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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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<title>bioRxiv</title>
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747290v1?rss=1">
<title>
<![CDATA[
The CoralAssist Plug: a novel device with built-in microrefugia for settling, rearing and rapidly outplanting corals 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747290v1?rss=1
</link>
<description><![CDATA[
Sexual coral propagation is an emerging technique capable of producing large numbers of corals for coral transplantation and reef rehabilitation. In contrast to asexual coral propagation, sexual propagation increases genotypic diversity and can be used for selective breeding to enhance coral heat tolerance or other desirable traits. However, implementation at meaningful ecological scales is hindered by high mortality during early life stages, high costs associated with nursery rearing facilities, and labour-intensive outplanting methods. To overcome these issues, we developed the CoralAssist Plug (CAP), a ceramic device designed for the rapid and cost-effective outplanting of sexually propagated corals in large numbers that maximises post-outplant survivorship. CAPs combine three important functional features: 1) built-in microrefugia to protect juvenile corals from grazing, 2) a relatively small size, 3 by 1 cm, that is easy to handle and stack efficiently without compromising the survivorship of corals, and 3) a hole in the middle that facilitates handling and attachment. CAPs were settled with Acropora aff. digitifera and outplanted to a reef crest after 1 to 6 months of ex situ nursery rearing. A 3-person dive team was able to outplant ~120 CAPs in one 90-minute shallow dive (just over 2 minutes per CAP per person). With longer nursery durations of 6 months, it was possible to achieve 36 % yield (i.e., the proportion of devices with a surviving coral) 4-years post-outplant. With nursery durations shortened to 1 month, we were able to attain 24 % yield 3-years post-outplant. Microrefugia significantly enhanced post-outplant survivorship leading to an 11 % increase in yield 4 years post outplant compared to devices without microrefugia. Outplanted corals that had reached adult size, were self-attached and were reproductively mature after 4 years. Our results suggest that CAPs can play a meaningful role in reef rehabilitation by efficiently introducing sexually propagated corals into natural populations with clear applications to assisted evolution techniques, such as selective breeding.
]]></description>
<dc:creator><![CDATA[ van der Steeg, E., Humanes, A., Bythell, J. C., Edwards, A. J., Golbuu, Y., Lachs, L., Miller, M. W., Guest, J. R. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747290</dc:identifier>
<dc:title><![CDATA[The CoralAssist Plug: a novel device with built-in microrefugia for settling, rearing and rapidly outplanting corals]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747664v1?rss=1">
<title>
<![CDATA[
Microcystis-triggered shifts in the symbiotic microbiome of Myriophyllum spicatum rapidly suppress Microcystis aeruginosa 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747664v1?rss=1
</link>
<description><![CDATA[
While the suppression of toxic cyanobacteria by aquatic plants has long been recognized, few studies have clearly differentiated between the allelopathic effects of the plant itself and the inhibitory influence of its associated microbiome. This study aimed to clarify the primary inhibitory agent by pre-culturing Myriophyllum spicatum (Eurasian watermilfoil) under three conditions: (1) BG11 medium, (2) live Microcystis aeruginosa KW culture, and (3) a Microcystis-symbiotic microbiome (excluding Microcystis cells). After a 7-day pre-culture, Myriophyllum shoots were transferred to fresh Microcystis culture. The Myriophyllum pre-cultured in Microcystis culture exhibited rapid inhibition against Microcystis (84% within day 1), whereas the Myriophyllum pre-cultured in BG11 medium showed delayed responses (89% by day 7). In contrast, inhibition remained below 50% in the Myriophyllum pre-cultured with the Microcystis-symbiotic microbiome. Notably, plant-derived soluble compounds exhibited weak inhibitory effects, whereas the microbiome showed stronger inhibitory activity, indicating that the plant-associated microbiome plays a more dominant role than the plant itself. Exposure to Microcystis triggered significant shifts in plant-symbiotic microbial community composition, leading to rapid enhancement of inhibitory activity in the Myriophyllum microbiome. Microbial community analysis identified 28 bacterial taxa closely associated with the inhibitory response, including strains involved in organic matter degradation, adhesion, biofilm formation, and predatory behavior. Meta-transcriptomic analysis further confirmed increased expression of genes related to bacterial adhesion, biofilm formation, and carbohydrate metabolism following Microcystis exposure, highlighting functional adaptations linked to cyanobacterial suppression. These findings underline the role of microbiome-mediated cyanobactericidal mechanisms, providing new insights into a nature-based solution for mitigating Microcystis-dominated harmful algal blooms.
]]></description>
<dc:creator><![CDATA[ Jeong, S., Lee, H., Ko, S.-R., Choi, D.-Y., Choi, W.-S., Shin, Y., Kim, K., Kim, H.-S., Ahn, C.-Y. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747664</dc:identifier>
<dc:title><![CDATA[Microcystis-triggered shifts in the symbiotic microbiome of Myriophyllum spicatum rapidly suppress Microcystis aeruginosa]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.28.747494v1?rss=1">
<title>
<![CDATA[
Beyond establishment: incorporating physiological performance into predictions of invasion risk 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.28.747494v1?rss=1
</link>
<description><![CDATA[
Biological invasions are a major driver of global change, reshaping ecosystems and threatening biodiversity worldwide. Anticipating where invaders will establish and where they will exert the strongest ecological impacts are key challenges for early detection and targeted management. Although Species Distribution Models (SDMs) are widely used to forecast biological invasions, they often provide uncertain estimates of establishment ranges and limited insight into invader performance, making it difficult to anticipate ecological impacts. Here, we address these limitations by integrating physiological information on invader performance with SDMs to identify regions of high invasion risk. Using the brown alga Rugulopteryx okamurae, one of the most prominent marine invaders in Europe, we first test alternative hypotheses of northern establishment limits: (i) a cold-survival constraint driven by winter temperatures and (ii) a growth constraint derived from the species' thermal performance. To identify the more likely scenario, we combine cold-tolerance experiments with seasonal growth comparisons between the invader and a native macroalga Dictyota dichotoma, whose established distribution allows physiological performance to be directly related to realised presence. Finally, we project seasonal growth of the invader across the predicted establishment range as a proxy for biomass accumulation and potential ecological impacts. Our results indicate that northern limit in Europe will be more likely constrained by winter survival rather than growth, extending the potential establishment range of Rugulopteryx to mid-Norway. In contrast, the highest impacts are likely to remain concentrated in southern Europe, where thermal conditions sustain high year-round growth. Overall, our approach illustrates how understanding the physiological response of invaders to their environment can improve the interpretation of SDM outputs and help identify areas at greatest risk of impact within their potential establishment range.
]]></description>
<dc:creator><![CDATA[ Vapillon, L., Delva, S., Bonafont Castelles, M., Assis, J., Strubbe, D., Adriaens, T., De Clerck, O., Vranken, S. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.28.747494</dc:identifier>
<dc:title><![CDATA[Beyond establishment: incorporating physiological performance into predictions of invasion risk]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.28.747010v1?rss=1">
<title>
<![CDATA[
Experimental flowering order shapes priority effects in plant-pollinator interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.28.747010v1?rss=1
</link>
<description><![CDATA[
Climate change is disrupting life's seasonal rhythms, altering the timing of key phenophases and reshaping how communities assemble. Beyond shifting flowering times, climate change can modify the extent of floral overlap and the sequence in which species bloom, generating novel assemblages with uncertain consequences for plant-pollinator interactions. Here, we ask whether flowering order generates priority effects in plant-pollinator communities, much like germination order does in plant communities. We tested how flowering order influences bee foraging behaviour and plant reproductive success in two co-flowering species, Hypochaeris radicata and Campanula rotundifolia, using a greenhouse experiment in which we manipulated the sequence of floral availability while allowing bees to forage repeatedly. We quantified changes in visit frequency, interspecific switches, handling time, and seed production. Our findings reveal priority effects in bee foraging that were strong enough to affect plant fitness: both species received more visits when flowering earlier than their co-occurring counterpart, and seed production declined when species flowered later. Overall, our results show that flowering order is an underappreciated driver of plant-pollinator interactions, suggesting that climate-driven phenological shifts could alter priority-effect dynamics with broader implications for community assembly. Key questions remain: How will climate-driven phenological shifts rearrange flowering sequences, and how will these priority effects emerge in more diverse communities in the wild? Our controlled experiment reveals strong flowering-order effects, underscoring the need to evaluate how widespread and impactful such dynamics are under accelerating climate change.
