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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 19 recordsLinked to original sources

bioRxiv2026

Beyond Single-Metric Assessments: Uncovering Masked Butterfly Declines via Multi-Scalar Analysis in Central Alberta

1. This study analyzed 21 years (2000-2025) of butterfly count data from Central Alberta, integrated with intensive 5-year (2021-2025) high-resolution intra-seasonal sampling. 2. Long-term macro-scale analysis revealed a significant decline in Shannon Diversity, a change that remained obscured when relying solely on traditional metrics of species richness and evenness. 3. This diversity decline was primarily driven by the severe, long-term collapse of the native Common Ringlet (Coenonympha tullia). 4. Four other dominant species--Cabbage White (Pieris rapae), Clouded Sulphur (Colias eriphyle), European Skipper (Thymelicus lineola), and Common Wood Nymph (Cercyonis pegala)--maintained long-term population stability, though their abundances were significantly constrained by extreme winter minimum temperatures and rapid spring warming. 5. High-resolution intra-seasonal analysis (2021-2025) demonstrated that community indices and species-specific abundances were strongly limited by daily weather, particularly wind velocity and temperature. 6. These findings illustrate that while traditional metrics like richness and evenness are fundamental to community ecology, they provide incomplete insights when applied in isolation; they are most effective when utilized as part of a complementary, multi-scalar framework. 7. This study highlights the necessity of coupling multi-decadal historical datasets with high-frequency, fine-scale sampling to accurately identify the mechanisms of community turnover that simpler metrics may overlook. 8. The results underscore the critical importance of standardized citizen science monitoring in quantifying environmental impacts and establishing conservation priorities for terrestrial insect groups.

ecology↗

bioRxiv2026

From concentration to export: resource contrasts and bee traits shape pollinator spillover to crops

Floral plantings can either concentrate bees or export them to adjacent crops, yet the ecological conditions influencing these outcomes remain unclear. Here, we develop a mathematical model as proof of concept for our previous integrative hypothesis: concentrator and exporter outcomes can arise as alternative, context-dependent outcomes of the same underlying resource-selection process. Using bees as a model and focusing specifically on spillover from floral plantings to crops, we identified resource-specific thresholds separating concentration- and export-favoring conditions. Our model translates differences in relative patch attractiveness into context-dependent concentration and export outcomes and generates resource-specific, testable predictions about the conditions favoring pollinator movement into crops. In our simulations, the concentrator-exporter transition occurred at a lower flowering-intensity contrast than at pollen or nectar contrasts, which suggests that flowering intensity may provide an initial cue for bee movement, whereas nectar and pollen rewards refine or sustain bee responses once crops are perceived as attractive. Spillover thresholds differed among resource contrasts, whereas response steepness varied across bee-trait and community scenarios. Under the model's trait-sensitivity formulation, predicted spillover probability responded more strongly to flowering contrast for specialists than for generalists; colony size amplified this response, whereas bee richness dampened it. Together, these patterns show how flowering and resource contrasts interact with bee traits and community context to shape predicted spillover. Our results confirm that the concentrator and exporter hypotheses can be understood as context-dependent outcomes of the same ecological process rather than as mutually exclusive alternatives. Experimental tests of the predicted thresholds conducted in the field could reveal when and where floral plantings are most likely to promote bee spillover to crops, potentially supporting crop pollination.

ecology↗

bioRxiv2026

A Computational Re-evaluation of Spatial Trials for Zoonotic Tuberculosis Control: Model Misspecification, Diagnostic Miss-classification, and the Illusion of Wildlife Culling Efficacy

