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bioRxiv2018

Variable Effects on Growth and Defence Traits for Plant Ecotypic Differentiation and Phenotypic Plasticity along Elevation Gradients

Along ecological gradients, ecotypes generally evolve as the result of local adaptation to a specific environment to maximize organisms fitness. Alongside ecotypic differentiation, phenotypic plasticity, as the ability of a single genotype to produce different phenotypes under different environmental conditions, can also evolve for favouring increased organisms performance in different environments. Currently, there is a lack in our understanding of how varying habitats may contribute to the differential contribution of ecotypic differentiation and plasticity in growth versus defence traits. Using reciprocal transplant-common gardens along steep elevation gradients, we evaluated patterns of ecotypic differentiation and phenotypic plasticity of two coexisting but unrelated plant species, Cardamine pratensis and Plantago major. For both species, we observed ecotypic differentiation accompanied by plasticity in growth related traits. Plants grew faster and produced more biomass when placed at low elevation. In contrast, we observed fixed ecotypic differentiation for defence and resistance traits. Generally, low elevation ecotypes produced higher chemical defences regardless of the growing elevation. Yet, some plasticity was observed for specific compounds, such as indole glucosinolates. We speculate that ecotypic differentiation in defence traits is maintained by costs of chemical defence production, while plasticity in growth traits is regulated by temperature driven growth response maximization.

ecology↗

bioRxiv2018

The biggest losers: Habitat isolation deconstructs complex food webs from top to bottom

Habitat fragmentation is threatening global biodiversity. To date, there is only limited understanding of how habitat fragmentation or any alteration to the spatial structure of a landscape in general, affects species diversity within complex ecological networks such as food webs. Here, we present a dynamic and spatially-explicit food web model which integrates complex food web dynamics at the local scale and species-specific dispersal dynamics at the landscape scale, allowing us to study the interplay of local and spatial processes in metacommunities. We explore how habitat fragmentation, defined as a decrease of habitat availability and an increase of habitat isolation, affects the species diversity patterns of complex food webs (-, {beta}-,{gamma} -diversity), and specifically test whether there is a trophic dependency in the effect of habitat fragmentation on species diversity. In our model, habitat isolation is the main driver causing species loss and diversity decline. Our results emphasise that large-bodied consumer species at high trophic positions go extinct faster than smaller species at lower trophic levels, despite being superior dispersers that connect fragmented landscapes better. We attribute the loss of top species to a combined effect of higher biomass loss during dispersal with increasing habitat isolation in general, and the associated energy limitation in highly fragmented landscapes, preventing higher trophic levels to persist. To maintain trophic-complex and species-rich communities calls for effective conservation planning which considers the interdependence of trophic and spatial dynamics as well as the spatial context of a landscape and its energy availability.

ecology↗

bioRxiv2018

The geometry of habitat fragmentation: effects of distribution patterns on short-term species persistence

Land-use changes cause habitat loss and fragmentation and are thus important drivers of anthropogenic biodiversity change. However, there is an ongoing debate about how fragmentation per se affects biodiversity in a given amount of habitat. We illustrate why it is important to distinguish two different aspects of fragmentation to resolve this debate: (i) geometric fragmentation effects, which exclusively arise from the spatial distributions of species and habitat fragments, and (ii) demographic fragmentation effects due to reduced fragment size, increased isolation, or edge effects. While most empirical studies are primarily interested in quantifying demographic fragmentation effects, geometric effects are typically invoked only as post-hoc explanations of biodiversity responses to fragmentation per se. Here, we present an approach to quantify geometric fragmentation effects on species persistence probability. We illustrate this approach using spatial simulations where we systematically varied the initial abundances and distribution patterns (i.e. random, aggregated, and regular) of species as well as habitat amount and fragmentation per se. As expected, we found no geometric fragmentation effects when species were randomly distributed. However, when species were aggregated, we found positive effects of fragmentation per se on persistence probability for a large range of scenarios. For regular species distributions, we found weakly negative geometric effects. These findings are independent of the ecological mechanisms which generate non-random species distributions. Our study helps to reconcile seemingly contradictory results of previous fragmentation studies. Since intraspecific aggregation is a ubiquitous pattern in nature, our findings imply widespread positive geometric fragmentation effects. This expectation is supported by many studies that find positive effects of fragmentation per se on species occurrences and diversity after controlling for habitat amount. We outline how to disentangle geometric and demographic effects of fragmentation, which is critical for predicting the response of biodiversity to landscape change.

ecology↗

bioRxiv2018

Response of Australian pied oystercatchers Haematopus longirostris to increasing abundance of the beach bivalve prey Donax deltoides