]]></description>
<dc:creator><![CDATA[ Torres, A., Chen, W.-L. C., Hille Ris Lambers, J., Waters, S. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.28.747010</dc:identifier>
<dc:title><![CDATA[Experimental flowering order shapes priority effects in plant-pollinator interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747580v1?rss=1">
<title>
<![CDATA[
Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747580v1?rss=1
</link>
<description><![CDATA[
Viral population dynamics are shaped by production and loss. For viruses of microbes, high standing levels of viral abundances are interpreted as evidence of high rates of viral-induced cellular loss and viral production, followed by rapid extracellular viral decay. Here we reassess assumptions of rapid extracellular decay in 17 curated datasets, finding that biphasic decay either fits better or is statistically indistinguishable from exponential decay in approximately half the datasets. In addition to intrinsic heterogeneity in decay rates, biphasic decay at population scales can arise generically through aggregation mechanisms, where single virions decay and viral aggregates are protected. Integrating aggregation-induced biphasic decay into a virus-host model reveals that accounting for aggregation can recapitulate joint observations of high virion abundances and low infection prevalence, without assuming significant levels of uniformly inefficient infection. Together, our results suggest that durable extracellular virion persistence is environmentally relevant in shaping virus-microbe population dynamics.
]]></description>
<dc:creator><![CDATA[ Arani, A., Fremont, P., Wachter, E. R., Weitz, J. S. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747580</dc:identifier>
<dc:title><![CDATA[Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747552v1?rss=1">
<title>
<![CDATA[
Soil microbial inoculants augment fertilizer performance across contrasting cropping systems in Rwanda 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747552v1?rss=1
</link>
<description><![CDATA[
Smallholder farming systems in sub-Saharan Africa are constrained by declining soil fertility, erosion, and rising fertilizer costs, creating an urgent need for scalable inputs that sustain yields while maintaining soil health. While there is some evidence that microbial inoculants may offer a promising complement to conventional fertility management, field-scale evidence in tropical cereal and tuber systems remains limited. Here, we evaluated a multi-species inoculant composed of 20-22 Bacillus and Streptomyces species on potato and maize across four sites in Rwanda over two growing seasons (2025A and 2025B). Treatments included the inoculant applied at two rates (150 and 250 g ha-1), both alone and in combination with standard fertilization (inorganic fertilizer plus manure), alongside untreated and fertilized controls. Co-application of the inoculant with standard fertilization increased yield and plant biomass beyond fertilization alone, with gains of 6-51% for maize and 3-58% for potato. However, while the inoculant applied alone outperformed untreated controls, it generally did not match standard fertilization. Responses were strongest and most consistent for large-grade potato tubers, and application rate interacted with crop type, whereby the lower dose maximized marketable tuber yield, while maize showed a positive dose-response for grain and biomass. Yield increases were not accompanied by reductions in crop nutrient density, which was instead governed by site-level differences. Altogether, these results indicate that multi-species microbial inoculants are an effective complement to existing fertility practices that may offer, pending further research, a potential pathway to partial fertilizer replacement while sustaining productivity and nutritional quality in smallholder tropical agriculture.
]]></description>
<dc:creator><![CDATA[ Hansen, P. M., Edlund, A., Bukombe, B., Grama, A., Mberwa, J. W., Makhalanyane, T. P., Jansson, J. K., Crowther, T. W., Gilbert, J. A. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747552</dc:identifier>
<dc:title><![CDATA[Soil microbial inoculants augment fertilizer performance across contrasting cropping systems in Rwanda]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.28.747639v1?rss=1">
<title>
<![CDATA[
Life history traits predict the contribution of transient dynamics to variation in population growth 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.28.747639v1?rss=1
</link>
<description><![CDATA[
The performance of any natural population in variable environments depends on contemporaneous changes in its vital rates (e.g., survival, reproduction) as well as legacies carried by its population structure. Yet whether the relative contribution of these two pathways can be predicted from life history remains unknown. Here, we use stochastic simulations of 1,986 matrix population models from 137 species to quantify the contribution of transient dynamics to variation in population growth rate, and test its associations with key life history traits. Longer generation times were associated with reductions in transient contributions, contrary to theoretical expectations. Greater stage-specific survival heterogeneities were associated with increases in transient contributions, whereas greater iteroparity was associated with decreases in plants but increases in animals. These associations were robust to body size, phylogenetic relationships, and vital-rate variability. Life history traits therefore provide a strong predictor for when population structure shapes population responses to environmental variability.
]]></description>
<dc:creator><![CDATA[ Lin, H.-w., Hernandez, C., Jaggi, H., ZUO, W., Tuljapurkar, S. D., Salguero-Gomez, R. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.28.747639</dc:identifier>
<dc:title><![CDATA[Life history traits predict the contribution of transient dynamics to variation in population growth]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.28.747721v1?rss=1">
<title>
<![CDATA[
Efficient capture-recapture inference for spatially varying natal dispersal,survival and recruitment 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.28.747721v1?rss=1
</link>
<description><![CDATA[
1. Natal dispersal is a key process in population ecology because it links local demographic processes to broader-scale population dynamics by redistributing individuals. When using capture-recapture data, multistate capture-recapture models using discrete spatial units as states are the gold standard for estimating natal dispersal among spatial units while accounting for spatial variation in survival, recruitment and imperfect detection. However, because their computational cost increases rapidly with the number of spatial units, applications have been limited to a small number of units. Therefore, in practice, these models cannot provide spatially detailed inference on natal dispersal across large landscapes. 2. We develop a computationally efficient Bayesian capture-recapture model, called the efficient natal dispersal (END) model, to estimate natal dispersal among discrete spatial units jointly with spatial variation in demographic parameters and detection probabilities. The END model relies on two key structural features: juveniles and breeders are separated into two arrays, and resightings outside the natal spatial unit are aggregated over time for individuals released as juveniles. 3. Using simulations, we show that the END model is considerably (up to 30 times) more computationally efficient than a conventional multistate model, while maintaining comparable parameter accuracy. We then apply the END model to white stork (Ciconia ciconia) capture-recapture data from Germany across 101 hexagonal spatial units, a spatial resolution at which a conventional multistate model is computationally infeasible. We estimate natal dispersal among units jointly with spatial variation in survival and recruitment. This allows us to identify areas of lower or higher survival, earlier or delayed recruitment, and dispersal probabilities among all units. By combining estimated dispersal probabilities with existing data on the number of juveniles born in each spatial unit, we estimate natal dispersal in terms of numbers of individuals and identify units with positive or negative net migration, sources and sinks. 4. Overall, our approach moves capture-recapture analyses from estimating natal dispersal among a few spatial units to inferring dispersal networks and assessing their demographic consequences across large domains. Our approach is applicable to many spatially structured capture-recapture datasets, opening new opportunities for studying spatial population dynamics.