1. Wildlife reservoir management frequently relies on the Randomised Badger Culling Trial's (RBCT) trade-off hypothesis, which posits that reductions in cattle herd infections are offset by a perturbation effect driven by disrupted host dispersal. This paper evaluates the computational and epidemiological robustness of this historical trial, which serves as the foundational empirical experiment guiding zoonotic tuberculosis (Mycobacterium bovis) control policies. 2. Using generalized linear mixed models with a generalized Poisson error distribution to explicitly address historical data overdispersion, this study contrasts traditional parametric inference against exact cluster-constrained permutation tests across distinct operational definitions of disease incidence. 3. Non-parametric diagnostics reveal that previously reported treatment and perturbation effects render as statistical artifacts under exact non-parametric permutation. Inside culling zones, parametric significance fails to withstand exact permutation verification due to extreme data leverage in localized cluster blocks. 4. Crucially, when diagnostic misclassification biases are eliminated by analysing total reactor datasets, all apparent culling effects disappear, and information criteria overwhelmingly favour nested null architectures. Unconfirmed reactors likely represent true biological infections missed by low-sensitivity post-mortem macro-necropsy, proving that host removal tracks observation noise rather than genuine zoonotic transmission pathways. 5. Finally, empirical scaling conducted in this study identifies a novel mathematical saturation effect, demonstrating that this sub-linear scaling is an operational artifact of unmodelled herd-level disease recurrence over time. 6. Policy implications. Because current zoonotic tuberculosis intervention frameworks are built upon a structurally misspecified statistical model, they have driven large-scale veterinary policies resulting in substantial, unevidenced ecological and economic interventions while failing to provide genuine public health, animal health, or disease control benefits.

ecology↗

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2026

Stepping-stone population structure and sidespread clonality of the mesophotic octocoral Swiftia exserta in the warm temperate northwest Atlantic

Isolated mesophotic banks form spatially discrete networks of patchy ecosystems along continental shelves. Their long-term persistence depends on connectivity among populations of the dominant coral species that structure these communities. Yet the scale of larval-mediated gene flow across these networks remains poorly characterized. Similarly, the extent to which clonal propagation shapes local population dynamics is unresolved, leaving the relative contributions of sexual and asexual reproduction to population maintenance an open question. Here, population genomics and high-resolution (1km) biophysical larval dispersal modeling are integrated to resolve the genetic connectivity and clonal dynamics of Swiftia exserta, a key habitat-forming octocoral, across 13 mesophotic banks spanning the U.S. Gulf and eastern coast within the Warm Temperate Northwest Atlantic (WTNWA) coastal and shelf biogeographic province. Genome-wide SNP markers derived from Restriction-site Associated Sequencing (RADseq) were genotyped across 288 individuals. About 40% of individuals belonged to clonal genets confined to single banks within meters of one another, indicating that asexual propagation sustains local density but plays no detectable role in inter-bank connectivity. Population genetic analyses pointed to isolation by distance as the primary structuring force, with the majority of molecular variance residing within rather than among populations. The west-most population, East Flower Garden Banks, was the most differentiated population in the WTNWA Northern Gulf ecoregion, reflecting its peripheral position within the bank network. The Edisto population from the WTNWA Carolinian ecoregion, was distinct from all others, implicating the Florida Peninsula as a phylogeographic barrier. Biophysical particle-tracking simulations independently recovered the same spatial structure, with modeled larval exchange consistent with the genomic signal across the bank network. These findings reveal that S. exserta persists across the northern WTNWA province through a dual reproductive strategy of clonality at the bank scale and episodic larval exchange at the network scale, with implications for the conservation and management of mesophotic octocoral metacommunities.

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bioRxiv2026

Physiological and anatomical leaf acclimation of understory trees subjected to a through-fall precipitation exclusion in a temperate rain forest in southern South America.