This study measured the response of Australian pied oystercatchers Haematopus longirostris on South Ballina Beach, New South Wales, Australia during a recovery in the stock of the primary prey species Donax deltoides, a large beach clam and commonly known as the pipi. It was predicted that oystercatcher counts would increase when pipi abundance increased (numerical response) and that oystercatcher feeding rates would also increase (functional response). Between Oct 2009 and Mar 2015, mean pipi density increased from c. zero to 30 pipis/m2. Mean oystercatcher feeding rates increased to an asymptote of c. 0.26 pipis/min. Breeding season mean counts of adult-plumage oystercatchers increased from 23 to 43, largely driven by non-territorial birds. Prey size selection was absent, both among different prey types and among pipis > 20 mm. This report provides some insights into the feeding ecology of oystercatchers on sandy ocean beaches that should be valuable in planning future studies.

ecology↗

bioRxiv2018

Local and landscape drivers of aquatic-to-terrestrial subsidies in riparian ecosystems: a worldwide meta-analysis

Cross-boundary fluxes of organisms and matter, termed \"subsidies\", are now recognized to be reciprocal and of roughly equal importance for both aquatic and terrestrial systems, even if terrestrial input to aquatic ecosystems has received most attention. The magnitude of aquatic to terrestrial subsidies is well documented, but the drivers behind these subsidies and their utilization by terrestrial consumers are characteristically local scale studies, limiting the inferences that can be drawn for broader geographic scales. We therefore built and analyzed a database of stable isotope data extracted from 21 studies worldwide, to identify both landscape and local scale variables that may affect the diet of terrestrial predators in riparian ecosystems. Our meta-analysis revealed a greater magnitude of aquatic-to-terrestrial subsidies (> 50%) than previously reported, albeit with large geographic and inter-annual variations. We demonstrated a large effect of landscape-scale factors on aquatic-to-terrestrial subsidies, particularly anthropogenic land use and tree cover. Local human population was the only relevant factor at the local scale. We also found that studies on landscape-scale and anthropogenic land use effects on aquatic-to-terrestrial subsidies are currently strongly under-represented in the ecological literature. Such studies are needed to improve our understanding of how land use and environmental change might influence future patterns of biodiversity and ecosystem function.

ecology↗

bioRxiv2018

Prediction of Algal Blooms in the Great Lakes through a Convolution Neural Network of Remote Sensing Data

Harmful algal blooms (HABs) are the proliferation of algae due to eutrophication and have severe repercussions to the ecological balance in many water bodies, due to the toxins the algae produce. Additionally, the identification and prediction of these HABs has been a challenge in the scientific community due to the interactions between both biological and physical processes that cause the HABs. Here, we used remote sensing data to bypass these issues; remote sensing data provides significant information about the coverage of chlorophyll which can be used to locate HABs. Using this indicator of HABs, we trained a Convolution Neural Network (CNN) to identify nine types of algal blooms, using 25 epochs of 900 images, which can predict algal bloom shapes with an 80 percent accuracy. This approach of HAB identification can easily be applied to other aquatic ecosystems where remote sensing data is present.

ecology↗

bioRxiv2018

Immigration from the metacommunity affects bdelloid rotifer community dynamics most

Dispersal is an important driver of local community dynamics. It has been proposed that, for communities composed of microscopic organisms, dispersal could well be the dominant process, outpacing local processes driven by environmental conditions and species interactions. This is because microscopic organisms often reproduce asexually, fostering rapid colonization, and are easily dispersed by water or air current. We studied the case of bdelloid rotifers belonging to the genus Adineta, microscopic asexual animals with dried stages that are easily dispersed by wind to investigate the relative effects of dispersal and local processes on their community dynamics. To this end, we constructed a classic competition model to theoretically examine how spatial and local biodiversity dynamics varied with fitness and dispersal characteristics of bdelloid Adineta species. Next, we compared our predictions with an experimental dataset containing spatio-temporal Adineta community dynamics from the wild. This comparison suggested that immigration from the local meta-community was the most critical parameter under the conditions tested. One Adineta vaga species, abundant in the surrounding area, rapidly colonized our experimental habitats and dominated most of the communities. We also ran the model under different levels of environmental conditions (permissive, intermediate and harsh) to simulate seasonal community variability and found that communities experience important bottlenecks yearly in winter but that the same community re-established. The dissimilarities observed between roof communities suggest differences in adaptation or immigration capacities. Besides their asexual reproduction and extreme desiccation tolerance, a key characteristic of bdelloid ecology identified here, is the spatio-temporal dynamic of abundant bdelloid clones present in the meta-community that rapidly colonize empty patches to establish new populations.

ecology↗

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

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

Resource supply dynamics control stability and chaos in complex ecosystems

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

ecology↗

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.

ecology↗

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.