]]></description>
<dc:creator><![CDATA[ Muller, M. H., Ketwaroo, F. R., Fiedler, W., Geiter, O., Herrmann, C., Schaub, M. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.28.747721</dc:identifier>
<dc:title><![CDATA[Efficient capture-recapture inference for spatially varying natal dispersal,survival and recruitment]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747286v1?rss=1">
<title>
<![CDATA[
Evaluating threshold management for willow grouse harvest: tracking open and closed areas during 12 years. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747286v1?rss=1
</link>
<description><![CDATA[
Managers must make decisions in the face of uncertainty, especially when available resources are limiting. Identifying thresholds when certain conditions are met or exceeded enable the potential to mitigate risks. In 2005, sustainable harvest levels of willow ptarmigan were identified to avoid harvest efforts exceeding three hunter days km2. Here we evaluate these recommendations by analyzing line transect counts and harvest data from six areas forming three open/closed pairs in a region of state managed willow ptarmigan harvest. We developed three sets of Bayesian hierarchical models, one static distance model, and two dynamics models. One mechanistic hazard model and a Gompertz phenomenological model. Adult and juvenile density showed pronounced year-to-year variation that was largely synchronous across all six sites regardless of hunting status. The harvest effort parameter shows a striking difference between the two models. In the Hazard model, is positive, and excludes zero with near certainty, but in the Gompertz model, the parameter is highly uncertain. However, the two models do not contradict each other but answer complementary questions with different sensitivity to the harvest signal, harvest mortality is additive at the individual level, but this additive mortality is masked at the level of population abundance. The demographic cost of harvest is therefore real and quantifiable through the survival chain, but bounded in the long run by the stabilizing dynamics. A fixed limit anchored to monitored effort and bag is not a crude substitute for adaptive management but the appropriate design under the information commonly at hand. It will be a precautionary instrument grounded in the one relationship this study establishes firmly, the translation of hunter effort into harvest mortality.
]]></description>
<dc:creator><![CDATA[ Willebrand, T., Hornell Willebrand, M., Brittas, R., Kleiven, E. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747286</dc:identifier>
<dc:title><![CDATA[Evaluating threshold management for willow grouse harvest: tracking open and closed areas during 12 years.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747059v1?rss=1">
<title>
<![CDATA[
Three-dimensional Imaging of Colonial Cyanobacteria with Optical Coherence Tomography 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747059v1?rss=1
</link>
<description><![CDATA[
The morphology of cyanobacterial colonies plays a key role in harmful cyanobacterial blooms, with implications for their vertical migration, resistance against grazing, and light availability. In this study, we introduce the use of Optical Coherence Tomography (OCT) to investigate the three-dimensional morphology of cyanobacterial colonies. The technique enables non-invasive 3D imaging of colonies up to several millimeters in size, providing access to detailed mesoscale morphological features. Gas vesicles inside cells were shown to strongly improve image quality. We describe the sample preparation and image acquisition protocol, as well as an image processing pipeline that extracts mesoscale morphological features and provides a volumetric visualization of colonies. The method was tested for representative colonies of different cyanobacterial species while a dataset of volumetric images and measured mesoscale features was acquired for natural colonies of Microcystis. We demonstrate the utility of 3D imaging by quantifying the effects of irregular colony morphologies on their flotation velocity and the light availability within colonies. We anticipate OCT to become a key imaging technique to monitor populations of cyanobacterial colonies and investigate colony formation, with potential extensions to other colonial and aggregated organisms in freshwater and marine environments.
]]></description>
<dc:creator><![CDATA[ Sinzato, Y. Z., Uittenbogaard, R., Visser, P. M., Huisman, J., Jalaal, M. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747059</dc:identifier>
<dc:title><![CDATA[Three-dimensional Imaging of Colonial Cyanobacteria with Optical Coherence Tomography]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747512v1?rss=1">
<title>
<![CDATA[
Female song and breeding phenology of the Nilgiri Flycatcher (Eumyias albicaudatus) in the Shola Sky Islands 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747512v1?rss=1
</link>
<description><![CDATA[
Assessing breeding phenology using singing intensity can potentially provide insights into a species' responses to climate or habitat change. Although male passerines are known to sing elaborate songs during the breeding season, females of several tropical passerines also sing. The Nilgiri Flycatcher (Eumyias albicaudatus) is an endemic dimorphic songbird found in the southern Western Ghats of India. Despite its limited distribution and its ecological significance as an indicator species of cloud forests, very little is known about its vocal behaviour and breeding ecology. To examine sex-specific differences in vocalisation patterns, we analysed 294 male and 102 female focal songs from two pairs of birds. We then used data from a year-long automated recorder placed near a breeding pair to study the species' singing phenology using the BirdNET Analyser. The two sexes broadly produced similar songs, although males' songs included more notes at a faster pace. The sex-specific detectors failed due to this high similarity among songs of the two sexes, but we were able to automate species-level detection (F1-score = 0.795 at a confidence threshold of 0.1). We found strong seasonality in vocal activity, with peaks in singing during the breeding season, and identified a diurnal peak at dawn. More data are required to parameterise differences in annual vocal activity between the sexes. These detection patterns provide a framework for a landscape-wide examination of Nilgiri Flycatcher phenology and occurrence. This study suggests that automatic detectors can be a reliable tool for assessing singing phenology in birds and provide insights into breeding periods.
]]></description>
<dc:creator><![CDATA[ Vyas, H., Arvind, C., Mangalasami, S., Vijayan, R. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747512</dc:identifier>
<dc:title><![CDATA[Female song and breeding phenology of the Nilgiri Flycatcher (Eumyias albicaudatus) in the Shola Sky Islands]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747521v1?rss=1">
<title>
<![CDATA[
Microplastic exposure alters immune-related gene expression in Culex quinquefasciatus mosquitoes and larval microbiota diversity 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747521v1?rss=1
</link>
<description><![CDATA[
Background: Microplastics have been detected in many freshwater ecosystems, including stagnant waters where mosquito larvae develop. Larvae are therefore exposed to microplastic pollution, which may affect their life history traits or microbiota along with immune gene expression. However, these effects have never been tested in mosquitoes, despite their major public health importance as vectors of numerous pathogens. Method: We exposed mosquito larvae, from hatching to adult emergence, to four concentrations of polyethylene microplastics (MPs): 0, 60, 200, and 600 MPs/mL. Fourth-instar larvae and newly emerged adult females were collected for each treatment. To investigate the effects of MPs on gene expression and bacterial microbiota, RNA sequencing and 16S metabarcoding approaches were performed on three biological replicates for each developmental stage. Results: Microplastic exposure induced a non-monotonic dose-dependent transcriptomic response. In larvae, only a limited number of genes were differentially expressed (five to eight per concentration), with immune-related genes downregulated at both low and high concentrations. In adult females, the intermediate concentration (200 MPs/mL) elicited the strongest response with 14 differentially expressed genes (DEGs). Regarding the microbiota, microplastic exposure reduced bacterial diversity in larvae, with the lowest diversity observed at the highest concentration. However, no significant changes were detected in the microbiota of adult females. Conclusion: Overall, this study shows that adult females are affected by larval exposure to MPs (i.e. differential expression in immune-related genes) and warrants further studies in this field. This includes: 1) investigating further the effects of MPs on mosquitoes' populations (e.g. through multi-generational studies), 2) gaining more environmentally relevant knowledge on MP effects (i.e. using MPs with a biofilm and/or adsorbed pollutants) and 3) focusing on the effects of MPs on mosquitoes' vectorial capacities.
