Data availability and model complexity, generality, and utility: a reply to Lonergan

Two decades of functional-structural plant modelling: now addressing fundamental questions in systems biology and predictive ecology

BACKGROUND

Functional-structural plant models (FSPMs) explore and integrate relationships between a plant's structure and processes that underlie its growth and development. In the last 20 years, scientists interested in functional-structural plant modelling have expanded greatly the range of topics covered and now handle dynamical models of growth and development occurring from the microscopic scale, and involving cell division in plant meristems, to the macroscopic scales of whole plants and plant communities.

SCOPE

The FSPM approach occupies a central position in plant science; it is at the crossroads of fundamental questions in systems biology and predictive ecology. This special issue of Annals of Botany features selected papers on critical areas covered by FSPMs and examples of comprehensive models that are used to solve theoretical and applied questions, ranging from developmental biology to plant phenotyping and management of plants for agronomic purposes. Altogether, they offer an opportunity to assess the progress, gaps and bottlenecks along the research path originally foreseen for FSPMs two decades ago. This review also allows discussion of current challenges of FSPMs regarding (1) integration of multidisciplinary knowledge, (2) methods for handling complex models, (3) standards to achieve interoperability and greater genericity and (4) understanding of plant functioning across scales.

CONCLUSIONS

This approach has demonstrated considerable progress, but has yet to reach its full potential in terms of integration and heuristic knowledge production. The research agenda of functional-structural plant modellers in the coming years should place a greater emphasis on explaining robust emergent patterns, and on the causes of possible deviation from it. Modelling such patterns could indeed fuel both generic integration across scales and transdisciplinary transfer. In particular, it could be beneficial to emergent fields of research such as model-assisted phenotyping and predictive ecology in managed ecosystems.

Stochastic disturbance regimes alter patterns of ecosystem variability and recovery

Altered ecosystem variability is an important ecological response to disturbance yet understanding of how various attributes of disturbance regimes affect ecosystem variability is limited. To improve the framework for understanding the disturbance regime attributes that affect ecosystem variability, we examine how the introduction of stochasticity to disturbance parameters (frequency, severity and extent) alters simulated recovery when compared to deterministic outcomes from a spatially explicit simulation model. We also examine the agreement between results from empirical studies and deterministic and stochastic configurations of the model. We find that stochasticity in disturbance frequency and spatial extent leads to the greatest increase in the variance of simulated dynamics, although stochastic severity also contributes to departures from the deterministic case. The incorporation of stochasticity in disturbance attributes improves agreement between empirical and simulated responses, with 71% of empirical responses correctly classified by stochastic configurations of the model as compared to 47% using the purely deterministic model. By comparison, only 2% of empirical responses were correctly classified by the deterministic model and misclassified by stochastic configurations of the model. These results indicate that stochasticity in the attributes of a disturbance regime alters the patterns and classification of ecosystem variability, suggesting altered recovery dynamics. Incorporating stochastic disturbance processes into models may thus be critical for anticipating the ecological resilience of ecosystems.

A comparison between data requirements and availability for calibrating predictive ecological models for lowland UK woodlands: learning new tricks from old trees

Woodlands provide valuable ecosystem services, and it is important to understand their dynamics. To predict the way in which these might change, we need process‐based predictive ecological models, but these are necessarily very data intensive. We tested the ability of existing datasets to provide the parameters necessary to instantiate a well‐used forest model (SORTIE) for a well‐studied woodland (Wytham Woods). Only five of SORTIE's 16 equations describing different aspects of the life history and behavior of individual trees could be parameterized without additional data collection. One age class – seedlings – was completely missed as they are shorter than the height at which Diameter at Breast Height (DBH) is measured. The mensuration of trees has changed little in the last 400 years (focussing almost exclusively on DBH) despite major changes in the nature of the source of value obtained from trees over this time. This results in there being insufficient data to parameterize process‐based models in order to meet the societal demand for ecological prediction. We do not advocate ceasing the measurement of DBH, but we do recommend that those concerned with tree mensuration consider whether additional measures of trees could be added to their data collection protocols. We also see advantages in integrating techniques such as ground‐based LIDAR or remote sensing techniques with long‐term datasets to both preserve continuity with what has been performed in the past and to expand the range of measurements made.

Allometry and growth of eight tree taxa in United Kingdom woodlands

As part of a project to develop predictive ecosystem models of United Kingdom woodlands we have collated data from two United Kingdom woodlands - Wytham Woods and Alice Holt. Here we present data from 582 individual trees of eight taxa in the form of summary variables relating to the allometric relationships between trunk diameter, height, crown height, crown radius and trunk radial growth rate to the tree’s light environment and diameter at breast height. In addition the raw data files containing the variables from which the summary data were obtained. Large sample sizes with longitudinal data spanning 22 years make these datasets useful for future studies concerned with the way trees change in size and shape over their life-span.

Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes

Background

Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose.

Results

We investigate the survival rates of ten tree species in a dataset designed to monitor growth rates. As some individuals were not included in the census at some time points we use capture-mark-recapture methods both to allow us to account for missing individuals, and to estimate relocation probabilities. Growth rates, size, and light availability were included as covariates in the model predicting survival rates. The study demonstrates that tree mortality is best described as constant between years and size-dependent at early life stages and size independent at later life stages for most species of UK hardwood. We have demonstrated that even with a twenty-year dataset it is possible to discern variability both between individuals and between species.

Conclusions

Our work illustrates the potential utility of the method applied here for calculating plant population dynamics parameters in time replicated datasets with small sample sizes and missing individuals without any loss of sample size, and including explanatory covariates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-015-0038-8) contains supplementary material, which is available to authorized users.