responses to environmental factors are not uniform across vertebrate taxa. Instead, species distributions are shaped by a combination of shared functional constraints and lineage-specific ecological traits. Our findings highlight the importance of vertical forest structure and suggest that habitat alteration affecting canopy structure may disproportionately impact certain taxa.
]]></description>
<dc:creator><![CDATA[ Nojiri, K., Sugeno, H., Inoshita, K. ]]></dc:creator>
<dc:date>2026-05-02</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.721856</dc:identifier>
<dc:title><![CDATA[Convergent gliding, divergent ecology: Environmental drivers of gliding vertebrates in Southeast Asia]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-02</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721557v1?rss=1">
<title>
<![CDATA[
Fungal-bacterial interaction unaffected by heatwave conditions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721557v1?rss=1
</link>
<description><![CDATA[
Climate change is reshaping soil microbial communities, yet the impact of warming in bacterial-fungal interactions (BFIs) remains underexplored. We investigated whether heatwave temperature influence BFIs and the mechanism supporting the interaction. Using co-culture experiments with two bacterial and two fungal strains isolated from heathland soil, we compared mono- and co-cultures final abundances under ambient (18{degrees}C) and heatwave (25{degrees}C) soil temperatures. Our results revealed strongly asymmetric interactions, where fungi benefited by around 5% from bacterial presence, while bacterial abundance was inhibited by around 68%, regardless of temperature. Analyses of pH confirmed that acidification by fungi was probably the main cause of this inhibition. Moreover, warming did not affect the strength or direction of these interactions, though it slightly increased fungal abundance. These findings provide direct experimental evidence that fungi can impact bacteria via acidification, and that the interaction is unaffected by temperature. Understanding these mechanisms is crucial for improving predictions of microbial community dynamics and ecosystem functioning in warming environments.
]]></description>
<dc:creator><![CDATA[ Moreno-Druet, M., Pardaens, S., Soudzilovskaia, N. A., De Laender, F., Rineau, F. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721557</dc:identifier>
<dc:title><![CDATA[Fungal-bacterial interaction unaffected by heatwave conditions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.720935v1?rss=1">
<title>
<![CDATA[
Large river eDNA sampling designs with remote-sensing-based clustering stratification 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.720935v1?rss=1
</link>
<description><![CDATA[
Environmental DNA (eDNA) provides a powerful tool for biodiversity monitoring in large river ecosystems. However, current studies often rely on subjective site selection and lack systematic sampling designs. This can limit the ability to capture the full spectrum of environmental conditions that species depend on, thereby compromising sampling efficiency. To address this challenge, we propose utilizing remote sensing-based clustering for environmental stratification of sampling designs, thereby enhancing detection capabilities and increasing the objectivity of eDNA sampling. Using GBIF-based fish species distribution models and simulated distributions along the Danube, we demonstrate that this approach enhances detection efficiency compared to conventional random and regular sampling methods. To facilitate practical implementation, we developed a tool to help fieldwork planners of river sampling campaigns automatically apply this method and select stratified sampling sites without the need for extensive data processing. Finally, we demonstrate that eDNA detection occurred most frequently within the range of 0-20 km downstream of the expected modeled distribution of species, suggesting that the diffusion of the signal should be further considered in the sampling design process. Our findings highlight the potential of remote sensing-based stratification to create more efficient and objective sampling designs but suggest that sampling design should be further combined with hydrological information to optimize cost-efficient sampling. The development of standard and robust sampling protocols will help advance more cost-effective eDNA-based biodiversity monitoring in riverine ecosystems.
]]></description>
<dc:creator><![CDATA[ Zong, S., Bauknecht, R., Seybold, H., Albouy, C., Pellissier, L. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.720935</dc:identifier>
<dc:title><![CDATA[Large river eDNA sampling designs with remote-sensing-based clustering stratification]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721682v1?rss=1">
<title>
<![CDATA[
Stopover departure decisions and movement patterns of migratory bats during autumn migration 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721682v1?rss=1
</link>
<description><![CDATA[
Migrating bats alternate between stopover periods and directed flights. When departing from a stopover site, bats select the night, the specific time within the night, and the flight direction to resume migration. Despite their ecological importance, the factors shaping these stopover departure decisions remain poorly understood. To identify the intrinsic and environmental factors driving departure decisions and movement patterns, we tagged Nathusius pipistrelles Pipistrellus nathusii at three coastal locations in the Netherlands and tracked 178 individuals during autumn migration, using the MOTUS Wildlife Tracking System. We examined movement patterns and analysed departure probability in relation to a set of individual and environmental covariates in a Bayesian capture-recapture model in state-space formulation. Additionally, we modelled within-night variation in departure timing. Seasonal patterns were strongly influenced by reproductive behaviour, with decreased migration probability during the mating period. Regardless of their seasonal timing, bats departed under moderate tailwinds and dry conditions, optimizing energy efficiency, while avoiding crosswinds and cloud cover, enhancing navigational safety. Most individuals departed shortly after sunset, whereas headwinds delayed nocturnal departure. Movement patterns were diverse, including migration towards lower latitudes, coastal barrier movements, and long-distance roundtrips, suggesting the use of multiple movement strategies. Our study demonstrates that migration patterns in bats emerge from the interaction between intrinsic factors and external conditions, and highlights the importance of both energy efficiency and safety in shaping stopover departure decisions. The presence of multiple movement strategies complicates predictions of spatiotemporal occurrence, emphasising the need to account for behavioural variability in conservation planning, for example in the context of wind energy developments.
]]></description>
<dc:creator><![CDATA[ Lagerveld, S., Karagicheva, J., Vries, P. d., Rakhimberdiev, E., Stienstra, K., Noort, B. C. A., Poot, M. J. M., Karwinkel, T., Ruppel, G., Brust, V., Mathews, F., Schmaljohann, H., Van Langevelde, F. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721682</dc:identifier>
<dc:title><![CDATA[Stopover departure decisions and movement patterns of migratory bats during autumn migration]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721193v1?rss=1">
<title>
<![CDATA[
Forecasting climate-driven distributional changes in the threatened Caribbean marine species Aliger gigas (Queen conch) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721193v1?rss=1
</link>
<description><![CDATA[
The queen conch (Aliger gigas) is a key native species of the Caribbean Sea and a primary source of income for thousands of fishers. Historically, it has been a highly valuable resource for the fishing sectors of countries such as the Bahamas, Turks and Caicos, Honduras, and Nicaragua. However, due to its high economic value, the species has been extensively overfished across the region. Overfishing, combined with limited larval dispersal, low recruitment, and poor population connectivity, has led to a drastic decline in population numbers of the species, resulting in its current classification as Threatened. Despite this status, likely impacts of climate change on its populations remain poorly understood, posing significant challenges to conservation efforts. To address this gap, we integrated occurrence records, climate data, and satellite-derived marine habitat data to develop ecological niche models estimating the current and future distribution of the queen conch under different climate change scenarios. We found substantial losses of suitable areas for queen conch along the northern Atlantic coast of South America and Central America, part of the Greater Antilles and the Lesser Antilles. The entire Caribbean region is projected to lose suitability entirely within 20-30 years under the moderate and most extreme climate scenarios. Conversely, our models estimate some suitable areas to persist or expand along the southeastern coast of the United States at least until sometime between 2040 and 2060. Overall, our results suggest a northward shift in the range of this species, with the magnitude of this shift closely tied to the severity of climate change impacts. This work aims to build upon and enhance existing knowledge about survival of queen conch populations in the Caribbean over time. Anticipating future habitat availability will be key to protecting this economically and ecologically important species.