]]></description>
<dc:creator><![CDATA[ Tchatakoura, A., Buysse, M., Setier Rio, M.-L., Roux, O., Loiseau, C., Aviles, A. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747521</dc:identifier>
<dc:title><![CDATA[Microplastic exposure alters immune-related gene expression in Culex quinquefasciatus mosquitoes and larval microbiota diversity]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.27.747453v1?rss=1">
<title>
<![CDATA[
Functional Robustness of Food Webs: A Dynamic Biomass Framework with Vital Species Sets and Cluster Influence 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.27.747453v1?rss=1
</link>
<description><![CDATA[
1. Species loss can erode food-web functioning not only through secondary extinctions, but also through biomass redistribution, weakened energy pathways, and threshold-like functional collapse. Common topology-, connectivity-, and extinction-based robustness metrics provide valuable summaries of structural disassembly and cascade risk, but they are not designed to quantify continuous biomass retention, collapse-associated species sets, and non-additive group-level effects within a single dynamic framework. 2. We develop a dynamic biomass-based framework for assessing food-web robustness under progressive species removal. The framework introduces Dynamic Area-based Robustness (DAR), which quantifies the weighted area between slow- and fast-collapse reference trajectories of total ecosystem biomass retention. Building on these trajectories, we operationally define the Minimal Vital Species Set (MVSS) as the smallest fast-collapse-prefix species set whose removal first drives biomass below a predefined functional-collapse threshold. We further propose Cluster Influence (CI), which compares the biomass effect of simultaneous group removal with the mean effect of removing the same species individually. 3. We evaluated the framework using 120 niche-model virtual food webs spanning controlled gradients of species richness and connectance, and further demonstrated its applicability on 16 empirical stream food webs. We compared DAR with AUC- and secondary-extinction-based robustness metrics and assessed the sensitivity of DAR, MVSS, and CI to key bioenergetic parameters and parameter uncertainty. 4. DAR captured biomass-based robustness patterns that were only partly aligned with structural and extinction-based metrics, indicating that dynamic functional degradation provides complementary information. In virtual food webs, MVSS subsets were strongly enriched in basal species or basal resource nodes, and smaller MVSS proportions were associated with stronger positive CI under fast-collapse trajectories. Together, DAR, MVSS, and CI provide a reproducible framework for linking food-web structure, biomass dynamics, collapse thresholds, and non-additive species-set effects, offering a practical tool for dynamic robustness assessment in theoretical and empirical food webs.
]]></description>
<dc:creator><![CDATA[ Qu, X., Guo, C., Fan, T., Lv, L. ]]></dc:creator>
<dc:date>2026-08-28</dc:date>
<dc:identifier>doi:10.64898/2026.08.27.747453</dc:identifier>
<dc:title><![CDATA[Functional Robustness of Food Webs: A Dynamic Biomass Framework with Vital Species Sets and Cluster Influence]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747389v1?rss=1">
<title>
<![CDATA[
Can an original be found? Mitochondrial species identity does not predict nuclear genome similarity in the photosymbiotic jellyfish Cassiopea andromeda and C. xamachana 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747389v1?rss=1
</link>
<description><![CDATA[
The Upside-Down Jellyfish, Cassiopea, has become a mainstay of cnidarian photosymbiosis research. Two nominal sister species, C. xamachana and the globally introduced C. andromeda, supply most of the medusae used in American and European laboratory research within this genus. As founder identity can shape experimental outcomes, here we utilize whole genome resequencing of 21 Cassiopea medusae spanning the Florida Keys, Bocas del Toro (Panama), and a European laboratory line, to ask whether mitochondrial species assignment predicts nuclear genome identity. Across multiple population structure analyses using the nuclear genome, Floridian Cassiopea carrying C. xamachana or C. andromeda mitotypes are indistinguishable, and geography is the dominant axis of nuclear genetic structure. A population tree that groups the two Floridian mitotypes as a single interbreeding unit is strongly supported (Patterson's D {approx} 0.0, Z = 0.02), whereas a tree that respects mitochondrial species boundaries is rejected (D = 0.42, Z = 20.8). Strikingly, the European "true" C. andromeda line clusters with Panamanian C. xamachana rather than with Floridian C. andromeda-mitotype animals. From the same sequencing effort, we recover evidence of symbiont community variability (Cladocopium) in Panama and assemble two near-complete Tenacibaculum and Endozoicomonas metagenomically-assembled genomes from Floridian host tissue. Together these results indicate that the C. andromeda/C. xamachana hybridization zone may extend across ocean basins, and that a "pure" original of either species may be difficult to find. We urge Cassiopea researchers to establish new European laboratory lines with described genomes.
]]></description>
<dc:creator><![CDATA[ Muffett, K. M., Sporre, M., Mammone, M., Miglietta, M. P. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747389</dc:identifier>
<dc:title><![CDATA[Can an original be found? Mitochondrial species identity does not predict nuclear genome similarity in the photosymbiotic jellyfish Cassiopea andromeda and C. xamachana]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747376v1?rss=1">
<title>
<![CDATA[
Bird functional dispersion predicts dengue vector presence across tropical working landscapes in Costa Rica 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747376v1?rss=1
</link>
<description><![CDATA[
Identifying reliable indicators of dengue vector habitat is critical for proactive surveillance and spatially targeted vector control. Bird communities are sensitive to habitat quality and landscape condition, and their functional diversity may track ecological conditions that support Aedes mosquito populations. We tested whether bird functional diversity predicts dengue vector presence across two working landscapes in Costa Rica, comparing bird-based predictors against landscape composition, vegetation structure, and plant diversity. Bird functional dispersion (FDis), the spread of species in multidimensional trait space, was the top-ranked predictor for Ae. aegypti and Ae. albopictus larval presence and for adult Ae. aegypti, outperforming all other predictor classes. Probability of presence declined with increasing FDis, where functionally homogeneous bird communities, characteristic of disturbed landscapes, co-occur with higher vector presence, consistent with shared habitat filtering. Functional diversity estimations may offer a practical signal for identifying habitats at elevated dengue vector risk.
]]></description>
<dc:creator><![CDATA[ Levey, D. R., Glidden, C. K., Shragai, T., Chamberlin, A. J., Fay, R. L., Chaves-Gonzalez, L. E., Figueroa-Sandi, J., Lazaro, J. E., Vasquez, V. N., Moreira-Soto, R. D., Osawa-Pivovarov, K., Daily, G. C., Rojas-Araya, D., Troyo, A., Mordecai, E. A. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747376</dc:identifier>
<dc:title><![CDATA[Bird functional dispersion predicts dengue vector presence across tropical working landscapes in Costa Rica]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.746844v1?rss=1">
<title>
<![CDATA[
Climate Impacts on Sockeye Salmon Productivity Vary Across Life Stages and Regions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.746844v1?rss=1
</link>
<description><![CDATA[
Many Sockeye salmon (Oncorhynchus nerka) populations have declined over recent decades, and climate change is likely to exacerbate these declines through direct and indirect ecological effects. The response to the associated environmental changes is likely to vary among life stages, populations, and regions. Quantitative estimates of climate change driven impacts that account for this variability could fill a critical gap and provide forward-looking insights into how sockeye are expected to respond to future climate-driven change across their lifecycle. To address this need we developed a hierarchical population dynamics model parameterized with juvenile, adult return and spawner abundance data from 13 sockeye salmon populations from Washington State to northern British Columbia. We used a formal causal inference framework that paired salmon abundance data with a suite of environmental covariates hypothesized to represent ecological conditions across the lifecycle. We used the model to estimate population-specific responses to each environmental driver, then combined parameter estimates with projections from down-scaled climate change models to estimate productivity responses to anticipated environmental change. We found that historical sockeye productivity was strongly associated with environmental covariates, which explained more interannual variability in return abundance than spawner abundance in most populations. However, the life stages and specific environmental covariates with the largest impacts differed among populations and regions, often displaying a latitudinal gradient. Increases in coastal ocean temperatures and mixed layer depth generally had negative effects though they varied among regions. Increased freshwater summer rearing and return migration temperatures had weaker but consistently negative effects. Under future climate conditions, projected changes in these environmental covariates are expected to result in substantial declines in productivity across most populations. Sockeye salmon display varying degrees of sensitivity to climate change across life stages, populations, and regions. Effective future management will require explicitly accounting for these life stage and population-specific responses.
