Biology subjects

Ke, P.-J.

Publications and source records attributed to Ke, P.-J..

13 recordsLinked to original sources

bioRxiv2026

Invasion analysis for structured populations: analytical principles and numerical workflows

All real populations show some form of structure--differences among individuals, such as life stage or physiological condition, that shape a species' ability to persist. Yet it remains challenging to incorporate population structure into models of species interactions. We provide a general framework for studying competition in structured populations by quantifying species' invasion growth rates. The crux of our approach is separation of timescales: the initial dynamics of a structured population depend on how exactly it is introduced, but these transient differences do not affect long-term invasion success. Depending on the research question, the relevant long-term growth rate when rare may equivalently be derived using analytical separation of timescales, matrix population theory, or numerical simulations. Using case studies spanning developmental stage, environmental state, and infection status, we illustrate how our methodology derives simple, ecologically meaningful invasion conditions for a variety of systems. Finally, we extend the approach to fluctuating resident dynamics, showing how to use simulations or a general mathematical framework known as Floquet theory to correctly quantify invasion growth. By unifying the quantitative methods of population biology and community ecology, our framework will allow ecologists to study species persistence and coexistence across a greater variety of demographically complex systems.

ecology↗

bioRxiv2026

High culturable diversity and climate-associated seasonal dynamics of Saccharomycotina yeasts in subtropical forest leaf litter

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.

microbiology↗

bioRxiv2026

Extending island biogeography theory to biotic islands: Microbial communities in epiphytic bird's nest fern Asplenium nidus

1. Biotic insular systems differ from conventional islands because patch attributes change dynamically as patch-forming organisms develop. It therefore remains unclear whether the assembly mechanisms predicted by island biogeography theory (IBT) operate in such systems. Here, using epiphytic birds nest ferns (BNFs, Asplenium nidus) as a model biotic island system, we tested whether fungal and bacterial community diversity conform to species-area relationships predicted by IBT. With a stratified sampling scheme, we further evaluated the underlying mechanisms (passive sampling, disproportionate effects, and environmental heterogeneity) of species-area relationships, and assessed isolation effects using distance-decay patterns in community similarity. 2. We treated each BNF individual as a microbial island and categorized 24 BNFs into three size classes. Microbial and humus samples from multiple litter layers within each BNF individual were collected; microbial communities were characterized using next-generation sequencing, and humus chemical properties (pH and C:N ratio) were measured to characterize microhabitat conditions. To investigate mechanisms underlying species-area relationships, we applied a multi-scale rarefaction framework to partition diversity components. Spatial distances among BNFs were quantified to evaluate isolation effects. 3. Consistent with IBT predictions, both fungal and bacterial communities exhibited positive species-area relationships, indicating that larger BNFs harbored greater microbial richness. Diversity partitioning suggested that fungal richness increased through both disproportionate effects and environmental heterogeneity, whereas bacterial richness was primarily driven by environmental heterogeneity. Within larger ferns, greater heterogeneity in litter pH was associated with increased species turnover across litter layers, suggesting that decomposition-driven pH gradients create diverse microhabitats that promote microbial diversity. In addition, both microbial communities exhibited distance-decay patterns, indicating that isolation contributes to community assembly through dispersal limitation. 4. Synthesis. Our results demonstrate that BNFs function as a biotic insular system, in which both patch size and spatial isolation structure microbial diversity, consistent with predictions from IBT. Furthermore, we show that environmental heterogeneity generated by the growth of the habitatforming BNF mechanistically links island area to microbial diversity. Our study integrates both local habitat heterogeneity and regional spatial structure, highlighting the potential to extend IBT and metacommunity theory to organism-formed habitats.

ecology↗

bioRxiv2025

Predator decision-making shapes the dynamics and stability of mimicry systems

Mimicry is an anti-predator strategy in which prey species (the mimic) resemble an unprofitable species (the model) to deceive predators. Despite theoretical expectations for perfect mimicry, imperfect mimicry, where the mimic resembles its model imperfectly, is widespread in nature. To understand how imperfect mimicry can persist ecologically, we studied the effect of different predator recognition processes on the dynamics and stability of various mimicry systems. Specifically, we extended a dynamical model that integrates optimal foraging and signal detection theories by introducing a novel abundance-dependent recognition mechanism, where predators perception of the similarity between mimic and model is influenced by the relative abundance of prey types. We demonstrate that intermediate similarity promotes stable community dynamics and increases mimic abundance in single Batesian mimicry systems. Moreover, abundance-dependent recognition leads predators to reduce attack on mimics with low morphological similarity, further contributing to system stability. Extending the framework to a multi-mimicry system, we find that Batesian and Mullerian mimics have contrasting effects: intermediate Batesian similarity continues to stabilize the system, while high Mullerian similarity provides additional protection and can off-set destabilization caused by highly similar Batesian mimics. Our study offers a novel explanation for the prevalence of imperfect mimicry in nature and highlights how recognition processes shape the ecological stability of mimicry systems.

