Biology subjects

Armitage, D. W.

Publications and source records attributed to Armitage, D. W..

12 recordsLinked to original sources

bioRxiv2026

Connectivity and dispersal mode shape the landscape genetics of a carnivorous pitcher plant-arthropod metacommunity

Dispersal differences between hosts and their symbionts can generate mismatched population structure, potentially destabilizing beneficial interactions across space. We tested this possibility in the carnivorous pitcher plant Darlingtonia californica and its obligate arthropod associates, the midge Metriocnemus edwardsi and the mite Sarraceniopus darlingtoniae, sampled across sites spanning the hosts patchy range in Oregon and northern California, USA. Comparing nuclear and chloroplast genomic data from D. californica with mitochondrial COI data from both arthropods, we tested how range position, landscape connectivity, and dispersal mode influence population genetic structure across this mutualistic metacommunity. Host plant populations supported the central-marginal hypothesis: nuclear diversity declined toward the range margins, and marginal populations showed greater nuclear genetic differentiation. Chloroplast variation was more weakly structured, most clearly separating the northern Oregon Coast populations and revealing cytonuclear discordance consistent with historical seed-mediated movement or chloroplast capture near the boundary between neighboring regions. Landscape connectivity estimated from an ecological niche model was also associated with genetic exchange. Circuit-theoretic current flow was positively related to effective migration inferred independently from plant genotypes. Further, landscape resistance explained variation in plant and mite differentiation beyond geographic distance alone. Both arthropods showed significant spatial congruence with the host plant but not with one another, a pattern inconsistent with co-dispersal and suggesting that each associate tracks the shared landscape according to its own dispersal biology. These results show that regional genetic concordance among obligate ecological partners can coexist with substantial differences in the processes governing their movement and local connectivity.

ecology↗

bioRxiv2026

Species responses to nutrient loading promote resistance but not temporal stability in floating macrophyte communities

Determining the drivers of ecological stability amid accelerating global environmental change is a critical goal of contemporary ecology. Various candidate drivers have been suggested, with recent attention turning to response diversity--the variation among organism-environment responses. However, despite conceptual interest in response diversity as a driver of stability, there remain few field tests of this relationship. Using multi-species competitive communities of floating aquatic macrophytes as an experimental model for measuring temporal stability and response diversity to nutrient loading, we show that response diversity does not promote temporal stability of total macrophyte cover, but that communities with an uneven distribution of species responses were more resistant to an exogenous shock. To quantify macrophyte composition and growth dynamics from photographic time series of our experimental communities, we developed an open-source, scalable, machine learning workflow (LeafMosaic) capable of classifying four species from noisy field data including variable lighting, resolution, and plant morphology. We measured response diversity as the balance of positive and negative biomass growth responses to dissolved nitrate concentration, weighted by species relative contributions to biomass, and tested its effect on temporal stability and resistance to an unexpected pulse disturbance (a large typhoon that disrupted our outdoor mesocosms). Response imbalance predicted typhoon resistance, but species asynchrony and mean population stability best predicted community stability, with no direct or indirect effect of species responses. Overall, our results provide new experimental evidence for how the structure of species responses promotes stability, and we aim our LeafMosaic workflow to empower future field experiments using floating macrophytes to study response diversity and ecological stability.

ecology↗

bioRxiv2025

Mutualism in disguise? Isotopic evidence for nutrient transfer from a carnivorous pitcher plant to its insect prey

Carnivorous pitcher plants are regarded as exploiters of arthropod prey, attracting them with nectaries which are densely clustered near the slippery peristome, putting visiting arthropods at risk of becoming trapped. However, most pitcher visitors are not captured and may benefit from access to concentrated, nutrient-rich rewards. This raises the possibility that pitcher plants and their arthropod visitors engage in an indirect mutualism in which both insects and plants incur some cost but reap net nutritive benefits, yet evidence that potential prey species derive measurable nutritional benefits from pitcher plants is currently lacking. To address this knowledge gap, we measured levels of nitrogen isotopic enrichment of vespulid wasps residing in dense stands of the naturally 15N enriched pitcher plant Darlingtonia californica relative to those from adjacent forest patches. Wasps occupying pitcher fens had elevated{delta} 15N values, suggesting they consume 15N-enriched nitrogen originating from Darlingtonia -- either directly through nectar or indirectly via 15N-enriched arthropod proteins. These findings contribute support for the hypothesized nutritional mutualism between pitcher plants and local insect populations.

