Biology subjects

Tonkin, J. D.

Publications and source records attributed to Tonkin, J. D..

14 recordsLinked to original sources

bioRxiv2026

Reduced-Rank Generalised Dissimilarity Modelling (RRGDM): Model-Based Ordination of Dissimilarity Data

(1) Dissimilarity indices offer an effective way to represent multivariate variability in community composition and to quantify beta diversity and its drivers. However, models that regress dissimilarities against environmental predictors face the challenge of linking site-level predictors to a pairwise response. (2) This mismatch is typically circumvented by regressing dissimilarities against distances in predictor values. But this approach does not reflect how environmental variables act on individual samples, complicates the inclusion of standard modelling features such as random effects, and conflates environmental effects on average composition with effects on compositional dispersion. (3) We propose Reduced-Rank Generalised Dissimilarity Modelling (RRGDM), a framework for model-based ordination that resolves the pair-to-site mismatch by reframing dissimilarity modelling as an ordination problem. RRGDM represents dissimilarities as the outcome of sample positions in a shared, low-dimensional latent space that captures community composition. These positions are in turn modelled as a linear function of predictors and error terms, with an associated dispersion sub-model. (4) Through a simulation study and two empirical examples, we show that RRGDM recovers known environmental effects and represents them as ecologically interpretable outputs. RRGDM enables inference on the relative importance of environmental gradients driving beta diversity and disentangles effects on composition versus dispersion. Although motivated by beta diversity, the approach is applicable to other pairwise dissimilarity data.

ecology↗

bioRxiv2026

Freshwater input and tidal position regulate species turnover and interaction rewiring in intertidal ecological networks

The effect that environmental conditions have on community and network assembly processes remains unclear, in part because these processes operate at multiple scales. Because marine primary producers and microinvertebrates have limited mobility, are susceptible to multiple stressors, and can be observed interacting in situ, their habitat-based interactions provide an informative system for disentangling network organising processes. We sampled 646 habitat-use networks, quantifying interactions involving habitat-users and biogenic habitat-formers over 12 months at 9 sites within Te Ihutai/Avon-Heathcote estuary in Christchurch, Aotearoa New Zealand. Using generalised dissimilarity mixed-effect models, we examined whether changes to species interactions - deconstructed into species turnover and interaction rewiring - were modulated by environmental covariates, including freshwater discharge, elevation, temperature, spatial location and season. We found that with increasing dissimilarity in sites proximity to freshwater, interaction change was more driven by rewiring, whereas differences in elevation (i.e., between channels and non-channel habitats) were driven by species turnover, with more sessile species inhabiting tidal channels. The proximity of habitats also played a strong role, with nearby networks comprising more similar interactions, and species turnover becoming more prevalent with increasing distance. Our results highlight that the relative influence and magnitude of rewiring and species turnover in controlling estuarine interaction networks was affected by the individual species distributions across the estuary and their responses to separate, but co-occurring, environmental factors. Quantification of habitat-former/user interaction networks offers robust, albeit understudied, measures of processes that can underpin community assembly, highlighting their potential importance in research, management and conservation. Open research statementData are provided for peer review. The code for produced from the project analysis and used to draft this manuscript is shared via a public GitHub repository hosted by the Tonkin Research group (repo name: EstInteractTurn). The data used in the formal analysis is hosted on Zenodo, under the corresponding authors profile (doi: 10.5281/zenodo.20619091). The data and code was prepared following strict adherence to the FAIR principles, meaning all data was saved as comma-separated values (.csv) or native R data structures (.rds).

ecology↗

bioRxiv2026

Effects of management on global crop pest damage depends on coevolutionary indicators