]]></description>
<dc:creator><![CDATA[ Finke, J. F., Tai, T. C., Freshwater, C., Connors, B., Holdsworth, A. M., Oldford, G. L., Selbie, D., Stiff, H. W., Thompson, P. L. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.746844</dc:identifier>
<dc:title><![CDATA[Climate Impacts on Sockeye Salmon Productivity Vary Across Life Stages and Regions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.739408v1?rss=1">
<title>
<![CDATA[
Guardians of our Rivers: transforming river health assessment through macroinvertebrate monitoring with citizen scientists 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.739408v1?rss=1
</link>
<description><![CDATA[
Freshwater ecosystems in Scotland are increasingly threatened by multiple interacting stressors, including pollution, hydrological alteration, land use change, and climate-driven pressures. Scotland's rivers are amongst the most physically diverse and dynamic in the UK, contributing significantly to the country-s economy and natural heritage. Monitoring 125,000 km of waterways presents an issue, with limited funding and capacity of environmental agencies creating an environmental monitoring deficit at a time when robust data are essential for delivering national and global biodiversity targets. Citizen science offers a scalable, community driven approach to strengthening environmental evidence. This study evaluates the development, implementation, and outcomes of Guardians of our Rivers (GooR), a nationwide citizen science programme using macroinvertebrate-based river health assessments based on the Anglers' Riverfly Monitoring Initiative (RMI) established by the Riverfly Partnership. Between 2022 and 2025, GooR trained more than 850 volunteers, established 123 monitoring sites across Scotland, and generated over 860 surveys-surpassing the previous 16 years of aquatic invertebrate monitoring efforts. Standardised field training, full equipment provision, and structured support enabled high-quality data collection across diverse catchments. The establishment of nationally applied trigger and target thresholds created a consistent mechanism for detecting ecological deterioration and ensured that verified trigger breaches (n = 39 in 2025) resulted in formal investigation or follow-up. Analysis of national abundance patterns revealed ecological and biogeographic trends across the eight RMI taxa, confirming data sensitivity to habitat differences, water quality, and regional pressures. A detailed case study of the Lothian Esk catchment demonstrated the programme's capacity to detect seasonal macroinvertebrate dynamics and site level ecological trajectories over time. Overall, GooR illustrates how well-designed and well-supported citizen science can deliver high resolution spatiotemporal datasets, enhance early warning systems, empower communities, and make a meaningful contribution to promoting river health. Importantly, GooR forged a working partnership with Scottish Environmental Protection Agency (SEPA) that allowed communities to not only gather data but also transformed the way citizen science is recognized as contributing to freshwater conservation. Continued investment and long-term support will be essential to sustain these gains and realise the full potential of citizen-driven freshwater stewardship.
]]></description>
<dc:creator><![CDATA[ Lewis, R., Dodd, K., Macadam, C., Matthews, I., Pulver, S. R. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.739408</dc:identifier>
<dc:title><![CDATA[Guardians of our Rivers: transforming river health assessment through macroinvertebrate monitoring with citizen scientists]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.746266v1?rss=1">
<title>
<![CDATA[
Longer projected droughts will impair the recovery of tropical seedlings and their leaf microbiota 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.746266v1?rss=1
</link>
<description><![CDATA[
The increasingly severe droughts in the Amazon Basin make it urgent to understand the resilience of tropical tree species and their microbiota. Plant-associated fungi and bacteria (i.e. extended phenotype) modulate drought stress for their hosts, but their role in recovery dynamics remains poorly understood. To test the impact of different drought durations on the recovery of both physiology and microbiota of tropical trees, we followed the responses of nearly 1,000 seedlings belonging to seven tropical tree species of seasonally flooded (SF) forests in a greenhouse experiment. Seedlings were subjected to different droughts, reflecting a current, a projected and an extreme drought scenario of the French Guiana climate. Plant responses were monitored after the drought and after rewetting. Plant performance was estimated through leaf gas exchange, photochemical functioning, leaf water potentials and water-related traits as well as morphological traits. Bacterial and fungal leaf communities were characterized with respectively 16S and ITS2 markers using high-throughput sequencing. Increasing the duration of the drought reduced the ability of plants to recover physiological functions, with differences among species which were only partially predicted by their drought tolerance strategies. Bacterial diversity increased in most plant host species after mild drought but not under the most severe stress. Bacterial dispersion and turnover responses were strongly host species-specific, without a general directional pattern across species. Fungal communities showed greater compositional stability, but exhibited consistently higher turnover compared to bacterial communities during both drought and recovery, with no convergence toward control composition. Finally, none of the recovery networks mirrored the architecture of the control network, regardless of prior drought duration, demonstrating that the integrated extended phenotype does not recover even when individual traits show signs of recovery. Our results reveal that both physiological recovery and microbial community recovery are strongly shaped by the plant host species identity and drought duration This study widens knowledge of SF tropical forests, vulnerable habitats in the context of climate change, through the lens of the associated microbial communities and functional traits. Beyond the effects of an increasingly uncertain climate combined with a rise in the frequency of extreme events, our study places emphasis on including tree species extended phenotypes in considering their recovery dynamics.
]]></description>
<dc:creator><![CDATA[ BOISSEAUX, M., Goret, J.-Y., Burban, B., Troispoux, V., Bordes, A., Cazal, J., Cazal, S.-O., Coste, S., Stahl, C., Schimann, H. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.746266</dc:identifier>
<dc:title><![CDATA[Longer projected droughts will impair the recovery of tropical seedlings and their leaf microbiota]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747079v1?rss=1">
<title>
<![CDATA[
Refining mechanistic models to better predict larval and nymphal activity patterns of Ixodes scapularis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747079v1?rss=1
</link>
<description><![CDATA[
The black-legged tick (Ixodes scapularis), a key vector of Lyme disease, anaplasmosis, and babesiosis, exhibits regionally distinct patterns of seasonal activity driven by climate. Consequently, the relative timing of larval and nymphal activity varies across geographic locations, influencing pathogen transmission dynamics. Early-emerging nymphs may increase pathogen transmission, whereas early-emerging larvae may reduce transmission. In addition, synchrony between the two life-stages facilitates co-feeding transmission, which contributes to pathogen maintenance and coinfection risk. Temperature is thought to be an important driver of tick phenology, but existing mechanistic models that incorporate temperature fail to accurately capture the timing of larval and nymphal tick activity. To address this limitation, we developed a mechanistic model that includes two additional factors: humidity-dependent questing and low rates of overwinter development. To assess the value of these factors for explaining real-world patterns, we fitted alternative models to tick collection data from the National Ecological Observatory Network. In doing so, we found that explicitly incorporating humidity is necessary to reproduce observed tick phenology, with larval ticks being especially sensitive to relative humidity compared to other life stages. In addition, we found that accounting for humidity had a larger effect at Mid-Atlantic sites than at Northeastern sites, underscoring the importance of region-specific interactions between temperature and humidity in shaping I. scapularis phenology. By more accurately capturing tick seasonality compared to existing mechanistic models, our model illustrates the importance of accounting for factors beyond temperature for investigating how climate variability influences seasonal tick activity and pathogen transmission.
