Biology subjects

Ray, C. A.

Publications and source records attributed to Ray, C. A..

4 recordsLinked to original sources

bioRxiv2026

Stage-dependent biotic interactions may not be important for stochastic competitive dynamics with little variation in stage structure

O_LIStage-dependent interactions, in which different life cycle stages (e.g., juveniles, adults) exert different per-capita competitive effects, are widespread across ecological communities. However, whether explicitly accounting for such ontogenetic variation improves forecasts of stochastic community dynamics remains unclear. We tested how the strength of stage dependence and species life-history strategy influence the predictive accuracy of community models that either include or ignore stage-specific interactions. C_LIO_LIWe constructed stochastic two-species competition models using stage-structured matrix population models spanning five virtual life histories along the fast-slow continuum. Density dependence was imposed separately on juvenile survival, adult survival, progression, retrogression, or fertility, and the strength of stage dependence varied from adult-driven to juvenile-driven competition. We then fitted deterministic projection models with and without stage-dependent interaction terms to simulated time series and quantified predictive performance over 100 time-step forecasts using mean absolute percentage error (MAPE). C_LIO_LIIncreasing stage dependence consistently reduced the predictive accuracy of models that ignored stage structure. However, absolute prediction errors remained small across all scenarios (MAPE < 0.7%), even under strong stage dependence. The influence of life-history strategy depended on which vital rate was density dependent: when juvenile survival was density dependent, faster life histories showed larger errors; when progression, retrogression, or fertility were density dependent, slower life histories exhibited greater errors; and when adult survival was density dependent, no consistent life-history effect emerged. Across simulations, temporal variation in population structure was low (coefficient of variation < 0.036), and prediction error was strongly associated with the magnitude of structural fluctuations rather than life-history pace per se. C_LIO_LISynthesis. Stage-dependent interactions can, in principle, alter stochastic competitive dynamics, but their practical importance for ecological forecasting depends on the extent to which population stage structure fluctuates through time. When environmental stochasticity dominates and stage structure remains near equilibrium, simpler models that ignore stage dependence provide robust approximations of community dynamics. Our results identify conditions under which demographic detail is necessary for forecasting and highlight the central role of structural variability in linking life-history strategy to community-level dynamics. C_LI

ecology↗

bioRxiv2026

Identification of transgene insertion sites via short- and long-read whole genome sequencing.

Transgenic mouse lines are essential to uncover organ or system level genotype-phenotype relationships. The generation of such lines via transgene addition may lead to the insertion into unknown genomic loci potentially leading not only to the disruption of native genes but also attenuation of transgene expression. Additionally, this often results in the inability to determine transgene zygosity which in turn complicates breeding and interpretation of experimental results. In this study we present two whole genome sequencing based pipelines that allow the identification and genotyping of even complex multi transgenic inserts. As they use widely available reagents and bioinformatic tools, they can easily be applied to develop genotyping strategies in potentially any species.

molecular biology↗

bioRxiv2022

Linking microenvironment modification to species interactions and demography in an alpine plant community

Individual plants can modify the microenvironment within their spatial neighborhood. However, the consequences of microenvironment modification for demography and species interactions remain unclear at the community scale. In a study of co-occurring alpine plants, we (1) determined the extent of species-specific microclimate modification by comparing temperature and soil moisture between vegetated and non-vegetated microsites for several focal species. We (2) determined how vital rates (survival, growth, fecundity) of all species varied in response to aboveground and belowground vegetative overlap with inter- and intraspecific neighbors as proxies for microenvironment modification. For (1), surface temperatures were buffered (lower maximums and higher minimums) and soil moisture was higher below the canopies of most species compared to non-vegetated areas. For (2), vegetative overlap predicted most vital rates, although the effect varied depending on whether aboveground or belowground overlap was considered. Vital rate response to microenvironment-modification proxies (vegetative overlap) was also frequently context dependent with respect to plant size and macroclimate. Microenvironment modification and spatial overlapping of individuals are key drivers of demography and species interactions in this alpine community.

ecology↗

bioRxiv2021

Frugivore gut passage increases seed germination: an updated meta-analysis

Many plants rely on animal mutualists for reproduction. Quantifying how animal mutualists impact plant performance provides a foundation for modelling how change in animal communities affects the composition and functioning of plant communities. We performed a meta-analysis of 2539 experiments, 6 times more than the last comprehensive meta-analysis, examining how gut passage by frugivores influences seed germination. We simultaneously analyzed multiple predictor variables related to study methodology, location, and frugivore identity to disentangle methodological from ecological impacts on effect sizes. We found that gut passage by birds, fish, reptiles, bats, primates, and other mammals on average increased seed germination, but that the magnitude varied across vertebrate groups. The positive effects of gut passage were largely explained by the de-inhibitory effects of pulp removal rather than by the scarification of seed tissues. Some previous studies and meta-analyses that found no effect of gut passage only tested scarification or did not distinguish between these tests of scarification and pulp removal. We found that, for a typical fleshy-fruited plant species, the lack of gut passage reduces germination by 60%. From an evolutionary perspective, this indicates a large risk associated with reliance on animal mutualists that is balanced against the benefits of animal-mediated seed dispersal. From a conservation perspective, this highlights the potential for large demographic consequences of frugivore declines on plant populations. Our database and findings advance quantitative predictions for the role of fruit-frugivore interactions in shaping plant communities in the Anthropocene.

ecology↗