Water input is a key component of the ecosystems. Water defines the functionality, composition, and structure of biomes; therefore, any change in its availability would have an impact on ecosystem features. Moreover, a change in the water balance of an ecosystem affects its persistence as well as biochemical cycles, such as the carbon and nitrogen. Forests are ecosystems structured using high amounts of water. Thus, trees, the oldest living plants, are the prime species in these ecosystems and are the main managers of this abiotic element. Trees uptake water from the soil, store it in their biomass, and exchange it with the environment through leaf stomata. They also intercepted rainfall and fog with their canopies. All of this water is also transmitted to the entire biological diversity that inhabits these ecosystems. Any change in water input affects the web described above. The ability of trees to modify their anatomy or processes, that is, to acclimate to novel climates, is of great advantage in maintaining the characteristics of ecosystems. In this study, we took advantage of a precipitation exclusion experiment to reveal the acclimation of shade-tolerant understory trees, which will be the main component of a cold temperate rainforest in the future. We evaluated different anatomical and physiological leaf traits involved in the use of water by these species. We hypothesized that, as observed in similar experiments, species would adopt more conservative water-use strategies by adjusting their functional traits accordingly. Contrary to our hypotheses, we found that understory tree species inhabiting this temperate ecosystem will not become more conservative when using water. In minimal, but significant differences, most of the studied species displayed traits, in the precipitation exclusion treatment, that were demonstrated to be water spender, rather than conservative. We attributed these contrasting changes to root metabolism alleviation due to the flooded soils of Chiloe inhabited by these forests.

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bioRxiv2026

Soils from different landscape elements diverge in response to multiple global change factors

Global change factors (GCFs) are known to affect terrestrial ecosystems across a range of land-use types, including farmlands, grasslands, and forests. However, it remains unclear whether different landscape elements within the same region respond differently to the same global change pressures. Here, we investigated this question using four soils collected from co-located farmland, grassland, pine forest, and oak forest, representing distinct landscape elements under the same regional climatic conditions. Each soil was exposed to one of six individual GCFs, warming, drought, nitrogen deposition, salinity, microplastics, and antibiotics, as well as to all six factors combined. We found that landscape elements exhibited strongly divergent responses to the same GCFs. The effects on soil functions also varied among soils under combined stress, with responses diverging from different null-model predictions depending on soils and response variable. Moreover, landscape-element specific response patterns became more pronounced under multiple concurrent stressors. Overall, our findings show that landscape heterogeneity represents a mosaic of different capacities to resist and respond to global change, even under shared climatic and geographic conditions. Global change assessments and ecosystem models should therefore better account for landscape-level heterogeneity, and management strategies aimed at enhancing ecosystem resilience should be tailored to individual landscape elements.

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bioRxiv2026

Environmental sensing capacity predicts bacterial ecological strategies and environmental preferences

The ability to sense environmental variation is a prerequisite for ecological success. Sensor domains enable bacteria to detect nutrients, neighboring organisms, and physicochemical conditions, but whether variation in these sensing systems reflects ecological specialization remains unresolved. Here, we analyzed sensor domains across 51,343 bacterial genomes and 255 soil metagenomes spanning a climatic gradient to determine whether sensory repertoires encode bacterial ecological strategies and environmental preferences. Sensory repertoires exhibited strong phylogenetic conservatism and revealed signatures of genome streamlining, indicating that environmental sensing reflects trade-offs associated with maintaining sensory complexity. Taxa occupying environmentally heterogeneous habitats, particularly free-living aerobic generalists, encoded the largest sensory repertoires, consistent with selection for expanded environmental information processing. To link sensory function with ecological adaptation, we mapped experimentally-characterized ligand-binding motifs (LBMs) across genomes and metagenomes. Distinct LBM profiles discriminated host-associated and free-living taxa, aerobic and anaerobic lineages, and generalists and non-generalists, revealing a tight coupling between sensory capacity and ecological strategy. Across soil communities, motifs associated with osmoprotection and oxygen sensing were consistently enriched under increasing aridity, linking sensory function to environmental filtering in natural ecosystems. These findings identify environmental sensing as an important organizational axis of bacterial trait-based ecology that integrates evolutionary history, ecological lifestyle, and adaptation to local conditions. Environmental sensing should be considered for predicting microbial niches and responses to environmental change.