]]></description>
<dc:creator><![CDATA[ Rojas-Ariza, D., Nunez-Penichet, C., Ruiz-Utrilla, Z. P. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721193</dc:identifier>
<dc:title><![CDATA[Forecasting climate-driven distributional changes in the threatened Caribbean marine species Aliger gigas (Queen conch)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.720302v1?rss=1">
<title>
<![CDATA[
Cell motility enhances metabolic coupling in spatially structured microbial communities 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.720302v1?rss=1
</link>
<description><![CDATA[
Metabolic interactions are central to the functioning of microbial communities. In spatially structured environments, such interactions typically require close physical proximity between partner cells. However, cell division drives spatial segregation of interaction partners, as the cells emerging from division remain adjacent and form clonal clusters, weakening these interactions. Here, we hypothesized that active cell motility can reduce this spatial segregation by enabling cells to leave clonal clusters and thereby enhance metabolic interactions. We tested this hypothesis by performing time-lapse single-cell imaging of a synthetic cross-feeding consortium growing in microfluidic chambers. We found that surface motility disrupted clonal clustering, enhanced spatial intermixing, and consequently increased the growth rates of individual cells and community productivity. Individual-based simulations further revealed that this effect is robust across motility modes and a wide range of ecological and physiological parameters. Together, our findings demonstrate that even non-directed, random motility, without chemotactic sensing, is sufficient to enhance metabolic interactions by separating cells from their clonal lineages and repositioning them in proximity to their metabolic partners, thereby acting as a key driver of community functioning in spatially structured microbial systems.
]]></description>
<dc:creator><![CDATA[ Wang, M., Schubert, O., Ackermann, M. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.720302</dc:identifier>
<dc:title><![CDATA[Cell motility enhances metabolic coupling in spatially structured microbial communities]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721765v1?rss=1">
<title>
<![CDATA[
Behavior-Driven Marine Larval Dispersal and Settlement with AI Agent-Based Modeling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721765v1?rss=1
</link>
<description><![CDATA[
Larval dispersal models are central to mapping and predicting ichthyoplankton dynamics in the ocean, yet despite decades of refinement they remain fundamentally limited by their ability to represent adaptive behaviors, relying instead on static trait parameterizations. This deficiency constrains our capacity to design effective restoration and mitigation strategies in an increasingly stressed ocean. SWARM (Simulating Waterborne Agent Routes for Marine connectivity) overcomes this barrier by integrating Large Language Model (LLM)-based behavioral agents with a standard biophysical model to simulate active decision making during the pelagic larval stage. In both idealized and realistic conditions focusing on Red Snapper larvae in the Gulf of Mexico, agents develop adaptive behaviors that improve settlement and generate explainable vertical distribution patterns. SWARM demonstrates that LLMs can overcome long standing limitations in dispersal modelling by explicitly representing behavioral drivers of movement, opening new pathways for predicting connectivity and designing effective marine-ecosystem restoration.
]]></description>
<dc:creator><![CDATA[ Zhou, X., Wang, G., Wu, R., Bracco, A. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721765</dc:identifier>
<dc:title><![CDATA[Behavior-Driven Marine Larval Dispersal and Settlement with AI Agent-Based Modeling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.722094v1?rss=1">
<title>
<![CDATA[
A three-dimensional carbon-nutrient functional balance model explains the formation of Root Economics Space 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.722094v1?rss=1
</link>
<description><![CDATA[
Root carbon (C)-nutrient functional balance underpins root economic strategies, yet previous models neglected the root-length dimension. Here, we develop a three-dimensional C-nutrient functional balance model for first-order roots that explicitly incorporates root length, and validates it using a global root trait dataset. For subtropical woody species, root cortex volume multiplied by root length scaled isometrically with the fourth power of stele diameter (slope{approx}1.0), supporting the model. Herbaceous species from the Qinghai-Tibetan plateau showed a significantly lower slope (0.61), likely due to extreme environmental impacts on transport or metabolism. Woody species preferentially invest in cortical area (thicker roots), supporting mycorrhizal symbiosis, whereas herbaceous species favor root length extension for autonomous soil exploration. By integrating root length, this model provides a novel mechanistic explanation for the formation of both the collaboration and conservation axes within the root economics space, advancing the theoretical framework of root functional strategies.
]]></description>
<dc:creator><![CDATA[ Zhou, B., Chen, G. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.722094</dc:identifier>
<dc:title><![CDATA[A three-dimensional carbon-nutrient functional balance model explains the formation of Root Economics Space]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721606v1?rss=1">
<title>
<![CDATA[
Forest expansion and open vegetation responses during the past 14 ka at Zhagaer Co on the eastern Tibetan Plateau 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721606v1?rss=1
</link>
<description><![CDATA[
Forest expansion and retreat are key drivers of alpine ecosystem dynamics, yet it remains unclear how forest expansion shapes alpine plant communities and whether alpine assemblages that re-emerge after forest decline resemble those of the Late Glacial. Here, we integrate sedimentary ancient DNA (sedaDNA) and pollen records from Zhagaer Co on the eastern Tibetan Plateau to reconstruct vegetation changes over the past ca.14 ka. Using Picea abundance as a proxy for forest cover, we apply constrained ordination of sedaDNA-inferred plant communities to identify plant taxa as "winners" and "losers" of forest expansion and compare the composition of loser taxa between the late Glacial and late Holocene cold-open phases. Our results show that forest expansion during the early to mid-Holocene favoured woody and forest-margin taxa (e.g. Rhododendron, Salicaceae), while suppressing alpine forbs and graminoids (e.g. Carex, Thalictrum), consistent with patterns expected under ecological filtering. However, late Holocene reopening did not fully restore a late Glacial-like alpine community; instead, it was characterised by a stronger contribution of alpine meadow and shrub taxa. This difference may reflect contrasting environmental backgrounds, including higher atmospheric CO2; levels during the late Holocene, ecological legacies of prior forest expansion, and increasing human influence. These findings suggest that forest expansion may lead to long-term restructuring of alpine plant assemblages, and that late Holocene cooling did not simply restore late Glacial alpine communities but instead produced a distinct alpine ecosystem state. Together, these results highlight the long-term legacy of treeline dynamics in shaping alpine ecosystem trajectories.