Pests and pathogens reduce yields of major food crops by 15% globally1. Interventions such as pesticides can mitigate yield loss, but pests can evolve resistance to pesticides over short timescales2,3. Pest damage to crops may also be determined by (co)evolutionary selection on pests by crops themselves and vice versa4, yet it is unclear whether the relative evolutionary potential of pests versus crops predicts the outcome of this arms race. Here we test whether readily available indicators of the evolutionary potential5-9 of crops and their pests or pathogens influence global yield loss10 and its response to agricultural management11-13. We find that evolutionary potential of the pest (measured as its genome size) and crop (measured as population density or proximity of wild relatives) moderated the effect of agricultural management (seed importation, fertiliser and pesticide use) on crop damage. Crucially, statistical interactions among crop and pest evolutionary potentials explained as much variation in yield loss as did agricultural management. Our results show a huge spatial variability in management effectiveness and suggest greatest benefit in places with a stronger imbalance in the evolutionary potential between crop and pest. More broadly, our findings reveal a key role of evolution in determining present-day pest damage.

evolutionary biology↗

bioRxiv2026

Population and community responses to the fast, slow, and seasonal components of environmental variation

Theory suggests that different components of environmental fluctuations, from daily and seasonal cycles to multidecadal trends, can have distinct and even opposing effects on species abundances and community dynamics, depending on their specific adaptations. But empirical research that deconstructs the influence of these different cycles on communities is lacking. Here, we used long-term biological monitoring data together with flow records of rivers across New Zealand to (i) investigate the role of fast, slow, and seasonal river-flow fluctuations in structuring macroinvertebrate communities; and (ii) to assess whether life-history and mobility traits mediate the response. Using joint species distribution models, we found striking differences in taxon and community responses to the different components of river flow variation. Responses to slow fluctuations were generally stronger and better predicted by traits, while responses to seasonal fluctuations were highly heterogeneous. Fast increases in flow, typical of flooding events, had pervasive negative effects on species abundances, but the severity of impact partly depended on mobility traits. Our results suggest that different ecological mechanisms underpin the response to distinct environmental fluctuations, highlighting the value of jointly considering multiple temporal scales of variation and species functional traits to understand and predict how communities reorganise under fluctuating environmental regimes.

ecology↗

bioRxiv2026

Partner fidelity with root symbionts impacts plant performance in the face of changing above- and belowground community context

Global environmental changes generate novel communities. Some species adapt to novel community contexts by demonstrating interaction fidelity, or consistently interacting with the same species, while others demonstrate interaction flexibility, or interacting with whichever partners are available (i.e., rewiring). However, the drivers and benefits of fidelity are unclear. Here, we use data from a large-scale mesocosm experiment to determine whether plant characteristics (e.g., provenance, functional group) and community contexts impact plant interaction fidelity to belowground mutualist and antagonist partners (i.e., root fungi and bacteria), and how this fidelity relates to plant performance. We found that the plant-antagonist relationships exhibited higher fidelity than plant-mutualist relationships with the strength of fidelity depending on a combination of plant characteristics and community context. Conversely, plant-mutualist fidelity impacted plant performance with competing effects depending on plant provenance and aboveground herbivore presence. Our study advances understanding of how species interactions influence plant performance in a changing world. Statement of authorshipAMM, JDT, JMT and DBS designed the concept. All authors contributed to refining the ideas. AM coded the analysis to produce the results with contributions from JDT, DBS, and BBM. HRL and DBS helped AMM with the statistical analysis. LPW, WJA, IAD, and JMT designed the experiment while LPW and WJA conducted the experiment. AMM wrote the first draft of the manuscript with assistance from all authors. IAD, JMT, and JDT obtained funding. All authors contributed to further editing of the manuscript.

ecology↗

bioRxiv2025

Climate-Driven Forest Reassembly Follows Divergent Functional Pathways in Cold- and Warm-Adapted Communities