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bioRxiv2026

Persistent but variable effect of experimental laboratory burns on microbial community resistance, resilience, and function across contrasting boreal forest soils

Boreal forests stretch across vast swaths of the northern hemisphere, are shaped by wildfire, and play an important role in the global carbon cycle. Microorganisms play a critical role in soil nutrient cycling in these ecosystems, yet there are many open questions about the impacts of wildfire on microbially mediated soil biogeochemical cycles. In this study, we used laboratory burns and soil incubations of intact soil cores collected from two distinct soil types -- Histosols and Gleysols -- from boreal forest within Wood Buffalo National Park, Alberta, Canada, to assess burn effects on soil bacterial and fungal community composition and function. We compared resistance and resilience to burning for microbial communities vs. resistance and resilience to burning for soil pH and soil respiration to assess the relationships between burn-induced shifts in microbial community composition, the soil environment, and microbial activity. To link shifts in microbial community composition to potential community function, we measured glucose-specific carbon use efficiency (CUE) and assessed its relationship with weighted mean predicted 16S rRNA gene copy numbers for bacterial communities and FUNGuild-estimated relative abundance of putative symbiotrophic and saprotrophic fungi in burned and unburned soils. Microbial community resistance and resilience to burning varied across soil type with higher resistance of both bacterial and fungal communities from Histosols compared to the O horizons of Gleysols. This may be explained by a larger impact of burning on microbes in the thinner Gleysol O horizons. The relatively low resilience of bacterial and fungal communities to burning as well as the failure of resilience to increase with time since burning supports previous reports of post-burn microbial community recovery occurring over years rather than months. Burning caused a decrease in CUE with larger decreases following longer, hotter burns, which correlated with an increase in weighted mean predicted 16S rRNA gene copy number, raising the possibility that copy number could serve as a proxy for post-fire CUE in boreal forest soils, though more research is needed to constrain the effects of environmental conditions, substrates, and time since fire on this relationship. These findings suggest several ways in which burn-induced shifts in microbial community composition reflect altered microbial community function in meaningful ways for soil carbon cycling.

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bioRxiv2026

Proteomic analysis of Stony Coral Tissue Loss Disease demonstrates coral-algal dysbiosis during disease progression

Stony Coral Tissue Loss Disease (SCTLD) has devastated Caribbean reefs, yet the host molecular response to infection is poorly understood. Previous gene expression studies of diseased corals identified shifts in the immune response, apoptosis, and coral-algal dysbiosis. Here, we characterized the proteomic response of Diploria labyrinthiformis to SCTLD by comparing protein abundance in healthy tissue from uninfected colonies and apparently healthy and neighboring diseased tissue from infected colonies. These results were compared with existing metagenomic data from the same samples that previously demonstrated significant shifts in the coral microbiome due to SCTLD. We identified 480 differentially abundant proteins when comparing diseased lesion and healthy tissues, but only 12 between apparently healthy and healthy tissues. Pathway-level analysis provides evidence of immune suppression in apparently healthy tissue, suggesting that host molecular responses precede visible disease progression. Diseased lesion tissues showed wound-healing responses combined with a decreased abundance of proteins involved in symbiosome maintenance and increased oxidative stress responses, consistent with host-algal dysbiosis. This result correlates with the previous metagenomic analysis of these samples which found that infected colonies exhibit distinct algal symbiont communities dominated by Symbiodinium necroappetens, whereas healthy colonies are dominated by Durusdinium trenchii and Breviolum spp. Comparison with existing transcriptomic studies revealed both shared and distinct molecular responses, underscoring the importance of integrating multi-omics approaches to understand coral diseases. Our results suggest that SCTLD in D. labyrinthiformis is associated with early immune suppression, coral-algal dysbiosis, oxidative stress, and subsequent wound-healing responses.

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bioRxiv2026

Why are fishers retaining manta and devil ray bycatch?