]]></description>
<dc:creator><![CDATA[ Zhang, Y., Cao, X., Stoof-Leichsenring, K. R., Chen, S., Tian, F., Herzschuh, U. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721606</dc:identifier>
<dc:title><![CDATA[Forest expansion and open vegetation responses during the past 14 ka at Zhagaer Co on the eastern Tibetan Plateau]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721552v1?rss=1">
<title>
<![CDATA[
Seed Microbiota Diversity and Culture Collection of Four Major Crops Covering Different Genotypes and Production Modes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721552v1?rss=1
</link>
<description><![CDATA[
Seed microbiota play a crucial role in plant health and development, yet remain understudied compared to other plant-associated microbial communities. This study aimed to characterize seed microbiota diversity across four major crops (common bean, rapeseed, tomato, and wheat) and establish a comprehensive strain collection of seed-borne microorganisms (bacteria and fungi). We employed a combination of culture-dependent and culture-independent approaches to analyze 68 seed samples representing diverse genotypes and production modes. Our results revealed highly variable seed microbiota, with bacterial colonization ranging from 10 to 100 million bacterial CFUs per gram of seeds, and microbial richness varying from 4 to 351 bacterial and 16 to 138 fungal amplicon sequence variants (ASVs) per sample. Both plant genotype and production mode significantly influenced microbiota composition, with each seed sample produced harboring a distinct microbial assemblage. Interestingly, seeds produced in confined environments exhibited lower bacterial colonization but higher microbial richness compared to field-produced seeds. We observed divergent ecological drivers shaping bacterial and fungal communities. Bacterial assemblages were more host-specific and variable, while fungal communities showed greater stability and a substantial core microbiome shared across plant species. Our culturomics approach yielded a collection of 2,510 bacterial and 837 fungal isolates, representing 10-21% of the seed microbiota diversity detected by metabarcoding and the majority of the prevalent and abundant taxa. Notably, 44-60% of cultured bacterial isolates were not detected by metabarcoding, highlighting the complementary nature of these approaches to detect rare or under amplified taxa in PCR. This study provides insights into the complexity and variability of seed microbiota across different crops and production conditions. Our findings emphasize the importance of combining culturomics and sequencing methods for comprehensive characterization of seed microbiota to uncover the potential of seed-borne microorganisms as bioinoculants for sustainable agriculture.
]]></description>
<dc:creator><![CDATA[ Simonin, M., Guschinskaya, N., Marchi, M., MARAIS, C., Preveaux, A., Briand, M., Kavunu, N., Bosc-Bierne, A., Labourgade, L., Dutrieux, C., BRAULT, A., Rolland, S., Koutouan, C.-E., Portier, P., Causse, M., Langin, T., Nesi, N., Chen, N. W., Sarniguet, A., BARRET, M. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721552</dc:identifier>
<dc:title><![CDATA[Seed Microbiota Diversity and Culture Collection of Four Major Crops Covering Different Genotypes and Production Modes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721390v1?rss=1">
<title>
<![CDATA[
Enhancing the Understanding of Environmental Microbiomes through Topic Modeling: A Quantitative and Qualitative Analysis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721390v1?rss=1
</link>
<description><![CDATA[
Background:Understanding ecosystem dynamics is essential for assessing ecosystem health, yet remains challenging due to complex biotic and abiotic interactions. Microbial communities are valuable indicators of environmental change, but the high dimensionality of microbiome data requires advanced analytical methods. This study explores the use of topic modeling (TM), an unsupervised machine learning approach initially designed for text analysis, to analyze microbiome data from the dynamic Warnow Estuary on the southern Baltic Sea coast. Results: We applied TM to estuarine microbiome data and compared its performance to traditional dimensionality reduction methods, Principal Component Analysis (PCA) and Principal Coordinate Analysis (PCoA). Quantitative results indicate that TM performs comparably to conventional approaches in preserving ecological and functional information, and in certain aspects even superior. In addition, we show qualitatively that NNMF, a TM method, captures latent patterns in the data providing an interpretable perspective on the microbiome. In this exploratory framework, NNMF suggested five distinct sub-communities within the estuary that appear to follow a seasonal succession influenced by freshwater inflow. These sub-communities were associated with specific ranges of salinity and temperature and showed distinct taxonomic profiles, with shared characteristics across the estuarine system. Conclusions: Our findings suggest that TM is a useful tool for exploring complex environmental microbiome datasets, offering a complementary perspective that can provide additional ecological insights. TMs ability to highlight coherent microbial community patterns indicates its promise for supporting environmental monitoring and informing targeted ecosystem management in dynamic habitats, though further studies are needed to fully assess its applicability.
]]></description>
<dc:creator><![CDATA[ Kujat, A. S., Hassenrück, C., Lüdtke, S., Labrenz, M., Sperlea, T. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721390</dc:identifier>
<dc:title><![CDATA[Enhancing the Understanding of Environmental Microbiomes through Topic Modeling: A Quantitative and Qualitative Analysis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.720860v1?rss=1">
<title>
<![CDATA[
What do fishermen think? Local perspectives on human crocodile co-existence in Lake Nasser 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.720860v1?rss=1
</link>
<description><![CDATA[
The increasing impact of humans on natural habitats leads to an increase in human-wildlife conflict (HWC), specifically when there is competition for shared resources. In freshwater systems such as Lake Nasser, Egypt, co-occurrence of local fishermen communities with Nile crocodiles (Crocodylus niloticus) poses critical challenges for both livelihoods and biodiversity conservation. Understanding local perception of crocodiles by local fishermen is therefore essential for developing effective and socially accepted management responses. We used a structured questionnaire to assess how fishermen perceive and respond to crocodiles across three attitudinal domains: (1) perceived threats, (2) perceived economic benefits, and (3) conservation or co-existence values. Forty-two fishermen were interviewed across multiple khors (side arms of the lake). The responses showed a multifaceted picture: while many local fishermen associated crocodiles with gear damage, reduced catches, and livelihood risks, support for crocodile protection and recognition of their ecological role were also widespread. Interest in crocodile-based livelihood opportunities, such as harvesting or collecting the hatchlings, was generally low, suggesting social, cultural, or legal barriers to such approaches. Fishing experience influenced perceptions, with fishermen encountering crocodiles more frequently reporting decreased catches and greater concern. Cluster analysis further revealed three different respondent groups with different attitudes: conflict-oriented, moderate, and coexistence-oriented. Support for crocodile protection was the strongest predictor of belonging to the pro-co-existence group. Our findings underscore the complexity of human- crocodile co-occurrence in Lake Nasser and, on a wider scale, add to the existing cautions against simplistic mitigations of local HWC. Effective conservation and livelihood interventions will require participatory, context-sensitive approaches that integrate the different perceptions and attitudes of local people.