ecology↗

bioRxiv2025

Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome

Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae--but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives--especially in defensive, stress-tolerance, and secondary metabolite pathways--yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified (rather than relaxed) selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.

microbiology↗

bioRxiv2023

Widespread analytical pitfalls in empirical coexistence studies and a checklist for improving their statistical robustness

O_LIModern Coexistence Theory (MCT) offers a conceptually straightforward approach for connecting empirical observations with an elegant theoretical framework, gaining popularity rapidly over the past decade. However, beneath this surface-level simplicity lie various assumptions and subjective choices made during data analysis. These can lead researchers to draw qualitatively different conclusions from the same set of experiments. As the predictions of MCT studies are often treated as outcomes, and many readers and reviewers may not be familiar with the frameworks assumptions, there is a particular risk of "researcher degrees of freedom" inflating the confidence in results, thereby affecting reproducibility and predictive power. C_LIO_LITo tackle these concerns, we introduce a checklist consisting of statistical best-practices to promote more robust empirical applications of MCT. Our recommendations are organised into four categories: presentation and sharing of raw data, testing model assumptions and fits, managing uncertainty associated with model coefficients, and incorporating this uncertainty into coexistence predictions. C_LIO_LIWe surveyed empirical MCT studies published over the past 15 years and discovered a high degree of variation in the level of statistical rigour and adherence to best practices. We present case studies to illustrate the dependence of results on seemingly innocuous choices among competition model structure and error distributions, which in some cases reversed the predicted coexistence outcomes. These results demonstrate how different analytical approaches can profoundly alter the interpretation of experimental results, underscoring the importance of carefully considering and thoroughly justifying each step taken in the analysis pathway. C_LIO_LIOur checklist serves as a resource for authors and reviewers alike, providing guidance to strengthen the empirical foundation of empirical coexistence analyses. As the field of empirical MCT shifts from a descriptive, trailblazing phase to a stage of consolidation, we emphasise the need for caution when building upon the findings of earlier studies. To ensure that progress made in the field of ecological coexistence is based on robust and reliable evidence, it is crucial to subject our predictions, conclusions, and generalizability to a more rigorous assessment than is currently the trend. C_LI

ecology↗

bioRxiv2023

Habitat degradation homogenizes ecological responses to typhoons across a subtropical island

Climate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenise ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawas diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.

ecology↗

bioRxiv2022

To remain modern, the coexistence program requires modern statistical rigor

A recent study by Van Dyke et al.1 paired experimental drought manipulations with demographic models and trait measurements to project major shifts in coexistence among a number of annual plant taxa. However, re-analysis of the data under alternative, more predictive competition models reveals that the authors original conclusions are very sensitive to slight variations in model form. Furthermore, propagating model parameter error into coexistence predictions results in relatively weak support for the majority of coexistence shifts predicted by the authors original model. These results highlight the need for increased statistical rigor when treating binary predictions of species coexistence as observed experimental outcomes, as is commonly practiced in empirical coexistence studies.

ecology↗

bioRxiv2022

Global maps of lake surface water temperatures reveal pitfalls of air-for-water substitutions in ecological prediction

In modeling species distributions and population dynamics, spatially-interpolated climatic data are often used as proxies for real, on-the-ground measurements. For shallow freshwater systems, this practice may be problematic as interpolations used for surface waters are generated from terrestrial sensor networks measuring air temperatures. Using these may therefore bias statistical estimates of species environmental tolerances or population projections - particularly among pleustonic and epilimnetic organisms. Using a global database of millions of daily satellite-derived lake surface water temperatures (LSWT), I trained machine learning models to correct for the correspondence between air and LSWT as a function of atmospheric and topographic predictors, resulting in the creation of monthly high-resolution global maps of air-LSWT offsets, corresponding uncertainty measures, and derived LSWT-based bioclimatic layers for use by the scientific community. I then compared the performance of these LSWT layers and air temperature-based layers in population dynamic and ecological niche models (ENM). While generally high, the correspondence between air temperature and LSWT was quite variable and often nonlinear depending on the spatial context. These LSWT predictions were better able to capture the modeled population dynamics and geographic distributions of two common aquatic plant species. Further, ENM models trained with LSWT predictors more accurately captured lab-measured thermal response curves. I conclude that these predicted LSWT temperatures perform better than raw air temperatures when used for population projections and environmental niche modeling, and should be used by practitioners to derive more biologically-meaningful results. These global LSWT predictions and corresponding error estimates and bioclimatic layers have been made freely available to all researchers in a permanent archive.