Increasing fishing pressure, including from small-scale fisheries, has caused declines in more than one-third of all elasmobranch species. Tackling conservation issues in small-scale fisheries requires interdisciplinary approaches due to the coastal community's interdependence on marine resources. To support inclusive policy change and fisher engagement, an understanding of the motivations driving fishers' operational choices (i.e., the retention of elasmobranch bycatch) is needed. We assess the motivational drivers behind bycatch retention of one of the slowest-growing and most vulnerable elasmobranch groups, manta and devil rays (collectively, mobulids), through a case study in India, their largest fishery in the world. We conducted a best-worst scaling survey in the fishery-intensive states of Tamil Nadu and Andhra Pradesh, which make significant contributions to mobulid landings on India's east coast. Our results suggest that fishers exhibit varied motivations for retaining mobulid bycatch across states. Financial motivation to sell mobulids for additional revenue was the most important motivator for bycatch retention in both states. In Tamil Nadu, the top three motivators were all financially driven, whereas in Andhra Pradesh, the top three motivators included both financial and non-financial attributes, such as nutritional importance and storage optimisation. As the first socio-economic study of mobulid fisheries in India, we show that motivations underlying bycatch retention decisions vary geographically and may be influenced by cultural differences between states and the socio-economic characteristics of decision makers. Based on identified fisher motivations, we provide context-specific recommendations to align conservation strategies with the values fishers derive from the mobulid fishery and encourage participation in conservation. These include subsidies for net repair to encourage mobulid release; promotion of a minimum price measure for sustainably sourced alternative species; quality improvement of target species; and increased awareness of national and international regulatory obligations (e.g., CITES, CMS, IOTC).

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bioRxiv2026

Deep sequencing artificially inflates estimates of microbial diversity

Sequencing artifacts challenge accuracy and reproducibility when quantifying microbial diversity. To track error propagation in microbiome analyses, we analyze no-diversity amplicons, which are amplified from host genes with limited genetic diversity or from synthetic spike-ins. We find that sequencing at greater than 104 reads exponentially increased no-diversity amplicon sequence variant (ASV) richness, with hundreds of ASVs observed per sample. This striking pattern was shared with microbial amplicons (16S rRNA, ITS, gyrB, rpoB), which revealed inflated Shannon diversity with an increase in read counts for both the community and within taxa. Comparing sequencing error profiles between no-diversity and microbial amplicons showed that truncating reads to shorter lengths and use of the AVITI Element platform can mitigate, but not abolish, the impacts of artificial inflation; we recommend caution when read depths vary orders of magnitude between samples. Overall, utilizing no-diversity amplicons can help optimize parameters to improve estimates of microbial diversity.

ecology↗

bioRxiv2026

Division of labor and low temperatures predict geographic variation in thermal tolerance of a North American paper wasp (Mischocyttarus mexicanus cubicola)

The biogeographic study of organismal thermal performance is fundamental to our understanding of how climate drives evolution. However, despite highly social insects being popular models for such studies, biogeographic comparisons of thermal functional traits seldom consider division of labor. Individuals within cooperative societies can operate in different microclimates, exposing different task groups to different selection pressures. Here we present a study of how thermal tolerance limits in a social paper wasp vary broadly across temperate and subtropical climates in eastern North America, testing whether division of labor between foundresses and non-reproductive workers generates adaptive variation in thermal performance within the colony. Cold tolerance rather than heat tolerance varied more predictably with environmental temperatures across latitudes, with temperate populations experiencing bouts of winter cold coma, unlike in subtropical populations. Within colonies, reproductive foundresses were also more cold-tolerant than workers, enabling them to remain mobile at cooler periods of early spring during crucial tasks of nest construction, before workers emerge. Together, these results broaden our understanding of how climate shapes thermal performance on both biogeographic and social scales.

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bioRxiv2026

Structural characteristics of important daily movement corridors for waterbirds in urban areas: A case study on Black-headed Gulls