]]></description>
<dc:creator><![CDATA[ Ezat, M. A., Van Langevelde, F., Naguib, M. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.720860</dc:identifier>
<dc:title><![CDATA[What do fishermen think? Local perspectives on human crocodile co-existence in Lake Nasser]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721369v1?rss=1">
<title>
<![CDATA[
Thermophilization, climatic debt, and consequent declines in primary productivity 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721369v1?rss=1
</link>
<description><![CDATA[
Species have optimal environmental conditions, and ongoing climate warming is reshaping community composition. In particular, many ecosystems exhibit thermophilization, a shift toward species adapted to warmer conditions. However, this process is often slower in forests, leading to a mismatch between community composition and ambient temperature, referred to as climatic debt. Despite increasing attention, its effects on forest productivity remain unclear. Quantifying tree community responses to warming is therefore essential for predicting future forest dynamics and informing biodiversity conservation. In this study, we analyzed natural forests across Japan using data from the 3rd and 4th National Forest Inventory periods (2009 to 2018). We first assessed compositional consistency between survey periods using the Bray Curtis index and excluded plots with high dissimilarity. Specific thermal optima for species were estimated using species distribution models and used to calculate the Community Temperature Index (CTI). Thermophilization was quantified as the temporal change in CTI, while climatic debt was defined as the difference between CTI and mean annual temperature. We then examined the relationship between climatic debt and changes in aboveground biomass, used as a proxy for productivity, using linear mixed-effects models. We found a mean thermophilization rate of 0.005 degree Celsius per year. Despite this shift, climatic debt increased at an average rate of -0.022 degree Celsius per year, indicating a growing mismatch between climate warming and community thermal composition. Although thermophilization showed no statistically significant association with stand structure, it tended to vary with the proportion of small-diameter trees, suggesting the influence of multiple interacting drivers. Importantly, increasing climatic debt was significantly associated with declines in forest primary productivity, even after accounting for stand structure and regional variation. These results demonstrate that delayed thermal adjustment of tree communities can constrain forest productivity under ongoing climate warming, highlighting the importance of evaluating community level thermal responses for sustaining forest ecosystem functioning.
]]></description>
<dc:creator><![CDATA[ Daido, Y., Konrai, K., Tatsumi, S., Onoda, Y. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721369</dc:identifier>
<dc:title><![CDATA[Thermophilization, climatic debt, and consequent declines in primary productivity]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721440v1?rss=1">
<title>
<![CDATA[
WolfPackR: An R package for identifying wolf packs based on genetic and spatial data 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721440v1?rss=1
</link>
<description><![CDATA[
The global expansion of grey wolf (Canis lupus) populations, particularly in Europe, underscores the need for robust tools to study their social structure, territory use, and genetic relatedness. Wolf packs are dynamic, evolving through dispersal, mortality, and reproductive success, and their accurate identification is crucial for effective conservation and conflict mitigation. Traditional methods for estimating wolf populations and pack structures--such as snow tracking or howling surveys--are labor-intensive and often unreliable. Noninvasive genetic sampling and spatial capture-recapture models have improved monitoring, but integrating genetic and spatial data remains a challenge.

We introduce WolfPackR, an R package designed to integrate genetic relatedness and spatial data for identifying wolf packs, lone individuals, and spatially isolated but genetically linked "ugly ducklings." WolfPackR uses pairwise relatedness estimators to define genetic groups and refines these groups through spatial overlap analysis based on Minimum Convex Polygons (MCPs). The package provides a comprehensive toolkit for analyzing population structure, territoriality, and social organization, including functions for genetic grouping, spatial clustering, summary statistics, and interactive visualization.

We demonstrate the utility of WolfPackR using a case study of 505 genotyped and geospatialized wolf scat samples from Romania. By combining genetic and spatial data, WolfPackR accurately identifies pack structures that align with expert assessments and family tree reconstructions. The package modular design and reliance on widely used R libraries (dplyr, igraph, sf, leaflet) ensure flexibility and ease of integration into existing workflows. While sampling heterogeneity may limit territory delineation in some cases, WolfPackR offers a cost-effective and reproducible framework for studying wolf pack dynamics, with potential applications for other social species.
]]></description>
<dc:creator><![CDATA[ Boncourt, E. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721440</dc:identifier>
<dc:title><![CDATA[WolfPackR: An R package for identifying wolf packs based on genetic and spatial data]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.720532v1?rss=1">
<title>
<![CDATA[
Estimating avian wingspan from wing length: an order-level regression approach 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.720532v1?rss=1
</link>
<description><![CDATA[
Wingspan is a key parameter in avian collision risk models but is rarely measured systematically, meaning for many species, collision risk remains largely unquantified due to a lack of morphological and flight data required to parameterise models. Folded wing length scales predictably with wingspan and is available for all extant bird species, yet no widely available method has been published for predicting wingspan from wing length; here we compiled a global wingspan dataset for 1,442 species across 25 orders and fitted order-level linear regression models predicting wingspan from wing length. Order-level models performed well, with 85% achieving R2 [&ge;] 0.95 (global model R2 0.96); cross-validation identified that model predictions generally fell within the intraspecific variation in wingspan, resulting in wingspan estimates for 9,194 species. Our models and accompanying wingspan data provide a transparent, reproducible, and validated method for generating species-level wingspan estimates from widely available wing length data, with direct applications to collision risk modelling, flight performance research, and macroecological analyses of avian morphology.
