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Background and Aims Many studies exist in the literature dealing with mathematical representations of root systems, categorized, for example, as pure structure description, partial derivative equations or functional--structural plant models. However, in these studies, root architecture modelling has seldom been carried out at the organ level with the inclusion of environmental influences that can be integrated into a whole plant characterization. Methods We have conducted a multidisciplinary study on root systems including field observations, architectural analysis, and formal and mathematical modelling. This integrative and coherent approach leads to a generic model (DigR) and its software simulator. Architecture analysis applied to root systems helps at root type classification and architectural unit design for each species. Roots belonging to a particular type share dynamic and morphological characteristics which consist of topological and geometric features. The DigR simulator is integrated into the Xplo environment, with a user interface to input parameter values and make output ready for dynamic 3-D visualization, statistical analysis and saving to standard formats. DigR is simulated in a quasi-parallel computing algorithm and may be used either as a standalone tool or integrated into other simulation platforms. The software is open-source and free to download at http://amapstudio.cirad.fr/soft/xplo/download. Key Results DigR is based on three key points: (1) a root-system architectural analysis, (2) root type classification and modelling and (3) a restricted set of 23 root type parameters with flexible values indexed in terms of root position. Genericity and botanical accuracy of the model is demonstrated for growth, branching, mortality and reiteration processes, and for different root architectures. Plugin examples demonstrate the model's versatility at simulating plastic responses to environmental constraints. Outputs of the model include diverse root system structures such as tap-root, fasciculate, tuberous, nodulated and clustered root systems. Conclusions DigR is based on plant architecture analysis which leads to specific root type classification and organization that are directly linked to field measurements. The open source simulator of the model has been included within a friendly user environment. DigR accuracy and versatility are demonstrated for growth simulations of complex root systems for both annual and perennial plants. [ABSTRACT FROM AUTHOR]

Summary: If trees minimize self‐shading, new foliage in shaded parts of the crown should remain minimal. However, many species have abundant foliage on short shoots inside their crown. In this paper, we test the hypothesis that short shoots allow trees to densify their foliage in self‐shaded parts of the crown thanks to reduced costs.Using 30 woody species in Mediterranean and tropical biomes, we estimated the contribution of short shoots to total plant foliage, calculated their costs relative to long shoots including wood cost and used 3D plant simulations calibrated with field measurements to quantify their light interception, self‐shading and yield.In species with short shoots, leaves on short shoots account for the majority of leaf area. The reduced cost of short stems enables the production of leaf area with 36% less biomass. Simulations show that although short shoots are more self‐shaded, they benefit the plant because they cost less. Lastly, the morphological properties of short shoots have major implications for whole plant architecture.Taken together, our results question the validity of only assessing leaf costs to understand leaf economics and call for more integrated observations at the crown scale to understand light capture strategies in woody plants. [ABSTRACT FROM AUTHOR]

Background and Aims: AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. [ABSTRACT FROM PUBLISHER]

The origin of xylem in the Silurian was a major step in plant evolution, leading to diverse growth forms with various mechanical and hydraulic properties. In the fossil record, these properties can only be investigated using models based on extant plant physiology. Regarding hydraulics, previous studies have considered either the properties of a single tracheid or of a set of independent tubes. Here, we use the analogy between the flow of water under tension in a plant and an electrical circuit to develop an extension of Wilson's single tracheid model to the tissue scale. Upscaling to the tissue-level allows considering wood as a heterogeneous tissue by taking into account differences in tracheid density and the presence of rays. The new model provides a more biologically accurate representation of fossil wood hydraulic properties. The single tracheid and new tissue models are applied to two conspecific specimens of Callixylon (Progymnospermopsida, Archeopteridales) from the Late Devonian of Morocco. Differences are shown at the tissue level that cannot be suspected at the single tracheid level. Callixylon represents the first trees with a conifer-like wood and is a major component of Late Devonian floras world-wide. Our results show that the anatomical disparity of its wood might have led to hydraulic plasticity, allowing growth in various environmental conditions. More generally, the new tissue-model suggests that the various combinations of tracheid and ray sizes present in Palaeozoic plants might have led to a higher variety of ecophysiologies than suspected based solely on the properties of individual tracheids. [ABSTRACT FROM AUTHOR]

As description of enamel microstructure in mammals is mainly performed through 2D sections, interpretations of its formation and development can be misinterpreted by neglecting the complexity of its 3D arrangement. Through Simulenam, a novel software dedicated to the simulation of enamel prisms, and an updated, integrative model of decussation formation, we managed to transform 2D observations of enamel sections into full 3D representations of hippopotamoid enamel microstructure. This allowed us to reinterpret the 2D morphological characters of these taxa into geometric parameters and put a new light on how they evolved through time, with potential implications on their cellular origins - essential steps for furthering our understanding of enamel. Indeed, we also demonstrated that some of these characters could actually be non-homologous across taxa, and that there is at least two fundamentally different ways to produce enamel prism decussation in mammals. [ABSTRACT FROM AUTHOR]

Background and Aims: Light interception is a critical factor in the production of biomass. The study presented here describes a method used to take account of architectural changes over time in sunflower and to estimate absorbed light at the organ level. [ABSTRACT FROM PUBLISHER]