]]></description>
<dc:creator><![CDATA[ Mowry, S., Perkins, A. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747079</dc:identifier>
<dc:title><![CDATA[Refining mechanistic models to better predict larval and nymphal activity patterns of Ixodes scapularis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747326v1?rss=1">
<title>
<![CDATA[
Hierarchical Value of Information in Microbial Predator-Prey Interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747326v1?rss=1
</link>
<description><![CDATA[
Information is fundamental to biological survival, but the amount of information and its biological value are not equivalent. Shannon information quantifies uncertainty reduction, whereas Volkenstein's value of information measures how information changes the probability of a biologically relevant outcome. Although originally developed for molecular biology contexts, the latter concept has rarely been applied to environmental sensing and ecological interactions. Here we develop a value-of-information framework for microbial predator-prey interactions based on hydrodynamic sensing, in which prey detect fluid disturbances generated by approaching predators. Using a mechanistic model that incorporates sensory thresholds, memory, false alarms, biological benefits and costs, and predator encounter probability, we characterize mutual information from three hierarchical measures of biological value: encounter-conditional value, ecological value, and lifetime fitness value. The framework reveals how small amounts of sensory information can produce disproportionately large survival benefits during predator encounters, generating encounter-level value amplification in which biological value exceeds Shannon information. However, although global sensitivity analysis shows that such amplification is common, it is not universal and becomes progressively diluted at broader ecological and lifetime scales by encounter rarity, background noise, and sensory costs. Across most parameter combinations, the encounter-conditional value exceeded the ecological value, which in turn exceeded the lifetime fitness value. These results demonstrate that environmental sensing should be evaluated not only by how accurately it represents the external world, but by how strongly it changes biologically relevant outcomes. More broadly, the framework extends Volkenstein's concept of information value to ecological interactions and provides a quantitative framework for predicting when environmental information enhances survival and fitness, thereby providing a platform for explaining the evolution, maintenance, diversification, and loss of sensory systems.
]]></description>
<dc:creator><![CDATA[ Fahimi, P., Lynch, M. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747326</dc:identifier>
<dc:title><![CDATA[Hierarchical Value of Information in Microbial Predator-Prey Interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.25.728853v1?rss=1">
<title>
<![CDATA[
SatCHM (Satellite Canopy Height Model): Leveraging deep learning for site-specific sub-meter canopy height predictions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.25.728853v1?rss=1
</link>
<description><![CDATA[
High-resolution monitoring of forest structure and productivity is essential for effective natural resource management. However, monitoring approaches such as field-based forest inventories or extensive lidar campaigns are costly, time-intensive, and spatially limited. Therefore, inexpensive and accessible methods are needed. SatCHM (Satellite Canopy Height Model) was developed to be an accessible and open-source tool for researchers, allowing for site-specific and temporally flexible predictions of canopy height with limited computational resources. SatCHM requires four inputs: panchromatic satellite imagery, solar and sensor angle metadata of satellite imagery, digital elevation models (DEMs), and lidar-produced CHMs for an area of interest. After SatCHM pre-processes inputs, data is loaded into a collection of convolutional neural networks (CNNs) for image-to-image regression. This ensemble cooperates to yield high-resolution predictions (up to 0.5-meter) of three-dimensional tree structure with discernible tree crowns across a broader defined area of interest. After calculating the mean absolute error for each prediction output, the median of these mean absolute errors was 6.06 meters.
]]></description>
<dc:creator><![CDATA[ Mitchell, M., Abolt, C., Crennen, Z., Marcato, A., Atchley, A. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.25.728853</dc:identifier>
<dc:title><![CDATA[SatCHM (Satellite Canopy Height Model): Leveraging deep learning for site-specific sub-meter canopy height predictions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.25.746390v1?rss=1">
<title>
<![CDATA[
The devil in citizen science data: observation processes invalidate the causal inference that photovoltaic policy reduces bird diversity 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.25.746390v1?rss=1
</link>
<description><![CDATA[
Citizen science data are increasingly used to infer biodiversity change, but causal claims based on such data are credible only if sampling effort and its temporal shifts are explicitly modeled. Zhang et al. (1) used citizen science data to conclude that greater photovoltaic policy stringency, measured using the photovoltaic policy stringency index (PSI), reduced county-level bird diversity in China. We reproduced their fixed effects and instrumental variable estimates. However, the observed Shannon diversity derived from pooled citizen science records reflects both bird communities and sampling effort, which the authors' controls do not adequately capture. Accounting for observer count changed the reported statistically significant 2.10% decline in Shannon index to a nonsignificant 0.58% increase (P = 0.288) per one-standard-deviation increase in PSI, and rendered the instrumental variable estimate statistically indistinguishable from zero (P = 0.912). Yet observer count is only one of many sources of sampling bias. PSI was also associated with multiple dimensions of sampling effort, consistent with sampling effort acting as a potential mediator in the PSI-diversity chain. The sampling domain also shifted markedly from 2014 to 2023: recorded county-months increased almost 24-fold, median observer count rose from one to three, and zero-duration records declined from 57.2% to 0.17%. Without adequate adjustment, these shifts confound estimates of temporal change in observed bird diversity. Beyond its inadequate treatment of sampling effort, the original study also misinterpreted its statistical results. Although the reported R{superscript 2} values are high, they are dominated by county and year-month fixed effects, with PSI contributing a partial R{superscript 2} of only 0.048% on observed Shannon index. The PSI-photovoltaic-area correlation is also weak (r = 0.0414) and vanishes after accounting for fixed effects (P = 0.977). Furthermore, the released bird observation data contain many erroneous outliers, raising significant concerns about insufficiently rigorous data preprocessing and quality control. These results show that the released data cannot properly distinguish ecological change from sampling effort change. Robust inference from citizen science data requires checklist-level effort metadata, explicit correction for spatiotemporal sampling shifts, and close collaboration among researchers with complementary methodological and ecological expertise.
]]></description>
<dc:creator><![CDATA[ Chen, Y., Zhang, W., Zou, H.-X., Shi, X., Liu, Y. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.25.746390</dc:identifier>
<dc:title><![CDATA[The devil in citizen science data: observation processes invalidate the causal inference that photovoltaic policy reduces bird diversity]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747239v1?rss=1">
<title>
<![CDATA[
The geography of nocturnality: emergence patterns of bats on a latitudinal gradient 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747239v1?rss=1
</link>
<description><![CDATA[
Animals often attempt to resolve the trade-off between foraging and predation by regulating their activity timings and patterns. Driven by individual energetic requirements and the local environment, onset of activity in a species varies across space and time. These differences are particularly enhanced on a latitudinal gradient, influenced by varying lengths of daylight, temperature and seasonality. For a nocturnal mammal like the bat, such patterns translate to shorter activity windows at higher latitudes, both on a nightly and a seasonal basis. This constructs the timing of activity onset as a crucial variable for a successful night of foraging. While roost exit timings and influence of local conditions on bat activity have been extensively studied across species inhabiting a variety of locations around the world, our understanding of bat emergence behaviour on a global scale remains limited. To investigate emergence patterns in bats across a latitudinal gradient, we conducted a meta-analysis spanning 91 species from across 13 Chiropteran families. We evaluated how timing and luminosity (i.e., sun altitude) at exit varied across latitudes and species. Results revealed that bats across the globe tended to emerge under conserved thresholds of brightness, a pattern that was facilitated by a temporal delay in roost exits at higher latitudes. By maintaining emergence within the confines of nautical twilight (sun altitude between 0{degrees} to -12{degrees}), bats across the phylogeny thus seemed to balance the dilemma of predation versus foraging. This pattern was mirrored across the two broad dietary types (frugivores and insectivores) as well as different social structures (maternal v. non-maternal colonies). Furthermore, our models indicated that while local conditions dictate final exit decisions, shared ancestry was potentially influencing the extent of plasticity seen in emergence patterns. Taken together, these results highlight how broad-scale latitudinal gradients of light can influence the foraging strategies in a globally distributed nocturnal mammal.