]]></description>
<dc:creator><![CDATA[ Fox, M. R., Brunton, E. A., Shephard, J. M. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.720532</dc:identifier>
<dc:title><![CDATA[Estimating avian wingspan from wing length: an order-level regression approach]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721321v1?rss=1">
<title>
<![CDATA[
Forty-four years of change: Capercaillie and Black grouse responses to changes in forestry, climate and vole decline in icentral Sweden 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721321v1?rss=1
</link>
<description><![CDATA[
Human land use has greatly affected the natural landscapes in most parts of the world, and Scandinavian industrial forestry has substantially altered the age structure of the boreal forest over the last 75 years. In this study, we analyzed 44 years of line transect counts of Capercaillie and Black grouse collected in an industrial forest landscape in central Sweden between 1980 and 2024. The area was heavily logged in the 1960s and 1970s, followed by large-scale replanting. A hierarchical Gompertz state-space model to assess long-term population dynamics of both species. The adult state model included a brood production submodel, and forest age structure, snow depth, vole abundance, and spring frost were covariates. Our results reveal strong density dependence and temporally variable environmental effects. Capercaillie and Black grouse exhibited contrasting decadal trends: Capercaillie increased markedly during the early study years, whereas Black grouse declined steeply before recovering later in the series. Increasing proportions of forest aged 21-40 years had a clearly positive effect on Capercaillie, whereas snow depth in the previous winter negatively influenced Capercaillie but not Black grouse. Brood production exhibited substantial interannual unexplained variation, although late spring frost reduced brood size in Capercaillie. Toward the end of the study, the two species reached similar levels of latent adult abundance, demonstrating that both can persist at sustainable densities across a broader range of forest structures than suggested in earlier studies.
]]></description>
<dc:creator><![CDATA[ Willebrand, T., Brittas, R., Kindberg, J. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721321</dc:identifier>
<dc:title><![CDATA[Forty-four years of change: Capercaillie and Black grouse responses to changes in forestry, climate and vole decline in icentral Sweden]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.719373v1?rss=1">
<title>
<![CDATA[
Climate change velocity drives rapid evolution of foliar phenology in trailing edge populations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.719373v1?rss=1
</link>
<description><![CDATA[
Here we tested the overarching hypothesis that climate change velocity drives rapid evolution in bud break phenology. With field and common garden studies, we used age cohorts within 17 populations of a foundation riparian tree species distributed across multiple strong environmental gradients in the western US. We provide evidence of contemporary evolution, as young trees in trailing-edge populations have evolved to break bud approximately six days earlier than old trees in these same populations. These populations experience greater water stress than populations at the core of the species' distribution, and the magnitude of genetic divergence in bud-break phenology is related to the velocity of change in climate water deficit over the last 100 years. This relationship to climate change velocity did not exist in core populations, suggesting that, despite similar rates of change, a threshold of water deficit stress has yet to be surpassed in those regions. Overall, the interactive effects of old trees and trailing edge populations can provide useful insight into centuries of environmental history and each independently represent important benchmarks for understanding the context for contemporary environmental change.
]]></description>
<dc:creator><![CDATA[ Bayliss, S. L. J., Ware, I. M., Schweitzer, J. A., Bailey, J. K. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.719373</dc:identifier>
<dc:title><![CDATA[Climate change velocity drives rapid evolution of foliar phenology in trailing edge populations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.720987v1?rss=1">
<title>
<![CDATA[
Biotic niche expansion constrains the fundamental abiotic niche: Evidence from experimental evolution 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.720987v1?rss=1
</link>
<description><![CDATA[
In an ever-changing world, organisms are subject to selective pressures that shape their ecological niches. Niche theory predicts that environmental heterogeneity selects for niche expansion, yet niches are inherently multidimensional, and expansion in one dimension may impose severe constraints on others. In this study, we employed rigorous experimental evolution to investigate these cross-dimensional trade-offs in the wheat curl mite, Aceria tosichella. By adapting replicated lineages to either stable (single-host) or alternating (two-host) environments for hundreds of generations, we successfully expanded the mites' fundamental biotic host niche, enabling lineages to exploit diverse host species, including those unencountered during their evolutionary history. Crucially, however, this biotic generalization incurred a significant cost in the abiotic niche dimension. Lineages adapted to alternating hosts exhibited significantly reduced thermal tolerance compared to host specialists, which maintained superior performance across a wider thermal range. This trade-off appears to be driven by a combination of genetically based metabolic constraints and behavioral dispersal strategies. Our results provide compelling experimental evidence for the "Jack-of-all-trades is master of none" hypothesis across niche dimensions. We demonstrate that physiological trade-offs between biotic versatility and abiotic resilience strictly constrain the evolution of the multidimensional niche, with critical implications for forecasting species' distributions and invasion potential under climate change.
]]></description>
<dc:creator><![CDATA[ Askarova, G., Skoracka, A., Puchalska, E., Lewandowski, M., Sexton, J. P., Kuczynski, L. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.720987</dc:identifier>
<dc:title><![CDATA[Biotic niche expansion constrains the fundamental abiotic niche: Evidence from experimental evolution]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721325v1?rss=1">
<title>
<![CDATA[
Silvicultural practices and interannual variation shape ectomycorrhizal fungal diversity and community composition in an oak-hornbeam forest in northern Hungary 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721325v1?rss=1
</link>
<description><![CDATA[
Ectomycorrhizal (ECM) fungi are well-known for their crucial roles in forest health and productivity, yet their responses to various forest management practices are understudied, particularly in oak-dominated forests. The purpose of this study was to better understand the effects of silvicultural treatments on the diversity and community composition of ECM fungi in an oak-hornbeam forest in northern Hungary. We analyzed ITS2 rDNA metabarcoding data of soil-borne fungi to compare richness and community composition of ECM fungi among forest treatment types (clear-cutting, gap-cutting, preparation-cutting, tree retention in clear-cut areas, and control) and between sampling years (2020 and 2021). We found 268 ECM fungal genotypes, with the most diverse phylogenetic clades being /russula-lactarius (52), /tomentella-thelephora (47), /inocybe (40), /sebacina (27), and /cortinarius (20). We found significant compositional difference of ECM fungi among silvicultural treatments in both years, with some variations in richness. There were also small, but still significant compositional differences between the two years. Treatment effect was partly explained by altered environmental variables, such as relative humidity and soil temperature. These results highlight the importance of forest structure and the abiotic environment in driving community dynamics of plant-symbiotic fungi, with potential implications for forest health and productivity.