ecology↗

bioRxiv2025

Plant-soil feedback persists beyond host death to shape density-dependent plant competition

Background and AimsPlant-soil feedback (PSF) shapes plant competition, yet classic PSF experiments often overlook the density dependence and temporal complexities of PSFs, especially after host death. We ask whether microbial effects vary after host death and mediate density dependence in seedling competition. MethodsWe combined forest inventory data from a subtropical forest with a density-gradient greenhouse experiment to evaluate seedling competition among two tree species with different mycorrhizal associations (ectomycorrhizal versus arbuscular mycorrhizal). In 2023, we collected soil inocula from living and dead trees (died between 2014 and 2019) with unsterilized and sterilized treatments. We applied invasion analysis to infer seedling competitive outcomes and used bootstrapping to evaluate uncertainty. ResultsSoil microbial communities shaped seedling competition, favoring the ectomycorrhizal species. Using soils collected from living versus dead hosts as live inocula, we found similar plant competitive outcomes, indicating that PSF persists for over 4-9 years following host death. In contrast, when using sterilized inoculum, we found shifts in competition after host death, suggesting underlying abiotic changes which might masked by microbial effects. Moreover, we found significant evidence that soil microbes can mediate nonlinear density dependence in seedling competition. ConclusionWe provide experimental evidence of persistent microbial legacies that benefit ectomycorrhizal tree species in a subtropical forest. Our study demonstrates how integrating field-based census data with density-gradient experiments and explicit uncertainty estimation can better capture the temporal dimensions, complexities of density dependence, and uncertainties of PSF.

ecology↗

bioRxiv2025

General predictions for the effects of warming on competition

Understanding the effects of climate change on ecological communities has been limited by a lack of general theory for how temperature affects competition. To fill this knowledge gap, we integrated Modern Coexistence Theory and the Metabolic Theory of Ecology by incorporating empirically-derived temperature sensitivities into Modern Coexistence Theorys central model. We then simulated warming in consumer-resource systems and found that warming reduced both niche and fitness differences, making species more ecologically similar and competitive interactions more neutral. The greatest shifts in competition occurred when temperature sensitivities among species were highly asymmetrical. Effects of warming on competition via niche differences were comparable to those on fitness differences, suggesting that the emphasis on vital rates in global change research may overlook key biodiversity drivers. This general theory expands the domains of two prominent ecological theories and provides predictions for how warming may alter competition even in benign regions of species thermal niches.

ecology↗

bioRxiv2024

Functional coexistence theory: a mechanistic framework linking biodiversity to ecosystem function

Theory and experiments show that diverse ecosystems often have higher levels of function (for instance, biomass production), yet it remains challenging to identify the biological mechanisms responsible. We synthesize developments in coexistence theory into a general theoretical framework linking community coexistence to ecosystem function. Our framework, which we term functional coexistence theory, identifies three components determining the total function of a community of coexisting species. The first component directly corresponds to the niche differences that enable pairwise species coexistence, and to the complementarity component from the additive partition of biodiversity effects. The second component measures whether higher functioning species also have higher competitive fitness, providing a missing link between the additive partitions selection effect and modern coexistence theorys concept of equalization. The third component is least well-studied: reducing functional imbalances between species increases niche differences positive effect on function. Using a mechanistic model of resource competition, we show that our framework can identify how traits drive the effect of competition on productivity, and confirm our theoretical expectations by fitting this model to data from a classic plant competition experiment. Furthermore, we apply our framework to simulations of communities with multiple ecosystem functions or more than two species, demonstrating that relationships between niche, fitness, and function also predict total function beyond the case studied by classical theory. Taken together, our results highlight fundamental links between species coexistence and its consequences for ecosystem function, providing an avenue towards a predictive theory of community-ecosystem feedbacks.

ecology↗

bioRxiv2024

Realistic time-lags and litter dynamics alter predictions of plant-soil feedback across generations

Plant-soil feedback is a critical process in natural plant communities. However, it remains unclear whether greenhouse-measured microbial effects manifest in natural systems with temporally separated growing seasons as classic experiments often overlook seasonal time lags and litter dynamics. We modified the classic two-phase experiment to study plant-soil feedback for three Californian annual plant species. Our response phase used soil inoculum obtained either immediately after plant conditioning, after a six-month dry period with the conditioning plant removed, or after a dry period with the litter of the conditioning plant. We characterized soil bacterial and fungal communities in different treatments and employed recent advancement in plant-soil feedback theory to predict plant coexistence. Temporal delays and the presence of litter caused distinct responses in the fungal and bacterial communities, resulting in divergent microbial compositions at the end of the response phases. The delayed response treatments also affected microbially mediated stabilization, fitness differences, and invasion growth rates differently across species pairs, influencing predictions of plant coexistence. Our study highlights that the interplay between seasonal delays and litter dynamics prevents the direct extrapolation of plant-soil feedback measurements across multiple seasons, emphasizing the necessity of considering natural history when predicting microbially mediated plant coexistence.