AimClimate change leads to the widespread rearrangement of forests predominantly towards warm-adapted lower-elevation species. However, understanding the context-specific community assembly mechanisms that underlie these changes requires a mechanistic understanding of plant responses. Here, we use functional traits and diversity indices to identify distinct responses of warm- and cold-adapted forest communities. MethodsOur analysis used seven traits, including leaf morphology, size, nutrient content, and foliar isotopes across 3,625 sites over 49 years. We derived functional strategies from community-weighted mean trait values, assessed assembly mechanisms using five multi-trait functional diversity indices, and estimated structural change and turnover rates using abundance-based dissimilarity metrics. ResultsForest composition shifted significantly towards warm-adapted, lowland species with increasing temperature (+0.12 {degrees}C/decade) and decreasing precipitation (0.87%/decade). Communities concurrently increased in functional and species richness, but became functionally more similar, indicating niche packing. Disturbance recruitment shifted warm-adapted forests towards acquisitive traits, and increases in anisohydric strategies, reflecting possible effects of CO2 fertilisation under drought stress. Cold-adapted forests, in contrast, shifted to conservative strategies and were subject to stronger abiotic filtering. Moreover, changes in nitrogen isotope ratios point towards the importance of ectomycorrhizal associations to persist under climate change. Ecotonal mixed forests showed both responses and experienced the highest turnover. Main conclusionsNew Zealand forests follow biome-specific trajectories, characterised by distinct assembly mechanisms and context-dependent ecological responses. While uniform trends obscure these responses, they can be disentangled using a functional diversity framework that incorporates isotopic traits, offering a practical means to detect and interpret community reassembly under climate change.

ecology↗

bioRxiv2025

Accounting for the influence of dissimilarity gradientson community uniqueness

Compositional uniqueness has become increasingly relevant for understanding how local communities contribute to regional biodiversity. The most widely used metric is the Local Contribution to Beta Diversity (LCBD), which is typically regressed against environmental predictors. However, LCBD can vary either because of environmental processes that affect the overall variance in community composition, or because communities change directionally along environmental gradients. The latter implies that LCBD-environment relationships can strongly depend on how the environment is sampled. To address this issue, we introduce Generalised Dissimilarity Uniqueness Models (GDUM), a framework that embeds effects on community uniqueness within pairwise dissimilarity modelling. GDUMs are consistent with conventional uniqueness models, while explicitly accounting for directional changes in composition. This distinction disentangles directional and non-directional drivers of beta diversity, such as environmental filtering versus stochastic processes. By improving interpretability and generalizability, GDUM is a useful tool for understanding beta diversity patterns and projecting biodiversity responses.

ecology↗

bioRxiv2025

Disturbance provides limited respite for native fish against invaders

Understanding how flow-related disturbance regimes influence species interactions is critical for conserving threatened species in freshwater ecosystems, where both the alteration of these regimes and the invasion of non-native species pose major threats. Using 30 years of sampling data from a well-studied river system in Aotearoa New Zealand, we applied empirically- parameterized Lotka-Volterra competition models across a gradient of flood disturbance regimes to assess the potential for coexistence between threatened native galaxiids and invasive trout. Our models suggest trout dominate under low disturbance regimes, leading to galaxiid extinction. Coexistence peaks at intermediate disturbance regimes, though native fish densities are highly suppressed. Only at high disturbance regimes do native fish prevail, but priority effects are likely. Thus, restoration and conservation efforts focused solely on high disturbance habitats without accompanying biological interventions may not ensure native fish persistence. Further, prioritizing such habitats at the expense of others risks misdirecting resources towards sub-optimal conditions, particularly under climate change.

ecology↗

bioRxiv2024

Introduced trout hinder the recovery of native fish following an extreme flood disturbance