]]></description>
<dc:creator><![CDATA[ Ododa, K. O., Odor, P., Kovacs, B., Tinya, F., Aszalos, R., Leal, C. M., Geiger, A., Molnar, A., Geml, J. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721325</dc:identifier>
<dc:title><![CDATA[Silvicultural practices and interannual variation shape ectomycorrhizal fungal diversity and community composition in an oak-hornbeam forest in northern Hungary]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721384v1?rss=1">
<title>
<![CDATA[
Labyrinthula merlionensis sp. nov.: a novel labyrinthulid infecting marine diatoms 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721384v1?rss=1
</link>
<description><![CDATA[
Labyrinthulomycetes are a class of fungus-like heterotrophic protists from the Stramenopiles lineage, recognized for their ecological role as decomposers and contributors to nutrient cycling. They colonize various substrates, from seaweed to terrestrial environments, utilizing ectoplasmic networks for nutrient absorption. This study characterized a novel Labyrinthula strain associated with the marine diatom Biddulphia. Phylogenetic analysis of the full-length 18S rRNA gene positioned this strain as a new species, Labyrinthula merlionensis sp. nov. Scanning electron and light microscopy observations revealed bi-flagellated zoospores and spindle-shaped vegetative cells with ectoplasmic networks. Time-series observations of the interactions between L. merlionensis and Biddulphia were categorised into different phases: establishment, infection, and aggregation. Scanning electron and confocal microscopy observations during the infection phase established the use of ectoplasmic nets to target the marginal ridge regions between diatoms, and the detection of labyrinthulid cells within diatom frustules. These findings enhance the understanding of the diversity, morphology, and ecological roles of Labyrinthulomycetes, particularly their intra- and extra-cellular interactions with diatom hosts.
]]></description>
<dc:creator><![CDATA[ Sim, C. W. H., Walde, M., Strindberg, H., Kaur, A., le Panse, S., Gourvil, P., Jahren, J., Vaulot, D., Lopes dos Santos, A. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721384</dc:identifier>
<dc:title><![CDATA[Labyrinthula merlionensis sp. nov.: a novel labyrinthulid infecting marine diatoms]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721297v1?rss=1">
<title>
<![CDATA[
Too Soon to Save: structural uncertainty inverts the value of precautionary conservation action 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721297v1?rss=1
</link>
<description><![CDATA[
Conservation policy often assumes that acting early is safer than waiting. We show that this intuition can fail when ecological structure is uncertain and protection decisions are difficult to reverse. We compare a precautionary strategy that protects early under uncertainty with an adaptive strategy that learns before committing protection, using both synthetic and real ecosystems. In synthetic ecosystems with uncertain trophic structure, the adaptive learn then commit strategy achieves higher protected area phylogenetic diversity than the main precautionary baseline, with Rao Q PD equal to 5.23 versus 4.41, P less than 0.0001, and Cohen d equal to 0.54. It also achieves higher functional diversity, 1.39 versus 1.25, P less than 0.0001, and d equal to 0.93, although it remains below the full knowledge oracle, 5.34 and 1.43 respectively. This adaptive advantage is greatest when errors in structural allocation are most costly, especially in highly connected ecosystems. It is also stronger in highly modular systems, although this effect is secondary. In a real ecosystem, North East Atlantic fish communities, we find the same conditions for such an advantage. Structural importance is largely decoupled from abundance, rho equal to -0.05 and P equal to 0.77, and trophic uncertainty declines markedly through time, R squared equal to 0.95 and P less than 0.000001. Consistent with this mechanism, adaptive spatial allocation also outperforms a precautionary Marxan like baseline in the empirical analysis, with Shannon diversity equal to 1.70 versus 1.44 at K equal to 10 and P less than 0.00001. Together, these results show that the value of waiting in conservation does not come from delay itself, but from the opportunity to learn which components of an ecosystem matter most. When ecological structure is uncertain and protection is hard to reverse, precaution can lock conservation into avoidable mistakes.
]]></description>
<dc:creator><![CDATA[ Gurchani, M. U., Montoya-Teran, J.-M., Bourgeois-Gironde, S. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721297</dc:identifier>
<dc:title><![CDATA[Too Soon to Save: structural uncertainty inverts the value of precautionary conservation action]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721338v1?rss=1">
<title>
<![CDATA[
Comparative efficiency of eDNA, camera traps and scat surveys to detect a semi-aquatic mammal across multiple catchments 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721338v1?rss=1
</link>
<description><![CDATA[
Semi-aquatic mammals lie at the intersection of several key conservation issues such as wetland deterioration or species invasions, and monitoring their distribution in space and time is essential to inform conservation strategies. However, gathering information about their presence is challenging due to their elusive lifestyle and generally low abundance. The Eurasian otter (Lutra lutra), a near-threatened and strictly protected species in Europe, is currently recolonizing part of its historical range. Its high conservation interest, combined with a dynamic more commonly associated with range-expanding or invasive species, makes it a particularly compelling case study. Otter monitoring has traditionally relied on scat surveys, but recent environmental DNA (eDNA) and camera-trapping initiatives have emerged offering promising complementary tools. Yet, these approaches have rarely been formally compared, either to one another or across regions. Here, we compared the efficiency of spraint surveys, camera traps, and eDNA for detecting otters, and assessed how their performance varied among four catchments in southern France where the species is known to be present. All three methods provided otter detections with varying efficiency. Scat surveys were the most effective method, with an average detection probability of 0.71 and no strong variability between catchments. Although camera-traps had the lowest detection rate, they provided detections at two of the four sites where no spraint was found, highlighting the complementarity of these two approaches. Detection rates varied greatly between individual cameras rather than between catchments, underscoring sensitivity to camera-placement. eDNA showed important variability between catchments, with detection probabilities differing by roughly sixfold across regions. All in all, our results highlight differences in efficiency between methods and across environmental conditions, and show the value of combining approaches for future monitoring programs.
]]></description>
<dc:creator><![CDATA[ Lacombe, S., Devillard, S., D'Hollande, L., Raulet, Y., Sablain, V., Barbu, L., Didier, G., Mathevet, R., Miaud, C., Oyon, C., Le Pommelet, E., Richarte, S., Rouviere, S., Valentini, A., Vazzoler-Antoine, N., Gimenez, O. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721338</dc:identifier>
<dc:title><![CDATA[Comparative efficiency of eDNA, camera traps and scat surveys to detect a semi-aquatic mammal across multiple catchments]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.721176v1?rss=1">
<title>
<![CDATA[
Evaluating eDNA Detection from Live and Dead Control Sources 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.721176v1?rss=1
</link>
<description><![CDATA[
Environmental DNA (eDNA) methods offer a powerful tool for monitoring aquatic species, yet field applications remain challenged by uncertainty in DNA transport, mixing, and detection, particularly in flowing or tidally influenced systems. One approach to improve confidence in eDNA surveys is the use of controlled DNA sources (positive controls), but questions remain regarding how the biological condition of the source influences eDNA release and detectability. This study evaluated differences in eDNA concentrations emitted from live versus dead fish in a controlled, shallow, well-mixed channel. Using a fixed point-sampling design, we measured eDNA concentrations over time and modeled the effects of treatment, sampling time, temperature, and water velocity. Dead fish consistently released significantly higher concentrations of eDNA than live fish, while eDNA concentrations declined over time in both treatments. Water temperature and velocity did not significantly influence detection, and the rate of eDNA decline was similar between live and dead treatments. These findings highlight the importance of source condition and site-specific mixing dynamics when interpreting positive control experiments and underscore the value of site characterization when designing eDNA sampling protocols.