]]></description>
<dc:creator><![CDATA[ Santusht, S., Fjelldal, M. A., Chakravarty, R., Appel, G., Bobrowiec, P., Lilley, T. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747239</dc:identifier>
<dc:title><![CDATA[The geography of nocturnality: emergence patterns of bats on a latitudinal gradient]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747178v1?rss=1">
<title>
<![CDATA[
ELAplus: Fast and accurate analysis platform for energy landscape analysis facilitated by fine-tuning optimization algorithm. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747178v1?rss=1
</link>
<description><![CDATA[
1. Large-scale community-composition datasets, especially from microbiome studies, increasingly provide opportunities to identify major community compositional types (e.g., enterotypes in human microbiomes) and potential transitions depending on environmental factors. Energy landscape analysis based on maximum entropy models has emerged as a promising framework for characterizing such multi-stability in ecological communities. However, its application to diverse, high-dimensional compositional datasets remains limited by computational inefficiency, insufficient evaluation of predictability, and lack of systematic assessment of uncertainty. 2. Here, we present a computationally tractable inference framework for energy landscape analysis of multispecies communities, implemented in the R package ELAplus. We introduce a framework combining cross-validation-based selection of optimization settings, enabling accurate and computationally efficient model fitting across a wide range of simulated community datasets. In addition, we incorporate a bootstrap-based approach to quantify the reliability of inferred stable states, providing a systematic measure of uncertainty in landscape structures. 3. Simulation analyses demonstrate improved predictive performance and robustness compared to existing implementations. Applications to empirical datasets further illustrate how the framework can reveal stable states, basins of attraction, and potential tipping points under varying environmental conditions. The package also provides visualization tools, including disconnectivity graphs and energy surface plots, to facilitate intuitive interpretation of complex ecological landscapes. 4. Our framework enables robust and computationally efficient inference of ecological stability from compositional and environmental data, expanding the applicability of energy landscape approaches in diverse natural communities.
]]></description>
<dc:creator><![CDATA[ Takano, S., Fujita, H., Ayabe, F., Sato, Z., Masuya, H., Toju, H., Suzuki, K. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747178</dc:identifier>
<dc:title><![CDATA[ELAplus: Fast and accurate analysis platform for energy landscape analysis facilitated by fine-tuning optimization algorithm.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.745935v1?rss=1">
<title>
<![CDATA[
Extended pregnancy during matrotrophy in cockroaches increases progeny survival during dry periods 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.745935v1?rss=1
</link>
<description><![CDATA[
Animals reproduce across a spectrum from oviparity to viviparity. Internal gestation and live birth have inherent advantages despite their costs. However, comparative analyses of key drivers, such as resilience to dehydration, lack taxonomic breadth. In this study, we assessed whether live birth improves the ability to proliferate in environments with limited access to water. To do so, we used the viviparous cockroach, Diploptera punctata, as a model of viviparity to assess dehydration-induced damage during extended periods of water deprivation. During pregnancy, maternal survival did not decline during dry periods compared with non-pregnant individuals, suggesting that pregnancy has minimal impact on resistance to dehydration stress. When mothers are deprived of water for 2 weeks, they show an increase in osmolality after one week, while their embryos show no change in osmolality until after two weeks, at which point abortions occur. Periods of dehydration increased the duration of pregnancy, likely due to a slower production of in utero milk, but there was no change in the size of progeny. After birth, viviparous D. punctata newborns showed increased survival under dry conditions compared to two other ovoviviparous species, which are much smaller and dehydrate more quickly. The combined impact of increased dehydration resistance during pregnancy and during the first independent phase indicates a benefit of prolonged viviparity in Diploptera punctata. This study provides evidence that viviparity in animal systems could enable progeny survival during drought.
]]></description>
<dc:creator><![CDATA[ LeFevre, G., Hendershot, J., Shemas, S., Cavanaugh, J., Bernhardt, L., Korthauer, M., Frigard, R., Jennings, E. C., Jansen van Rensburg, A., English, S., Benoit, J. B. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.745935</dc:identifier>
<dc:title><![CDATA[Extended pregnancy during matrotrophy in cockroaches increases progeny survival during dry periods]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747315v1?rss=1">
<title>
<![CDATA[
Introducing entropy-based metrics for quantifying edge- and macro-shape complexity in leaves and beyond 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747315v1?rss=1
</link>
<description><![CDATA[
Leaf shape is a fundamental trait of plant ecological strategies, influencing biotic interactions and ecosystem functioning. However, established quantitative metrics fail to capture subtle variations and irregularities, require user-based reference points or are challenging to compare among taxa with broadly different leaf shapes. In addition, established metrics typically conflate (aggregate) leaf edge complexity and macro-shape complexity, despite their independent functional significance and genetic foundations. Here, we introduce an entropy-based framework to quantify two new complexity metrics: edge complexity and macro-shape complexity. Based on three case studies, we show that these metrics outperform aggregate metrics in predicting Quercus robur chemical traits, provide more intuitive interspecific classifications, and strongly align with human perception. In addition, edge and macro-shape complexity show high complementarity, while aggregate metrics are highly redundant and typically strongly related to leaf area. Emerging as the strongest predictor of leaf chemistry and key visual cue for complexity as perceived by humans, the effects of edge complexity highlight the under-appreciated functional significance of leaf margins. Our framework and the proposed entropy-based complexity metrics thus promise to help unlock the potential of growing digital image archives of leaves, including images from herbaria and fossils, and are technically readily applicable to shapes of algae, bacteria, pollen, and beyond. The accompanying package ShapeComplexity enables the broad application of entropy-based metrics, providing a powerful tool to explore how the shape of organisms and biological structures influences ecological strategies, biotic interactions, and ecosystem functioning while tracking spatial and temporal variation.
