Biology subjects

Lai, H. R.

Publications and source records attributed to Lai, H. R..

10 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

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

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

Mobile species' responses to surrounding land use generate trade-offs among nature's contributions to people

Agricultural landscapes provide material, non-material and regulating contributions that affect human wellbeing. The responses of these natures contributions to people (NCP) to land-use patterns depend on supporting biota with different habitat requirements, generating trade-offs and synergies. Predictions of NCP trade-offs could inform land-use decisions, but these do not typically account for the effects of land-use patterns on the movement of NCP-providing species, nor for interactions among NCP providers. To explore spatial trade-offs and synergies in eight indicators of NCP, we used Bayesian models that allow for interactions among land uses and among NCP using data from 150 grassland sites across rural Germany. We found that spatial arrangements of forest and open habitat influenced many NCP: acoustic diversity, birdwatching potential, natural enemy abundance and pollination. In particular, the amount and proximity of land uses in the surrounding landscape, especially forest and open habitat, drove the supply of most NCP. However, NCP provided by smaller-bodied taxa (herbivory and pathogen infection) responded weakly to landscape factors. Multiple NCP provided by a given taxon responded differently to their surrounding landscape (e.g. bird-provided caterpillar predation and seed predation), leading to trade-offs among NCP over short distances ([≤]60 m). These were caused by different rates and directions of response to amount and location of land uses. Resulting spatial predictions revealed that grassland-dominated or mixed forest-grassland areas better maximize beneficial NCP and minimize detrimental NCP across landscapes than purely forest-dominated areas. This suggests promoting semi-natural vegetation in agricultural landscapes to provide greater-than-additive benefits to net NCP supply. Significance StatementLand use affects natures contributions to people (NCP), including those provided by mobile species, in complex ways. Variation in the responses of species to the amount and location of land uses results in NCP trade-offs across landscapes, but decision-makers lack the capacity to spatially predict these trade-offs. We predict how the supply of both beneficial and detrimental NCP and associated trade-offs vary across diverse rural landscapes and find that grassland-dominated or mixed forest-grassland areas deliver higher net NCP supply than forest-dominated areas in our study system. Our findings support policies for promoting semi-natural vegetation cover in agricultural landscapes, as these may provide non-additive benefits for NCP.

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↗

bioRxiv2024

Eltonian niche modelling: applying joint hierarchical niche models to ecological networks

There is currently a dichotomy in the modelling of Grinnellian and Eltonian niches. Despite similar underlying data, Grinnellian niches are modelled with species-distribution models (SDMs), whereas Eltonian niches are modelled with ecological-network analysis, mainly because the sparsity of species-interaction data prevents the application of SDMs to Eltonian-niche modelling. Here, we propose to adapt recently developed joint species distribution models (JSDMs) to data on ecological networks, functional traits, and phylogenies to model species Eltonian niches. JSDMs overcome sparsity and improve predictions for individual species by considering non-independent relationships among co-occurring species; this unique ability makes them particularly suited for sparse datasets such as ecological networks. Our Eltonian JSDMs reveal strong relationships between species Eltonian niches and their functional traits and phylogeny. Moreover, we demonstrate that JSDMs can accurately predict the interactions of species for which no empirical interaction data are available, based solely on their functional traits. This facilitates prediction of new interactions in communities with altered composition, e.g. following climate-change induced local extinctions or species introductions. The high interpretability of Eltonian JSDMs will provide unique insights into mechanisms underlying species interactions and the potential impacts of environmental changes and invasive species on species interactions in ecological communities.

ecology↗

bioRxiv2024

Discordant changes in foliar and reproductive phenology of tropical dry-forest trees under increasing temperature and decreasing wet-season rainfall

O_LIPlant phenology drives population dynamics and forest productivity; it is also impacted by shifting environmental cues under climate change such as more prevalent drought. It is imperative to better understand how species and community phenology respond to climate change in leaf turnover and reproduction, both of which are required to integrate phenology into full life-cycle assessments. C_LIO_LIHowever, relatively few studies to-date examined the quantity and timing of phenology simultaneously. We demonstrate that the simultaneous assessment of phenological quantity and timing across multiple organs reveals more nuanced and holistic insights into the consequences of climate change. C_LIO_LIExtending a regression approach based on Fourier series, we decomposed the long-term (2004-2020) monthly leaf shedding, leaf flush, flowering and fruiting of 617 trees across 94 taxa at a Nigerian seasonally dry tropical forest into three periodic components--mean intensity, amplitude and phase--which respectively represents the total quantity, pulse concentration and peak timing of phenology. We then related each periodic component to warming minimum temperature and drying wet-season rainfall. C_LIO_LIWe found that climate explained more variation in phenological amplitudes (14-66%) compared to mean intensity and timing (6-49%). In drier years, more species (18%) shed leaves earlier (changing timing) or in more concentrated pulses (changing amplitude), while only a few (2%) shed leaves in greater total amounts (changing mean intensity). This combined with the decreased mean intensity of leaf flush imply a lower primary productivity as trees deployed fewer leaves for a shorter period. Some species (30%) produced fewer fruits despite no change or even increase in flowering; in a few species this could be explained by a shortened flowering period that limited pollination. At the community level, reproduction became more synchronous, potentially creating periods of scarcity for consumers. C_LIO_LISynthesis: Our findings highlight several contrasting yet complementary phenology- climate insights, indicating that assessments of forests climate resilience necessitate multiple aspects of phenology rather than a single performance indicator. The decline of leaf and fruit productions, as well as the temporal mismatches in leaf turnover and reproduction, will have cascading impacts on trophic interactions and nutrient cycling. C_LI

ecology↗

bioRxiv2020

The role of higher-order biotic interactions on tropical tree growth

Growth in individual size or biomass is a key demographic component in population models, with wide-ranging applications from quantifying species performance across abiotic or biotic conditions to assessing landscape-level dynamics under global change. In forest ecology, the responses of tree growth to biotic interactions are widely held to be crucial for understanding forest diversity, function, and structure. To date, most studies on plant-plant interactions only examine the additive competitive or facilitative interactions between species pairs; however, there is increasing evidence of non-additive, higher-order interactions (HOIs) impacting species demographic rates. When HOIs are present, the dynamics of a multi-species community cannot be fully understood or accurately predicted solely from pairwise outcomes because of how additional species interfere with the direct, pairwise interactions. Such HOIs should be particularly prevalent where species show nonlinear functional responses to resource availability and resource-acquisition traits themselves are density dependent. With this in mind, we used data from a tropical secondary forest--a system that fulfills both of these conditions--to build a ontogenetic diameter-growth model for individuals across ten woody-plant species. We allowed both direct and indirect interactions within communities to influence the species-specific growth parameters in a generalized Lotka-Volterra model. Specifically, indirect interactions entered the model as higher-order quadratic terms, i.e. non-additive effects of conspecific and heterospecific neighbour size on the focal individuals growth. For the whole community and for four out of ten focal species, the model that included HOIs had more statistical support than the model that included only direct interactions, despite the former containing a far greater number of parameters. HOIs had comparable effect sizes to direct interactions, and tended to further reduce the diameter growth rates of most species beyond what direct interactions had already reduced. In a simulation of successional stand dynamics, the inclusion of HOIs lead to rank swaps in species diameter hierarchies, even when community-level size distributions remained qualitatively similar. Our study highlights the implications, and discusses possible mechanisms, of non-additive density dependence in highly diverse and light-competitive tropical forests.

ecology↗