]]></description>
<dc:creator><![CDATA[ Blankenship, S., Dean, C., Karpenko, K., Johnston, M., Espe, M., Schumer, G. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.721176</dc:identifier>
<dc:title><![CDATA[Evaluating eDNA Detection from Live and Dead Control Sources]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.720981v1?rss=1">
<title>
<![CDATA[
The flaws of fitness functions in changing environments 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.720981v1?rss=1
</link>
<description><![CDATA[
When predicting species' responses to changing environments, one can use mathematical functions that describe how individual fitness components depend on the environment, or a single "composite" function that directly links fitness to the environmental state. The former approach is a cornerstone of process-based modelling, but the latter remains standard for developing fundamental theory and making ecological predictions. Yet, fitness is not a single instantaneous trait, but an integrated outcome of multiple underlying processes accruing throughout an organism's life. We show that by ignoring the distinct environmental dependence of the underlying processes, predictions from composite fitness functions become inherently flawed in variable environments. We explore the magnitude of this error by leveraging empirical thermal reaction norms for four important life-history processes in an insect pest, the seed beetle Callosobruchus maculatus. We parameterize two fitness functions: one explicitly modelling the temperature-dependence of the four life-history traits independently (the "ground truth") and one composite function, which treats fitness as a single, instantaneous outcome of the environment. By combining these two functions with hourly temperature data, we projected demographic responses under different warming scenarios across 300 sites over three beetle population origins (California, USA; Yemen; Brazil). We show that the composite function over- or underestimates fitness depending on subtle climatic differences and whether fitness is assumed to accumulate additively or multiplicatively, highlighting the problems of applying composite fitness functions to variable conditions. We conclude that explicitly modeling trait-specific processes will become increasingly important for accurate eco-evolutionary forecasting under future environmental change.
]]></description>
<dc:creator><![CDATA[ von Schmalensee, L., Rueffler, C., Lancaster, L., Bocedi, G., Berger, D. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.720981</dc:identifier>
<dc:title><![CDATA[The flaws of fitness functions in changing environments]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.24.720762v1?rss=1">
<title>
<![CDATA[
Core Bacterial and Host Fruit-Specific Yeast Microbiota in a Polyphagous Fly Pest 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.24.720762v1?rss=1
</link>
<description><![CDATA[
Holometabolous polyphagous insects undergo complete metamorphosis and exploit multiple host plants, exposing them to highly variable ecological conditions across both life stages and host plants. Whether these species, like specialist ones, harbour a stable core microbiota, or whether life stages or host plants act as the primary drivers of microbiota assembly remain open questions. Here, we characterized the fungal and bacterial communities associated with Drosophila suzukii across life stages and host fruits using 16S and ITS metabarcoding. We tested the relative influence of life stage and host fruit on microbiota composition, using community and network-based analyses. We first identified that host fruit significantly structured fungal communities, but not bacterial ones. Yeast communities were rather fruit-specific: Hanseniaspora and Pichia mostly associated with cherries and strawberries, contrary to Metschnikowia with blackberries. In contrast, bacteria and filamentous fungi were shared across fruits, constituting for fruits a core microbiota dominated by Gluconobacter cerinus, Tatumella and Cladosporium. Second, we found that both bacterial and fungal D. suzukii communities were structured by life stage, and that fungal, but not bacterial communities, were also structured by host fruits. D. suzukii individuals harboured a core bacteria composed of G. cerinus and a niche-specific microbiota composed of yeasts: Hanseniaspora typical in individuals related to cherry and strawberry, and Metschnikowia to blackberry. Components of both core and niche-specific microbiota were most likely horizontally acquired by D. suzukii from host fruits. Taken together our results underline the importance of meta-community approaches to investigate tripartite interactions among insects, host plants and microbiota.

IMPORTANCEThe role of gut microbiota in mediating interactions between phytophagous insects and their host plants has been well illustrated in specialist species. However, it has been less comprehensively studied in polyphagous species, which infest multiple host plants, and across life stages for holometabolous species experiencing separate ecological niches through development. We tested the existence of a core, a niche-specific and a stage-specific microbiota in a polyphagous holometabolous species, D. suzukii. We examined both fungal and bacterial communities in larvae, pupae and emerging flies infesting three host fruits. Our results showed first that the assembly of bacteria, filamentous fungi and yeasts on fruits is driven by different ecological processes. Second, that D. suzukii harbours a core bacterial microbiota, a niche-specific microbiota constituted by yeasts and no stage-specific microbiota. Our study emphasizes the importance of considering jointly the assembly of host plant and polyphagous insect microbial communities to better understand the ecology and evolution of insect-microbe interactions.
]]></description>
<dc:creator><![CDATA[ Dunis, S., Lapegue, M., Deschamps, C., Cesari, L., Loiseau, A., Facon, B., Rode, N. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.24.720762</dc:identifier>
<dc:title><![CDATA[Core Bacterial and Host Fruit-Specific Yeast Microbiota in a Polyphagous Fly Pest]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.26.718926v1?rss=1">
<title>
<![CDATA[
Faunal and Floral Assemblages of the Zavitan (Zvitan) Stream near Katzrin (Central Golan Heights, Israel) and Their Influence on Amphibians 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.26.718926v1?rss=1
</link>
<description><![CDATA[
The Zvitan (Zavitan) Stream is one of the major basaltic drainage systems of the Levant Region in Israel. The present short communication focuses specifically on the sector adjacent to Katzrin, integrating geomorphological, hydrological, ecological, and amphibian distribution data within the broader watershed context. The stream originates in the central Golan plateau and flows westward into the Yehudiya Reserve before joining the Meshushim Stream and ultimately draining into Lake Kinneret. In the Katzrin sector, the stream is characterized by deeply incised basalt canyons, winter spring discharge and semi-permanent pools sustained by springs and seepage. Seasonal hydrological fluctuations strongly influence aquatic habitats and amphibian breeding success. Amphibian species documented in the Golan Heights include Salamandra salamandra infraimmaculata, Triturus vittatus (currently Ommatotriton vittatus), Hyla savignyi, Bufotes viridis, Pelophylax bedriagae (formerly Rana ridibunda), and Pelobates syriacus. Their distribution is closely associated with water availability, elevation, temperature, and hydroperiod, as demonstrated in northern Israel habitats. The Katzrin sector of Zvitan represents an intermediate ecological zone where Mediterranean and steppe elements converge, creating heterogeneous amphibian assemblages. This observation, carried out at a specific site in the Zavitan Stream, aimed to examine the ecological conditions and identify which amphibian species inhabit this pool, where environmental conditions may differ from those in the main stream channel.