Landscape management facilitating animal movement is essential for sustaining urban wildlife populations and ecosystem services. Although linear vegetation corridors effectively conserve terrestrial animal movements, it remains unclear which landscape elements serve as pathways for aquatic organisms. Urban waterbirds frequently utilize rivers, but the specific characteristics that render certain river segments crucial as movement corridors have yet to be elucidated. This study aims to identify the characteristics of river segments functioning as critical corridors based on waterbird movement strategies. We tracked the movement behaviors of the Black-headed Gull (Chroicocephalus ridibundus), a river-dependent species in daily movements, and identified key movement corridors in highly urbanized Tokyo, Japan. Using GPS tracking data from gulls, we evaluated how river sinuosity and surrounding feature heights influenced tendencies to follow rivers across various temporal scales and perceptual ranges. Furthermore, we predicted and mapped these tendencies across individual river segments in central Tokyo. Gulls tended to fly along river segments with tall features during instantaneous to mid-term decision-making. In contrast, they utilized straight channels for long-term decisions. Although results varied slightly depending on the spatial scale they can perceive, this overarching trend remained consistent. Furthermore, our model predicted that the lower reaches of the Sumida River serve as critical movement corridors. This predictive tendency was also highly robust across all time scales. While straightened river segments with high feature heights may provide unsuitable habitats for diverse taxa, we emphasize their ecological value and argue that they should be conserved as essential movement corridors for waterbirds.

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bioRxiv2026

Early establishment acts as a selective filter shaping climate-associated genomic variation in European beech

Climate change is increasing drought and heat stress in European forests, raising concerns about the capacity of long-lived tree species to respond to rapidly changing environmental conditions. While local adaptation has been documented in many forest trees, it remains unclear whether newly established seedlings, which form the forests of the future, are able to persist and adapt to these new climatic conditions. Here, we investigated genomic differences between naturally regenerated seedlings and trees of European beech (Fagus sylvatica) across the three regions of the German Biodiversity Exploratories using low-coverage whole-genome sequencing (5x) of 1,032 individuals. Population structure was primarily driven by geographic region, whereas genetic diversity was similar across life stages. Despite this genome-wide similarity, we detected allele frequency shifts between trees and seedlings, concentrated in narrow genomic windows. These shifts were strongest in surviving seedlings, suggesting that environmental filtering during early establishment may contribute to shaping the genetic composition of regenerating populations. The strongest signals were observed within the Swabian Alb, where sampled seedlings were 2-years old and had experienced a longer period of potential filtering prior to sampling. Genotype - environment association analyses identified loci associated with climatic variables, and subsequent GO enrichment analyses of genes linked to these loci revealed significantly more enriched GO terms in seedlings than in trees, suggesting stronger environmental filtering by the current climate in seedlings. In particular, we found associations with maximum air temperature, relative humidity, soil moisture, and precipitation, affecting genes involved in stress responses, growth, metabolism, and developmental processes. Together, our results demonstrate that young cohorts of European beech differ genetically from trees and reveal genomic patterns consistent with life-stage-dependent environmental filtering. These findings suggest that the genetic composition of early life-stages is already altered by current environmental conditions, possibly contributing to adaptation to new climatic conditions.

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bioRxiv2026

Burning down the mouse: Effects of wildfire and post-fire reseeding on Sin Nombre virus prevalence in its reservoir host

Worldwide, physical habitats and biological communities are being reshaped by wildfire. Such changes have obvious potential to alter pathogen ecology, yet few studies, outside of those focused on ectoparasites, have tested the effects of wildfire on pathogen prevalence in wildlife. Even fewer have focused on the impacts of strategies for post-fire remediation on pathogen circulation. Here, we investigated the effect of wildfire and wildfire mitigation on the prevalence and viral load of Sin Nombre virus (SNV) infection in its reservoir host, the western deer mouse, using a study design of matched burned, unburned, and post-burn reseeded sites in northern New Mexico. In total, we screened 411 individual deer mice for SNV via RT-qPCR and analyzed the effect of wildfire and wildfire mitigation on relative mouse abundance, individual infection probability, site-level prevalence and viral load. Relative abundance was highest at reseeded sites, and model selection indicated that habitat structure, particularly the gradient from closed canopy to open-herbaceous habitat, was consistently associated with increased relative abundance. Similarly, SNV prevalence was significantly higher in reseeded sites than either burned or unburned sites but did not differ in burned versus unburned sites. Viral load did not differ between burn history types, and zero-inflated gamma hurdle models did not identify any strong predictors of viral load. Serendipitously, we were also able to investigate the impacts of an El Nino Southern Oscillation (ENSO) cycle on patterns of infection in a subsample of sites that were studied during and one year after an ENSO year and found that SNV prevalence increased significantly post-ENSO. Both reseeding and ENSO deliver resource pulses that can support increases in mouse density and thereby enhance SNV transmission. The impacts of post-fire management practices on SNV prevalence in its reservoir host that were revealed in this study should be considered when implementing such strategies and when utilizing treated areas.

