An overview of models of stomatal conductance at the leaf level

Stomata play a key role in plant adaptation to changing environmental conditions as they control both water losses and CO₂ uptake. Particularly, in the context of global change, simulations of the consequences of drought on crop plants are needed to design more efficient and water‐saving cropping systems. However, most of the models of stomatal conductance (g_s) developed at the leaf level link g_s to environmental factors or net photosynthesis (A_net), but do not include satisfactorily the effects of drought, impairing our capacity to simulate plant functioning in conditions of limited water supply. The objective of this review was to draw an up‐to‐date picture of the g_s models, from the empirical to the process‐based ones, along with their mechanistic or deterministic bases. It focuses on models capable to account for multiple environmental influences with emphasis on drought conditions. We examine how models that have been proposed for well‐watered conditions can be combined with those specifically designed to deal with drought conditions. Ideas for future improvements of g_s models are discussed: the issue of co‐regulation of g_s and A_net; the roles of CO₂, absissic acid and H₂O₂; and finally, how to better address the new challenges arising from the issue of global change.     

冬小麦叶片气孔导度模型水分响应函数的参数化

植物气孔导度模型的水分响应函数用来模拟水分胁迫对气孔导度的影响过程, 是模拟缺水环境下植物与大气间水、碳交换过程的关键算法。水分响应函数包括空气湿度响应函数和土壤湿度(或植物水势)响应函数, 该研究基于田间实验观测, 分析了冬小麦(Triticum aestivum)叶片气孔导度对不同空气饱和差和不同土壤体积含水量或叶水势的响应规律。一个土壤水分梯度的田间处理在中国科学院禹城综合试验站实施, 不同水分胁迫下的冬小麦叶片气体交换过程和气孔导度以及其他的温湿度数据被观测, 同时观测了土壤含水量和叶水势。实验数据表明, 冬小麦叶片气孔导度对空气饱和差的响应呈现双曲线规律, 变化趋势显示大约1 kPa空气饱和差是一个有用的阈值, 在小于1 kPa时, 冬小麦气孔导度对空气饱和差变化反应敏感, 而大于1 kPa后则反应缓慢; 分析土壤体积含水量与中午叶片气孔导度的关系发现, 中午叶片气孔导度随土壤含水量增加大致呈现线性增加趋势, 但在平均土壤体积含水量大于大约25%以后, 气孔导度不再明显增加, 而是维持在较高导度值上下波动; 冬小麦中午叶片水势与相应的气孔导度之间, 随着叶水势的增加, 气孔导度呈现增加趋势。根据冬小麦气孔导度对空气湿度、土壤湿度和叶水势的响应规律, 研究分别采用双曲线和幂指数形式拟合了水汽响应函数, 用三段线性方程拟合了土壤湿度响应函数和植物水势响应函数, 得到的参数可以为模型模拟冬小麦的各类水、热、碳交换过程采用。     

Use of a model of photosynthesis and leaf microenvironment to predict optimal stomatal conductance and leaf nitrogen partitioning

Abstract. A model of photosynthesis (PGEN) is presented. The model assumes that optimal use is made of the leaf nitrogen available for partitioning between the carboxylase and thylakoid components. This results in predictions of Rubisco and chlorophyll concentrations very similar to those measured elsewhere. A function is incorporated which represents the detrimental effects of negative leaf water potentials on the Calvin cycle, producing a quantitative and mechanistic trade-off between CO2 entering, and H₂O leaving, the leaf. Thus, an optimal stomatal conductance and associated internal partial pressure of CO₂ exists for any given set of environmental conditions. The model calculates this optimal state for the leaf, which is its output. The model was subjected to changes in the following parameters: soil water potential, irradiance, ambient CO2 partial pressure, leaf temperature, leaf-to-air vapour pressure deficit, wind speed, atmospheric pressure, leaf nitrogen content, root dry weight and leaf width. These perturbations resulted in changes in predicted optimal conductance which were very similar to what has been observed. In general, as the capacity of the leaf to fix CO₂ increased, so did the predicted optimal conductance, with the internal partial pressure of CO2 being maintained close to 22Pa.     