ecology↗

bioRxiv2022

Multiple climate change factors jointly increased the competitiveness of a C4 grass against its C3 competitor

C3 and C4 plants are the two major terrestrial plant groups that respond differently to temperature, water, and CO2. Although much research has focused on the individual effect of warming, water availability, and elevated CO2 on biomass production and competitive interactions between C3 and C4 plants, the joint effects of these factors remain underexplored. We grew naturally co-occurring C3 (Oplismenus composites) and C4 (Paspalum conjugatum) grass under three temperature warming scenarios (control, +2{degrees}C, and +4{degrees}C), two water supply intervals (normal 2 days vs. prolonged 7 days [drought]), and two CO2 concentrations (ambient 400 ppm vs. elevated 800 ppm) in growth chambers and measured their above- and below-ground dry biomass in monoculture and mixture to quantify their biomass performances and competitive responses. Warming and elevated CO2 together enhanced the above- and/or below-ground biomass of both C3 and C4 grass. Moreover, temperature, water, and CO2 interacted to increase the below-ground biomass of the C4 grass. Surprisingly, the C3 grass performed worse under interspecific competition (mixture biomass) relative to intraspecific competition (monoculture biomass) at elevated CO2 compared to ambient CO2, while the reverse is true for the C4 grass. Furthermore, the C4 grass was most competitive against the C3 grass under simultaneous 4{degrees}C warming, drought, and elevated CO2. Taken together, our results suggest that the competitive balance could potentially shift in favor of C4 plants under the projected temperature warming, increased drought frequencies, and rising atmospheric CO2, with an increase in C4 relative abundance in future plant communities.

ecology↗

bioRxiv2021

Different mycorrhizal nutrient acquisition strategies shape tree species competition and coexistence dynamics

Mycorrhizal fungi with different nutrient acquisition strategies influence the functional separation among plant species. This might drive resource competition dynamics that cumulatively impact tree species coexistence, but few manipulative experiments have directly tested this. Combining surveys and experiments in a modern coexistence theory framework, we tested how variation in mycorrhizal strategies and nutrient conditions affect competitive outcomes between co-occurring ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) tree species. The dependency on EM symbioses increased with latitude and nitrogen (N) limitation, matching global trends. Host-specific soil microbiome conditioning and N fertilization combined to qualitatively affect coexistence outcomes. Lower N conditions favored EM over AM trees, but N fertilization reversed this outcome for southern species, consistent with regional-scale forest mycorrhizal transitions. As the magnitude and outcome of microbially-mediated competition depends on mycorrhizal differentiation and soil nutrient availability, this strongly supports the importance of mycorrhizal symbioses in driving large-scale biogeographic patterns of tree species.

ecology↗

bioRxiv2021

Different methods for niche and fitness differences computation offer contrasting explanations of species coexistence

In modern coexistence theory, species coexistence can either arise via stabilizing mechanisms that increase niche differences or equalizing mechanisms that reduce fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. Several methods for quantifying niche and fitness differences exist, but it remains unknown to what extent these methods agree on the reasons why species coexist. Here, we apply four common methods to quantify niche and fitness differences to one simulated and two empirical data sets. We ask if different methods result in different insights into what drives species coexistence. We find that different methods disagree on the effects of resource supply rates (simulated data), and of plant traits or phylogenetic distance (empirical data), on niche and fitness differences. More specifically, these methods often do not agree better than expected by chance. We argue for (1) a better understanding of what connects and sets apart different methods, and (2) the simultaneous application of multiple methods to enhance a more complete insight into why species coexist.

ecology↗

bioRxiv2021

The effect of non-linear competitive interactions on quantifying niche and fitness differences

The niche and fitness differences of modern coexistence theory separate mechanisms into stabilizing and equalizing components. Although this decomposition can help us predict and understand species coexistence, the extent to which mechanistic inference is sensitive to the method used to partition niche and fitness differences remains unclear. We apply two alternative methods to assess niche and fitness differences to four well known community models. We show that because standard methods based on linear approximations do not capture the full community dynamics, they can sometimes lead to incorrect predictions of coexistence and misleading interpretations of stabilizing and equalizing mechanisms. Conversely, a more recently developed method to decompose niche and fitness differences, that accounts for the full nonlinear dynamics of competition, consistently identifies the correct contribution of stabilizing and equalizing components. This approach further reveals that when the true complexity of the system is taken into account, essentially all mechanisms comprise both stabilizing and equalizing components. Amidst growing interest in the role of non-additive and higher-order interactions in regulating species coexistence, we propose that the effective decomposition of niche and fitness differences will become increasingly reliant on methods that account for the inherent non-linearity of community dynamics.

ecology↗

bioRxiv2018

Coexistence theory and the frequency dependence of priority effects

Priority effects encompass a broad suite of ecological phenomena. Several studies have suggested reframing priority effects around the stabilizing and equalizing concepts of coexistence theory. We show that the only compatible priority effects are those characterized by positive frequency dependence.

ecology↗