ecology↗

bioRxiv2022

How to measure response diversity

O_LIThe insurance effect of biodiversity--that diversity stabilises aggregate ecosystem properties--is mechanistically underlain by inter- and intraspecific trait variation in organismal responses to the environment. This variation, termed response diversity, is therefore a potentially critical determinant of ecological stability. However, response diversity has yet to be widely quantified, possibly due to difficulties in its measurement. Even when it has been measured, approaches have varied. C_LIO_LIHere, we review methods for measuring response diversity and from them distil a methodological framework for quantifying response diversity from experimental and/or observational data, which can be practically applied in lab and field settings across a range of taxa. C_LIO_LIPrevious empirical studies on response diversity most commonly invoke response traits as proxies aimed at capturing species ecological responses to the environment. Our approach, which is based on environment-dependent ecological responses to any biotic or abiotic environmental variable, is conceptually simple and robust to any form of environmental response, including nonlinear responses. Given its derivation from empirical data on species ecological responses, this approach should more directly reflect response diversity than the trait-based approach dominant in the literature. C_LIO_LIBy capturing even subtle inter- or intraspecific variation in environmental responses, and environment-dependencies in response diversity, we hope this framework will motivate tests of the diversity-stability relationship from a new perspective, and provide an approach for mapping, monitoring, and conserving this critical dimension of biodiversity. C_LI

ecology↗

bioRxiv2020

Barriers to coexistence limit the poleward range of a globally-distributed plant

Species poleward ranges are thought to be primarily limited by climatic constraints rather than biotic interactions such as competition. However, theory suggests that a species tolerance to competition is reduced in harsh environments, such as at the extremes of its climatic niche. This implies that under certain conditions, interspecific competition near species range margins can prevent the establishment of populations into otherwise tolerable environments and results in geographic distributions being shaped by the interaction of climate and competition. We test this prediction by challenging an experimentally-parameterized mechanistic competition model to predict the poleward range boundaries of two widely co-occurring and ecologically-similar aquatic duckweed plants. We show that simple, mechanistic ecological niche models which include competition and thermal response terms best predict the northern range limits of our study species, outperforming competition-free mechanistic models and matching the predictive ability of popular statistical niche models fit to occurrence records. Next, using the theoretical framework of modern coexistence theory, we show that relative nonlinearity in competitors responses to temperature fluctuations maintains coexistence at the subordinate competitors poleward range boundary, highlighting the importance of this underappreciated fluctuation-dependent coexistence mechanism. Our results demonstrate the predictive utility of mechanistic niche models and support a more nuanced, interactive role of climate and species interactions in determining range boundaries, which may help explain the conflicting results from previous tests of classic range limit theory and contribute to a more mechanistic understanding of range dynamics under global change.

ecology↗

bioRxiv2019

How sample heterogeneity can obscure the signal of microbial interactions

Compositional data are commonly subjected to computational tools such as correlation networks, null models, and dynamic models, with the goal of identifying the ecological processes structuring microbial communities. Researchers applying these methods assume that the signs and magnitudes of species interactions and vital rates can be reliably parsed from compositional data. However, we contend that this assumption is violated when sample units contain any underlying spatial structure. Here, we show how three phenomena -- Simpsons paradox, context--dependence, and nonlinear averaging -- can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities. At the root of this issue is the fundamental mismatch between the spatial scales of species interactions (micrometres) and that of a typical marker gene sample (millimetres to centimetres). These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales, which will lead to more reliable inference of the ecological mechanisms structuring natural microbial communities.

microbiology↗

bioRxiv2016

Seasonal succession influences the functioning of a host-associated microbial food web

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leafs nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.\n\nStatement of authorshipDWA conceived this work, performed data collection and analysis, and wrote the manuscript

ecology↗