A coupled model of photosynthesis,stomatal conductance and transpiration for a rose leaf (Rosa hybrida L.)

The following three models were combined to predict simultaneously photosynthesis, stomatal conductance, transpiration and leaf temperature of a rose leaf: the biochemical model of photosynthesis of Farquhar, von Caemmerer and Berry (1980, Planta 149: 78-90), the stomatal conductance model of Ball, Woodrow and Berry (In: Biggens J, ed. Progress in photosynthesis research. The Netherlands: Martinus Nijhoff Publishers), and an energy balance model. The photosynthetic parameters: maximum carboxylation rate, potential rate of electron transport and rate of triose phosphate utilization, and their temperature dependence were determined using gas exchange data of fully expanded, young, sunlit leaves. The stomatal conductance model was calibrated independently. Prediction of net photosynthesis by the coupled model agreed well with the validation data, but the model tended to underestimate rates of stomatal conductance and transpiration. The coupled model developed in this study can be used to assist growers making environmental control decisions in glasshouse production.     

Ozone exposure causes a decoupling of conductance and photosynthesis: implications for the Ball-Berry stomatal conductance model

Industrialization has significantly altered atmospheric chemistry by increasing concentrations of chemicals such as nitrogen oxides (NO( x )) and volatile organic carbon, which react in the presence of sunlight to produce tropospheric ozone (O(3)). Ozone is a powerful oxidant that causes both visual and physiological damage to plants, impairing the ability of the plant to control processes like photosynthesis and transpiration. Damage to photosynthesis and stomatal conductance does not always occur at the same rate, which generates a problem when using the Ball-Berry model to predict stomatal conductance because the calculations directly rely on photosynthesis rates. The goals of this work were to develop a modeling framework to modify Ball-Berry stomatal conductance predictions independently of photosynthesis and to test the framework using experimental data. After exposure to elevated O(3) in open-top chambers, photosynthesis and stomatal conductance in tulip poplar changed at different rates through time. We were able to accurately model observed photosynthetic and stomatal conductance responses to chronic O(3) exposure in a Ball-Berry framework by adjusting stomatal conductance in addition to photosynthesis. This led to a significant improvement in the modeled ability to predict both photosynthesis and stomatal conductance responses to O(3).     

Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England

A fundamental consideration for the conservation of a species is the extent of its native range, that is, regions naturally colonized. However, both natural processes and human‐mediated introductions can drive species distribution shifts. Ruling out the human‐mediated introduction of a species into a given region is vital for its conservation, but remains a significant challenge in most cases. The crucian carp Carassius carassius (L.) is a threatened freshwater fish thought to be native to much of Europe. However, its native status in England is based only on anecdotal evidence. Here, we devise an approach that can be used to empirically test the native status of English fauna. We use this approach, along with 13 microsatellite loci, population structure analyses, and Approximate Bayesian Computation (ABC), to test hypotheses for the origins of C. carassius in England. Contrary to the current consensus, we find strong support for the human‐mediated introduction of C. carassius into England during the 15th century. This result stimulates an interesting and timely debate surrounding motivations for the conservation of species. We discuss this topic, and the potential for continued conservation of C. carassius in England, despite its non‐native origins.     

Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central–marginal hypothesis

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold‐adapted species likely used two isolated glacial refugia in southern France, in permafrost‐free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses.     