]]></description>
<dc:creator><![CDATA[ Trauden, T., Rakotomalala, A. A. N. A., Junker, R. R., Sauressig, L., Trauden, K., Munoz Andres, M., Dannoritzer, R., Farwig, N., Pinkert, S. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747315</dc:identifier>
<dc:title><![CDATA[Introducing entropy-based metrics for quantifying edge- and macro-shape complexity in leaves and beyond]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747227v1?rss=1">
<title>
<![CDATA[
Projected ecosystem responses to environmental changes associated with offshore wind farms and ocean warming 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747227v1?rss=1
</link>
<description><![CDATA[
Offshore wind farms are rapidly expanding to meet growing demands for renewable energy, with development expected to extend further offshore into deeper waters. This expansion requires a robust understanding of the long-term ecological consequences of offshore wind farms (OWFs) and how these may interact with ongoing climate change. We used the coupled hydrodynamic-ecosystem-biogeochemical water-column model (GOTM-ERSEM-BFM) to investigate ecosystem-wide responses to environmental changes associated with OWFs and climate warming. Specifically, we examined OWF-related scenarios of reduced benthic suspension-feeding activity, representing potential effects of contaminant emissions from OWFs, and reduced wind forcing, together with increased sea surface temperature. The scenarios were simulated individually and in combination to explore potential interactive effects. These scenarios were simulated at two contrasting locations in the North Sea, representing a well-mixed coastal site and a seasonally stratified offshore site. The coastal site exhibited comparatively modest ecosystem responses across the scenarios, whereas responses were generally stronger at the deeper offshore site. At the offshore site, changes in stratification altered vertical nutrient dynamics and contributed to pronounced differences in ecosystem responses between the surface and bottom layers. Our results demonstrate that ecosystem responses to OWF-related and climate-driven environmental changes are strongly dependent on local environmental conditions, suggesting that ecological consequences may differ substantially as wind farm development expands into deeper offshore environments.
]]></description>
<dc:creator><![CDATA[ Dye, B., Peck, M. A., van der Molen, J. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747227</dc:identifier>
<dc:title><![CDATA[Projected ecosystem responses to environmental changes associated with offshore wind farms and ocean warming]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747351v1?rss=1">
<title>
<![CDATA[
Heatwaves do not impact bacteria within pollen provisions, despite accelerating blue orchard bee (Osmia lignaria) larval development 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747351v1?rss=1
</link>
<description><![CDATA[
Many insect populations are experiencing thermal stress as a result of global change, making it imperative to investigate how their relationship with other organisms will be impacted by heat disturbances. Microbial symbionts, such as bacteria, have the potential to enhance or inhibit an insect's thermal tolerance. Solitary bee larvae host bacteria within their food stores ("pollen provisions"), which have been shown to benefit survival and development; however, it is unclear how heatwaves brought about by climate change will impact their relationships with these bacterial partners. In this study, we subjected blue orchard bee (Osmia lignaria) eggs and larvae to a 4-day heatwave (35 {degrees}C daytime:22 {degrees}C nighttime) or kept them at control temperatures (25 {degrees}C daytime:15 {degrees}C nighttime), then returned all bees to control temperatures for a 5-day recovery period. We assessed bacterial communities within pollen provisions and larval development stage pre-heatwave (Day 0), immediately post-heatwave (Day 4), and following the recovery period (Day 9). Bacterial community composition, diversity, and abundance were resilient to heat stress, but larval bees developed faster when subjected to a heatwave. This finding refutes the hypothesis that bacteria within pollen provisions modulate blue orchard bee responses to heat, suggesting instead that developmental effects could be more largely shaped by bee physiology or interactions with microorganisms other than bacteria.
]]></description>
<dc:creator><![CDATA[ Martin, A. N. N., Williams, N. M., Vannette, R. L. ]]></dc:creator>
<dc:date>2026-08-27</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747351</dc:identifier>
<dc:title><![CDATA[Heatwaves do not impact bacteria within pollen provisions, despite accelerating blue orchard bee (Osmia lignaria) larval development]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.22.746414v1?rss=1">
<title>
<![CDATA[
Predation of small nocturnal primates (Microcebus) on Madagascar; insights into predator preferences in Andohahela National Park 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.22.746414v1?rss=1
</link>
<description><![CDATA[
Predation is a major selective force shaping lemur behaviour and population dynamics, yet direct observations remain rare, particularly for small nocturnal species. Here, we document predation on mouse lemurs (Microcebus spp., Cheirogaleidae) in Andohahela National Park, south-eastern Madagascar, and using complementary evidence from radio-telemetry and owl pellet analyses. Two radio-collared individuals were confirmed as prey of endemic snakes, Ithycyphus oursi and Madagascarophis meridionalis (both Pseudoxyrhophiidae), representing the first documented records of Microcebus predation by these species. Examination of owl pellets and prey remains from three sites and from three owl species revealed a single predation event by Asio madagascariensis (Strigidae), likely involving M. tanosi, no evidence of mouse lemur predation by Tyto alba (Tytonidae) despite high local prey availability, and a single and first predation record from Athene superciliaris (Strigidae). Material from A. superciliaris roosts was otherwise dominated by invertebrates, indicating that primate predation is likely opportunistic. Together, these findings expand the known predator guild of mouse lemurs and suggest that snake predation is rarely detected, and its contribution to mouse lemur mortality and population dynamics is likely underestimated. Our findings demonstrate how combining behavioural field observations with dietary evidence can uncover otherwise undetected predation events and clarify predator prey relationships in nocturnal primates.
]]></description>
<dc:creator><![CDATA[ Hyde Roberts, S., Segami, J. C., Harinala, V. J. N., Rajemison, B., Rasoarinoro, E., Goodman, S. M., Yoder, A. D. ]]></dc:creator>
<dc:date>2026-08-26</dc:date>
<dc:identifier>doi:10.64898/2026.08.22.746414</dc:identifier>
<dc:title><![CDATA[Predation of small nocturnal primates (Microcebus) on Madagascar; insights into predator preferences in Andohahela National Park]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-26</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.08.26.747214v1?rss=1">
<title>
<![CDATA[
Vertical profile of airborne microbial communities in the Southern Ocean atmospheric boundary layer 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.08.26.747214v1?rss=1
</link>
<description><![CDATA[
Aerobiological studies have largely focused on near-surface sampling and horizontal biogeographic patterns, while vertical structuring of airborne microbial communities within the atmospheric boundary layer (ABL) remains poorly understood. Here, we investigated microbial communities across the lower and upper ABL in a low-orography coastal site on the Antarctic Peninsula, representative of the Southern Ocean marine ABL and with low direct human influence. Airborne microorganisms were sampled simultaneously using ground-based and aerial platforms on five occasions. Community composition, abundance, and cell morphometry were assessed using metabarcoding and epifluorescence microscopy and interpreted alongside atmospheric observations. Airborne bacterial and eukaryotic communities showed consistent vertical stratification, although partial taxonomic overlap indicates vertical connectivity between atmospheric layers. Lower ABL communities were more diverse than upper ABL counterpart, compositionally homogeneous, and dominated by marine-associated taxa, reflecting strong influence from local sources and turbulent mixing. In contrast, upper ABL communities were less diverse but more heterogeneous among sampling events, enriched in stress-tolerant, terrestrial and plant-associated taxa, consistent with atmospheric filtering, selective upward transport, and long-range atmospheric inputs. Upper-layer samples also exhibited higher microbial abundance and greater prevalence of elongated cell morphologies, suggesting particle accumulation aloft and aerodynamic selection permanence. Together, these findings identify the Southern Ocean ABL as a vertically structured microbial habitat organized into two partially decoupled sublayers, in which atmospheric dynamics regulate microbial dispersal, ecosystem connectivity, and biogeographic patterns.
]]></description>
<dc:creator><![CDATA[ Galban, S., Kim, W. Y., Sanz, P., Pletzer, T., Banon, M., Higuera, J. A., Mendez, J., Kang-Ho, A., Gonzalez-Herrero, S., Justel, A., Quesada, A. ]]></dc:creator>
<dc:date>2026-08-26</dc:date>
<dc:identifier>doi:10.64898/2026.08.26.747214</dc:identifier>
<dc:title><![CDATA[Vertical profile of airborne microbial communities in the Southern Ocean atmospheric boundary layer]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-08-26</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