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bioRxiv2026

The emerging medium-scale: Prioritising fisheries management for elasmobranch conservation.

Fishing pressure has substantially increased over time and elasmobranchs are among the most vulnerable marine taxa impacted. 'Small-scale' and 'large-scale' are terms frequently used to describe fisheries, yet definitions used across the globe are inconsistent. The global impact of small-scale fisheries on elasmobranch decline is increasingly evident. However, ambiguous vessel-capacity classifications undermine effective conservation management. Technological advancements have led to the emergence of medium-capacity vessels that sit between small and large-scale classifications, creating regulatory gaps that increase bycatch impacts on vulnerable elasmobranchs. Beyond vessel size, the gear specificities and practices also affect interaction with species caught incidentally, and can alter bycatch risk for vulnerable elasmobranchs. Manta and devil rays (collectively, mobulids) represent a pelagic ray group that includes species listed as Critically Endangered with high risk of extinction, largely due to bycatch threats. To prioritise fisheries management for conservation, we assess the contribution of fishing gear specifications and practices to mobulid bycatch as a case study in their largest fishery globally. We use a Huber-robust extension to a Hurdle negative binomial model to assess the impact of fishery characteristics and operational specificities on mobulid bycatch risk. We find that within the Food and Agriculture Organization (FAO) of the United Nations' broad international fleet classification of small-scale vessels based on overall length ([≤]24 m), the 'medium-capacity vessels' in India are twice as likely to catch mobulids than small-scale vessels. Further, increased fishing intensity, measured in five-day increments, doubles mobulid bycatch risk. Our results indicate the emergence of a distinct medium-capacity fishery class in rapidly developing blue-economy nations, shaped by rising technological capacity and exemptions from large-scale management measures. We propose a comprehensive re-conceptualisation of small-scale fisheries to ensure that advanced medium-capacity vessels are subject to management measures commensurate with their bycatch impact. Our recommended re-conceptualisation is complementary to FAO's SSF characterisation matrix and would promote fishery-level sustainability and enable bycatch risk mitigation for elasmobranchs, including manta and devil rays. Further, for congruence between elasmobranch demography and regulations, we recommend that fisheries management measures distinguish vessel capacities for elasmobranch bycatch risk and apply biologically relevant regulations to the associated fisheries scale.

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bioRxiv2026

Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates

Understanding the processes that shape microbial biodiversity and community structure is a key objective of the field of microbial ecology. The processes driving assembly of benthic biofilm bacteria on functionally important reef substrates, such as crustose coralline algae (CCA) and calcium carbonate, are not well understood, despite their critical contributions to the maintenance of biodiversity and ecosystem function on reefs. To characterize the patterns of community assembly and biogeography on these substrates, climax biofilm bacterial communities from 11 reef sites were collected, and full 16S small subunit rRNA genes were sequenced. Though CCA- and carbonate-associated communities demonstrated different diversity, composition, and correlations with environmental conditions, communities on both substrates were assembled according to similar processes. Stochastic processes dominated assembly on both substrates, primarily drift with moderate influence from dispersal limitation and selection. Sub-communities of habitat generalists and specialists, as well as rare and abundant taxa, experienced disparate patterns of assembly that remained consistent between substrates, highlighting the importance of individual taxa traits in shaping community assembly. These results provide insight into the factors shaping benthic biofilm bacterial assembly and biogeography in a tropical reef ecosystem and contribute to understanding of reef resilience in the face of environmental change.

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