ecology↗

bioRxiv2026

AWET -- Arthropod Weight Estimation Tool

Arthropods drive essential ecosystem processes such as pollination, decomposition, and nutrient cycling and are widely used as indicators of ecosystem condition and function. Among various arthropod-derived metrics, body weight is a key variable in functional ecology and frequently assessed as dry body weight. However, drying arthropod specimens limits the samples future potential for research, as it prevents further processing such as trait measurements or species identification. Here, we present AWET (Arthropod Weight Estimation Tool), an open-source application for automated estimation of individual fresh body weight and extraction of morphometric measurements from standardized images of pre-sorted arthropod samples. AWET combines automated image analysis with taxon-specific allometric regression models to estimate fresh body weight while simultaneously quantifying body length, width, area, and specimen abundance. The software operates with standard imaging equipment, requires no machine-learning-based classification or segmentation, and allows users to define taxonomic groupings according to their objectives. By preserving specimens for downstream analyses while processing large numbers of individuals within milliseconds, AWET provides an efficient, non-destructive, and cost-effective workflow for high-throughput arthropod phenotyping. The software is a practical and expandable tool for biodiversity monitoring projects investigating changes in arthropod biomass, abundance and individual morphometric measures.

ecology↗

bioRxiv2014

Population genomics of Saccharomyces cerevisiae human isolates: passengers, colonizers, invaders.

The quest for the ecological niches of Saccharomyces cerevisiae ranged from wineries to oaks and more recently to the gut of Crabro Wasps. Here we propose the role of the human gut in shaping S. cerevisiae evolution, presenting the genetic structure of a previously unknown population of yeasts, associated with Crohns disease, providing evidence for clonal expansion within humans gut. To understand the role of immune function in the human-yeast interaction we classified strains according to their immunomodulatory properties, discovering a set of genetically homogeneous isolates, capable of inducing anti-inflammatory signals via regulatory T cells proliferation, and on the contrary, a positive association between strain mosaicism and ability to elicit inflammatory, IL-17 driven, immune responses. The approach integrating genomics with immune phenotyping showed selection on genes involved in sporulation and cell wall remodeling as central for the evolution of S. cerevisiae Crohns strains from passengers to commensals to potential pathogens.

Evolutionary Biology↗

bioRxiv2014

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingmans coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life-history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so called multiple merger coalescent models are reviewed here ({Lambda}-coalescent, beta-coalescent, Bolthausen-Snitzman, {Xi}-coalescent). We explicit how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as 1) the skew in offspring production typical of marine species, 2) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, 3) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles, and 4) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.

Evolutionary Biology↗

bioRxiv2014

SINGLE NUCLEOTIDE POLYMORPHISMS SHED LIGHT ON CORRELATIONS BETWEEN ENVIRONMENTAL VARIABLES AND ADAPTIVE GENETIC DIVERGENCE AMONG POPULATIONS IN ONCORHYNCHUS KETA

Identifying the genetic and ecological basis of adaptation is of immense importance in evolutionary biology. In our study, we applied a panel of 58 biallelic single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus keta. Samples included 4164 individuals from 43 populations ranging from Coastal Western Alaska to southern British Colombia and northern Washington. Signatures of natural selection were detected by identifying seven outlier loci using two independent approaches: one based on outlier detection and another based on environmental correlations. Evidence of divergent selection at two candidate SNP loci, Oke_RFC2-168 and Oke_MARCKS-362, indicates significant environmental correlations, particularly with the number of frost-free days (NFFD). Important associations found between environmental variables and outlier loci indicate that those environmental variables could be the major driving forces of allele frequency divergence at the candidate loci. NFFD, in particular, may play an important adaptive role in shaping genetic variation in O. keta. Correlations between divergent selection and local environmental variables will help shed light on processes of natural selection and molecular adaptation to local environmental conditions.

Evolutionary Biology↗

bioRxiv2014

Differential gene expression and alternative splicing in insect immune specificity

Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris / trypanosome Crithidia bombi model system, we have carried out a transcriptome-wide analysis of gene expression and alternative splicing in bees during C. bombi infection. We have performed four analyses, 1) comparing gene expression in infected and non-infected bees 24 hours after infection by Crithidia bombi, 2) comparing expression at 24 and 48 hours after C.bombi infection, 3) searching for differential gene expression associated with the host-parasite genotype-genotype interaction at 24 hours after infection and 4) searching for alternative splicing associated with the host-parasite genotype-genotype interaction at 24 hours post infection. We found a large number of genes differentially regulated related to numerous canonical immune pathways. These genes include receptors, signaling pathways and effectors. We discovered a possible interaction between the peritrophic membrane and the insect immune system in defense against Crithidia. Most interestingly we found differential expression and alternative splicing of Dscam related transcripts and a novel immunoglobulin related gene Twitchin depends on the genotype-genotype interactions of the given bumblebee colony and Crithidia strain.

Evolutionary Biology↗

bioRxiv2014

A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection acting on all identified genes and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR \"gatekeeper\" loci sharing syntelogs across all analyzed genomes. In summary, we designed and implemented an easy-to-follow computational framework for super-gene family identification, and provide the most curated set of NB-LRR genes whose genetic versatility among twelve lineages can underpin crop improvement.

Genomics↗