O_LIIn rivers, we are seeing a shift away from natural flow regimes towards larger and more frequent extreme drought and flood events. However, it is unclear how increasing intensity and frequency of extreme flow disturbances will play out alongside existing biotic pressures, such as biological invasions, to impact aquatic biodiversity. In New Zealand, vulnerable native non-diadromous galaxiid fishes face pressure from introduced trout through interspecific competition and predation, which may influence the recovery of native galaxiids after flood disturbances. C_LIO_LIHere, we employed a capture-mark-recapture study across 12 sites, along a gradient of disturbance following a major flood event, to examine the impact of extreme flooding on the population structure of non-diadromous galaxiids (Galaxias vulgaris and G. paucispondylus), and the effect of trout presence on individual galaxiid growth rates recovering from this event. C_LIO_LIWe found a lower abundance of all non-diadromous galaxiid size classes under higher flood magnitudes, but smaller size classes (i.e., young-of-year and 1-2 year cohorts) were more impacted. C_LIO_LIFurthermore, the presence of trout, whether at low or high abundances, reduced the individual growth of native non-diadromous galaxiids, despite interspecific effects being a weaker regulator of individual growth compared to conspecific effects. Moreover, trout effects on galaxiids varied by both galaxiid size and density, such that growth of smaller individual galaxiids in low densities were most affected by the presence of trout regardless of trout density. C_LIO_LIIn summary, our results demonstrate that non-diadromous galaxiid population dynamics in future are likely to be affected by flood disturbance regimes and introduced trout presence, the outcome of which involves a complex balance between reduced population persistence and increased individual resistance of larger individuals. C_LIO_LIConservation efforts that focus on maintaining strategically placed trout-free source populations of adult galaxiids could therefore be an important tool to enable native dispersal into trout-affected habitat and maintain population resilience in the face of increasingly larger and more frequent extreme events, given that recruitment of non-diadromous galaxiids is higher in the absence of trout. C_LI

ecology↗

bioRxiv2023

Species interactions drive continuous assembly of freshwater communities in stochastic environments

Understanding the factors driving the maintenance of long-term biodiversity in changing environments is essential for improving restoration and sustainability strategies in the face of global environmental change. Biodiversity is shaped by both niche and stochastic processes, however the strength of deterministic processes in unpredictable environmental regimes is highly debated. Since communities continuously change over time and space -- species persist, disappear or (re)appear -- understanding the drivers of species gains and losses from communities should inform us about whether niche or stochastic processes dominate community dynamics. Applying a nonparametric causal discovery approach to a 30-year time series containing annual abundances of benthic invertebrates across 66 locations in New Zealand rivers, we found a strong asynchronous causal relationship between species gains and losses directly driven by predation indicating that niche processes dominate community dynamics. Despite the unpredictable nature of these system, environmental noise was only indirectly related to species gains and losses through altering life history trait distribution. Using a stochastic birth-death framework, we demonstrate that the negative relationship between species gains and losses can not emerge without strong niche processes. Our results showed that even in systems that are dominated by unpredictable environmental variability, species interactions drive continuous community assembly.

ecology↗

bioRxiv2022

Diversity-stability relationships become decoupled across spatial scales: a synthesis of organism and ecosystem types

