Cohort aggregation modelling for complex forest stands: Spruce-aspen mixtures in British Columbia

Mixed-species growth models are needed as a synthesis of ecological knowledge and for guiding forest management. Individual-tree models have been commonly used, but the difficulties of reliably scaling from the individual to the stand level are often underestimated. Emergent properties and statistical issues limit their effectiveness. A more holistic modelling of aggregates at the whole stand level is a potentially attractive alternative. This work explores methodology for developing biologically consistent dynamic mixture models where the state is described by aggregate stand-level variables for species or age/size cohorts. The methods are demonstrated and tested with a two-cohort model for spruce-aspen mixtures named SAM. The models combine single-species submodels and submodels for resource partitioning among the cohorts. The partitioning allows for differences in competitive strength among species and size classes, and for complementarity effects. Height growth reduction in suppressed cohorts is also modelled. SAM fits well the available data, and exhibits behaviors consistent with current ecological knowledge. The general framework can be applied to any number of cohorts, and should be useful as a basis for modelling other mixed-species or uneven-aged stands.Comment: Accepted manuscript, to appear in Ecological Modellin

A flexible geometric model for leaf shape descriptions with high accuracy

Accurate assessment of canopy structure is crucial in studying plant-environment interactions. The advancement of functional-structural plant models (FSPM), which incorporate the 3D structure of individual plants, increases the need for a method for accurate mathematical descriptions of leaf shape. A model was developed as an improvement of an existing leaf shape algorithm to describe a large variety of leaf shapes. Modelling accuracy was evaluated using a spatial segmentation method and shape differences were assessed using principal component analysis (PCA) on the optimised parameters. Furthermore, a method is presented to calculate the mean shape of a dataset, intended for obtaining a representative shape for modelling purposes. The presented model is able to accurately capture a large range of single, entire leaf shapes. PCA illustrated the interpretability of the parameter values and allowed evaluation of shape differences. The model parameters allow straightforward digital reconstruction of leaf shapes for modelling purposes such as FSPMs

Development and validation of computational models of cellular interaction

In this paper we take the view that computational models of biological systems should satisfy two conditions – they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of software issues

Ecohydrological Controls on Grass and Shrub Above-ground Net Primary Productivity in a Seasonally Dry Climate

Seasonally dry, water‐limited regions are often co‐dominated by distinct herbaceous and woody plant communities with contrasting ecohydrological properties. We investigated the shape of the above‐ground net primary productivity (ANPP) response to annual precipitation (Pa) for adjacent grassland and shrubland ecosystems in Southern California, with the goal of understanding the role of these ecohydrological properties on ecosystem function. Our synthesis of observations and modelling demonstrates grassland and shrubland exhibit distinct ANPP‐Pa responses that correspond with characteristics of the long‐term Pa distribution and mean water balance fluxes. For annual grassland, no ANPP occurs below a ‘precipitation compensation point,’ where bare soil evaporation dominates the water balance, and ANPP saturates above the Pawhere deep percolation and runoff contribute to the modelled water balance. For shrubs, ANPP increases at a lower and relatively constant rate across the Pa gradient, while deep percolation and runoff account for a smaller fraction of the modelled water balance. We identify precipitation seasonality, root depth, and water stress sensitivity as the main ecosystem properties controlling these responses. Observed ANPP‐Paresponses correspond to notably different patterns of rain‐use efficiency (RUE). Grass RUE exceeds shrub RUE over a wide range of typical Pa values, whereas grasses and shrubs achieve a similar RUE in particularly dry or wet years. Inter‐annual precipitation variability, and the concomitant effect on ANPP, plays a critical role in maintaining the balance of grass and shrub cover and ecosystem‐scale productivity across this landscape

A process-based model of conifer forest structure and function with special emphasis on leaf lifespan