]]></description>
<dc:creator><![CDATA[ Almozlino, M., Degani, G., Bercovich, D., Meerson, A. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.26.718926</dc:identifier>
<dc:title><![CDATA[Faunal and Floral Assemblages of the Zavitan (Zvitan) Stream near Katzrin (Central Golan Heights, Israel) and Their Influence on Amphibians]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.25.720805v1?rss=1">
<title>
<![CDATA[
Image surveys, agricultural landowners and residents hold the key: optimizing local ecological knowledge to reveal carnivore communities 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.25.720805v1?rss=1
</link>
<description><![CDATA[
The choice of appropriate methods to detect species is crucial for biodiversity monitoring. Camera trapping is currently one of the most widely used methods for characterizing mammal communities, although it requires substantial investment in equipment and personnel. In contrast, questionnaires administered to local populations provide a faster and more cost-effective alternative for assessing community composition, but may be influenced by respondent-related biases that compromise data reliability. This study evaluates the concordance between these approaches for characterizing the carnivore community in the Sierra de Segura (Jaen, southern Spain), using Cohens kappa coefficient, while also examining the individual and social factors shaping Local Ecological Knowledge (LEK). We deployed 24 camera-trap stations (144 trap nights) across a 25 km2 area to record carnivore presence. In parallel, we conducted two types of surveys with local residents (n = 103): (i) free-listing and (ii) image-based species recognition, while recording individual and social characteristics of respondents. Free-listing surveys tended to underreport species, whereas image-based surveys showed higher agreement with camera-trap data, although occasionally overestimating species presence. Higher concordance was associated with social factors indicative of closer and prolonged contact with the environment, such as permanent residence and ownership of agricultural land. Mammal communities differed between methods; however, agreement improved when respondents had higher LEK, while species-specific behavioral traits could also influence perception. Our findings demonstrate that image-based questionnaires can provide results comparable to camera trapping when respondents have strong connections to their natural surroundings. These results highlight the importance of both survey design and respondent selection in improving the accuracy of biodiversity monitoring, offering a transferable framework for integrating LEK into conservation protocols across diverse ecosystems.



O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/720805v1_ufig1.gif" ALT="Figure 1">
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]]></description>
<dc:creator><![CDATA[ Fernandez Vizcaino, E., Fernandez Lopez, J. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.25.720805</dc:identifier>
<dc:title><![CDATA[Image surveys, agricultural landowners and residents hold the key: optimizing local ecological knowledge to reveal carnivore communities]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.24.720639v1?rss=1">
<title>
<![CDATA[
Tipping points are typical in ecosystems with higher-order interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.24.720639v1?rss=1
</link>
<description><![CDATA[
Whether species-rich communities erode gradually or collapse abruptly under environmental change is a central question in ecology [1]. Classical pairwise theory predicts that coexistence is always lost gradually, through smooth declines to extinction [2], yet real ecological interactions are often strongly state-dependent - shaped by nonlinearities that fixed pairwise coefficients cannot capture [3]. Here we show that higher-order (nonlinear) interactions make abrupt, irreversible loss of coexistence a typical route to community collapse: across diverse random communities, the equilibrium supporting coexistence disappears suddenly at a fold bifurcation. Using polynomial homotopy continuation [4] to track equilibria as environmental conditions change, we find that folds progressively dominate the boundary of the coexistence domain as nonlinearity strengthens, replacing the gradual extinctions of pairwise theory. Furthermore, the sign structure of higher-order interactions controls both the onset of tipping-points and whether biodiversity buffers or amplifies collapse. Because higher-order and nonlinear interactions are intimately linked, tipping points also arise generically in pairwise models with strong nonlinearity. Applying our continuation framework to a canonical model of plant-pollinator collapse [5], we formally resolve its bifurcation structure as fold-mediated, and we show that fold bifurcations are typical across published multispecies models spanning mutualistic, competitive, and consumer-resource interactions. These results challenge the expectation that monitoring abundances suffices to anticipate collapse, and unify structural-stability theory, which delineates the safe operating space for coexistence, with critical transition theory, which characterizes the nature of its boundaries.
]]></description>
<dc:creator><![CDATA[ Lechon-Alonso, P., Miller, Z. R., Liaghat, A., Breiding, P., Pascual, M., Allesina, S. ]]></dc:creator>
<dc:date>2026-04-28</dc:date>
<dc:identifier>doi:10.64898/2026.04.24.720639</dc:identifier>
<dc:title><![CDATA[Tipping points are typical in ecosystems with higher-order interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.24.720520v1?rss=1">
<title>
<![CDATA[
Passive acoustic monitoring as a tool for early detection of invasive animal species: a systematic review and a case study 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.24.720520v1?rss=1
</link>
<description><![CDATA[
Invasive animal species are spreading rapidly across the globe, creating an urgent need for efficient early-detection and monitoring tools. Passive acoustic monitoring has become an established method in biodiversity research, but its application to invasive species monitoring has been less systematically explored. Here, we combine a systematic literature review with a field-based case study to evaluate the potential of passive acoustic monitoring for invasive animal detection. We identified 26 studies on acoustic monitoring of invasive animals, mainly addressing amphibians (11 studies), birds and fish (five each) with most studies from the USA and Australia. The use of acoustic monitoring of invasive species has increased during the past decade, with recent studies applying automated detection, machine learning, and large-scale monitoring frameworks. As a case study, we further tested the feasibility of low-cost acoustic monitoring of the invasive American bullfrog (Lithobates catesbeianus) in southwestern Germany, combined with automated identification using BirdNET. We successfully confirmed bullfrog presence in eight of the eleven monitored lakes, including sites close to a protected nature reserve. Our results highlight the growing potential of passive acoustic monitoring of invasive species under field conditions. In combination with automated species detection, manual validation, and emerging real-time monitoring devices, passive acoustic monitoring becomes an increasingly powerful tool for early intervention and scalable management of biological invasions.
]]></description>
<dc:creator><![CDATA[ Becker, D., Kasten, M. K., Weber, T., Grass, I., Hiller, T. ]]></dc:creator>
<dc:date>2026-04-28</dc:date>
<dc:identifier>doi:10.64898/2026.04.24.720520</dc:identifier>
<dc:title><![CDATA[Passive acoustic monitoring as a tool for early detection of invasive animal species: a systematic review and a case study]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-28</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