The relationship between biodiversity and stability, or its inverse, temporal variability, is multidimensional and complex. Temporal variability in aggregate properties, like total biomass or abundance, is typically lower in communities with higher species diversity (i.e., the diversity-stability relationship or DSR). Recent work has shown that, at broader spatial extents, regional-scale aggregate variability is also lower with higher regional diversity (in plant systems) and with lower spatial synchrony. However, it is not yet clear whether regional DSRs hold across a broad range of organisms and ecosystem types. Furthermore, focusing exclusively on aggregate properties of communities may overlook potentially destabilizing compositional shifts. To test these questions, we compiled a large collection of long-term spatial metacommunity data spanning a wide range of taxonomic groups (e.g., birds, fish, plants, invertebrates) and ecosystem types (e.g., deserts, forests, oceans). We applied a newly developed quantitative framework for jointly analyzing aggregate and compositional variability across scales. We quantified DSRs for composition and total abundance in local communities and metacommunities. At the local scale, compositional DSRs suggested that higher local () diversity was associated with lower variability in animal populations but higher variability in plant populations, while aggregate DSRs supported the classic stabilizing effects of diversity. Spatial synchrony differed among taxa (birds had the lowest, plants the highest), suggesting differences in stabilization by spatial processes. Spatial synchrony declined with higher diversity among sites ({beta}) for both compositional and aggregate properties. However, at the regional ({gamma}) scale, we found no aggregate DSR, but a positive compositional DSR. Across a broader range of taxa, our results suggest that high {gamma}-diversity does not consistently stabilize aggregate properties at regional scales without sufficient spatial {beta}-diversity to reduce spatial synchrony. Open research statementAll data sets are accessible via the Environmental Data Initiative, and a specific data package of the data sets used in this analysis will be made publicly available (doi: pending). Citations to original sources are included in Appendix S1. Code to reproduce the analyses is found in a Zenodo archive (doi: pending) of the GitHub repository for this project (https://github.com/sokole/ltermetacommunities/tree/master/Manuscripts/MS3).

ecology↗

bioRxiv2021

The dual nature of metacommunity variability

There is increasing interest in measuring ecological stability to understand how communities and ecosystems respond to broad-scale global changes. One of the most common approaches is to quantify the variation through time in community or ecosystem aggregate attributes (e.g., total biomass), referred to as aggregate variability. It is now widely recognized that aggregate variability represents only one aspect of communities and ecosystems, and compositional variability, the changes in the relative frequency of species in an assemblage, is equally important. Recent contributions have also begun to explore ecological stability at regional spatial scales, where interconnected local communities form metacommunities, a key concept in managing complex landscapes. However, the conceptual frameworks and measures of ecological stability in space have only focused on aggregate variability, leaving a conceptual gap. Here, we address this gap with a novel framework for quantifying the aggregate and compositional variability of communities and ecosystems through space and time. We demonstrate that the compositional variability of a metacommunity depends on the degree of spatial synchrony in compositional trajectories among local communities. We then provide a conceptual framework in which compositional variability of (i) the metacommunity through time and (ii) among local communities combine into four archetype scenarios: spatial stasis (low/low); spatial synchrony (high/low); spatial asynchrony (high/high) and spatial compensation (low/high). We illustrate this framework based on numerical examples and a case study of a macroalgal metacommunity in which low spatial synchrony reduced variability in aggregate biomass at the metacommunity scale, while masking high spatial synchrony in compositional trajectories among local communities. Finally, we discuss the role of dispersal, environmental heterogeneity, species interactions and suggest future avenues. We believe this framework will be helpful for considering both aspects of variability simultaneously which is important to better understand ecological stability in natural and complex landscapes in response to environmental changes.

ecology↗

bioRxiv2020

Designing flow regimes to support entire river ecosystems

Overcoming the challenges of water scarcity will require creative approaches to flow management and modeling approaches that forecast the effects of management actions on multiple ecosystem components simultaneously. Using a mechanistic multispecies modeling approach, we investigated the cross-ecosystem effects of environmental flow regimes designed for specific ecosystem outcomes. We reveal tradeoffs associated with flow regimes targeting riparian vegetation, fishes, and invertebrates. The different frequencies associated with each flow regime in some cases caused non-target ecosystem components to become locally extirpated within short (decadal) timespans. By incorporating multiple flow frequencies (from intraannual-scale pulses to large decadal-scale floods), the natural flow regime enabled a balanced but sub-optimal response of the three ecosystem components (mean 72% of designer flow). Although returning to a natural flow regime may not be possible in highly managed rivers, novel flow regimes must incorporate diverse frequencies inherent to such a regime and accommodate the sometimes conflicting requirements of different taxa at different times.

ecology↗

bioRxiv2016

Latitudinal metacommunity gradients in New Zealand stream invertebrates

That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealands two largest islands (~1300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealands dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.

ecology↗