We describe the University of Sheffield Conifer Model (USCM), a process-based approach for simulating conifer forest carbon, nitrogen, and water fluxes by up-scaling widely applicable relationships between leaf lifespan and function. The USCM is designed to predict and analyze the biogeochemistry and biophysics of conifer forests that dominated the ice-free high-latitude regions under the high pCO2 “greenhouse” world 290–50 Myr ago. It will be of use in future research investigating controls on the contrasting distribution of ancient evergreen and deciduous forests between hemispheres, and their differential feedbacks on polar climate through the exchange of energy and materials with the atmosphere. Emphasis is placed on leaf lifespan because this trait can be determined from the anatomical characteristics of fossil conifer woods and influences a range of ecosystem processes. Extensive testing of simulated net primary production and partitioning, leaf area index, evapotranspiration, nitrogen uptake, and land surface energy partitioning showed close agreement with observations from sites across a wide climatic gradient. This indicates the generic utility of our model, and adequate representation of the key processes involved in forest function using only information on leaf lifespan, climate, and soils

Elastic and plastic effects on heterogeneous nucleation and nanowire formation

We investigate theoretically the effects of elastic and plastic deformations on heterogeneous nucleation and nanowire formation. In the first case, the influence of the confinement of the critical nucleus between two parallel misfitting substrates is investigated using scaling arguments. We present phase diagrams giving the nature of the nucleation regime as a function of the driving force and the degree of confinement. We complement this analytical study by amplitude equations simulations. In the second case, the influence of a screw dislocation inside a nanowire on the development of the morphological surface stability of the wire, related to the Rayleigh-Plateau instability, is examined. Here the screw dislocation provokes a torsion of the wire known as Eshelby twist. Numerical calculations using the finite element method and the amplitude equations are performed to support analytical investigations. It is shown that the screw dislocation promotes the Rayleigh-Plateau instability.Comment: 16 page

Morphoelastic rods Part 1: A single growing elastic rod

A theory for the dynamics and statics of growing elastic rods is presented. First, a single growing rod is considered and the formalism of three-dimensional multiplicative decomposition of morphoelasticity is used to describe the bulk growth of Kirchhoff elastic rods. Possible constitutive laws for growth are discussed and analysed. Second, a rod constrained or glued to a rigid substrate is considered, with the mismatch between the attachment site and the growing rod inducing stress. This stress can eventually lead to instability, bifurcation, and buckling

Modelling understorey dynamics in temperate forests under global change : challenges and perspectives

The understorey harbours a substantial part of vascular plant diversity in temperate forests and plays an important functional role, affecting ecosystem processes such as nutrient cycling and overstorey regeneration. Global change, however, is putting these understorey communities on trajectories of change, potentially altering and reducing their functioning in the future. Developing mitigation strategies to safeguard the diversity and functioning of temperate forests in the future is challenging and requires improved predictive capacity. Process-based models that predict understorey community composition over time, based on first principles of ecology, have the potential to guide mitigation endeavours but such approaches are rare. Here, we review fourteen understorey modelling approaches that have been proposed during the last three decades. We evaluate their inclusion of mechanisms that are required to predict the impact of global change on understorey communities. We conclude that none of the currently existing models fully accounts for all processes that we deem important based on empirical and experimental evidence. Based on this review, we contend new models are needed to project the complex impacts of global change on forest understoreys. Plant functional traits should be central to such future model developments, as they drive community assembly processes and provide valuable information on the functioning of the understorey. Given the important role of the overstorey, a coupling of understorey models to overstorey models will be essential to predict the impact of global change on understorey composition and structure, and how it will affect the functioning of temperate forests in the future

The correlation space of Gaussian latent tree models and model selection without fitting

We provide a complete description of possible covariance matrices consistent with a Gaussian latent tree model for any tree. We then present techniques for utilising these constraints to assess whether observed data is compatible with that Gaussian latent tree model. Our method does not require us first to fit such a tree. We demonstrate the usefulness of the inverse-Wishart distribution for performing preliminary assessments of tree-compatibility using semialgebraic constraints. Using results from Drton et al. (2008) we then provide the appropriate moments required for test statistics for assessing adherence to these equality constraints. These are shown to be effective even for small sample sizes and can be easily adjusted to test either the entire model or only certain macrostructures hypothesized within the tree. We illustrate our exploratory tetrad analysis using a linguistic application and our confirmatory tetrad analysis using a biological application.Comment: 15 page