Long-term hoarding in the Paridae: a dynamic model

Using stochastic dynamic programming we modeled the hoardingand foraging behavior of tits and chickadees, Pandas, that areresident in the boreal forest at high latitudes. Here autumnshave a rich supply of seeds and temperatures are relativelymild, while winters are cold with short days and a low foodsupply. We assumed that parids have a memory of limited durationand that forgotten seeds accumulate in a bank that adds to thegeneral food supply in the hoarder's territory. Our model predictsthat birds should start "high-intensity" hoarding in early autumn,but not before that. Because of mass-dependent costs the birdswill keep their fat levels low during the autumn. When winterarrives they will carry more body fat, both for the long winternights and to hedge against the large effects of weather variationsin winter. After increasing the fat level at the start of winter,fat should gradually increase even more, to compensate for thediminishing food supply. Most hoarding occurs in autumn as away of building up the supply of long-term stores. Remembered,or short-term caches, may hedge against stochastic events inthe environment. Even though conditions are not beneficial forhoarding in winter, the birds still stored in winter to maintainlarger short and long-term hoards if environmental variationincreased. Almost all time in winter that not was spent foragingwas spent perching, mainly to avoid predation     

A model of stomatal conductance to quantify the relationship between leaf transpiration, microclimate and soil water stress

A model of stomatal conductance was developed to relate plant transpiration rate to photosynthetic active radiation (PAR), vapour pressure deficit and soil water potential. Parameters of the model include sensitivity of osmotic potential of guard cells to photosynthetic active radiation, elastic modulus of guard cell structure, soil‐to‐leaf conductance and osmotic potential of guard cells at zero PAR. The model was applied to field observations on three functional types that include 11 species in subtropical southern China. Non‐linear statistical regression was used to obtain parameters of the model. The result indicated that the model was capable of predicting stomatal conductance of all the 11 species and three functional types under wide ranges of environmental conditions. Major conclusions included that coniferous trees and shrubs were more tolerant for and resistant to soil water stress than broad‐leaf trees due to their lower osmotic potential, lignified guard cell walls, and sunken and suspended guard cell structure under subsidiary epidermal cells. Mid‐day depression in transpiration and photosynthesis of pines may be explained by decreased stomatal conductance under a large vapour pressure deficit. Stomatal conductance of pine trees was more strongly affected by vapour pressure deficit than that of other species because of their small soil‐to‐leaf conductance, which is explainable in terms of xylem tracheids in conifer trees. Tracheids transport water by means of small pit‐pairs in their side walls, and are much less efficient than the end‐perforated vessel members in broad‐leaf xylem systems. These conclusions remain hypothetical until direct measurements of these parameters are available.     

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world''s richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.     

Suitability of a combined stomatal conductance and photosynthesis model for calculation of leaf-level ozone fluxes

Currently, the most important source of uncertainty in stomatal ozone flux ( FO3) modelling is the stomatal conductance ( gst) factor. Hence FO3 model accuracy will strongly depend on the gst model being implemented. In this study the recently developed semi-empirical Gst model of Dewar was coupled to the widely known biochemical photosynthesis ( An) model of Farquhar. The Gst performance of this model combination was evaluated with a 4-month time series of beech ( Fagus sylvatica L.) measurements. The Gst model was hereto optimized in two steps to a 4-day and a 8-day period. A comparison between the modelled and measured gst to O(3) (gstO3) revealed a rather good overall performance (R(2)=0.77). Errors between the model combination and the measurements are thought to be largely caused by a moderate performance of the AN model, due to poor parameterization. Two 2-day periods with distinctly differing soil and meteorological conditions were chosen to give a picture of the daily gst performance. Although instant relative differences between modelled and measured gstO3 are sometimes high, the model combination is able to simulate the rough daily courses of gstO3 and hence FO3 reasonably well. Further improvement on full parameterization of the gst model and a well-parameterized An model to be linked to are needed to draw founded conclusions about its performance. Future efforts hereto are certainly justified since the model's mechanistic nature makes it a tool able to model gst variation in space and time, O(3) effects on gst, and effective FO3.     

Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red‐listed grasshopper

Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we use genomic data (restriction site‐associated DNA sequencing) to test biologically informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross‐backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species; (b) distributional shifts resulting from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles; and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation framework supported spatial configuration of topographic barriers to dispersal and human‐driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model‐based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.     

Comparing model predictions and experimental data for the response of stomatal conductance and guard cell turgor to manipulations of cuticular conductance, leaf-to-air vapour pressure difference and temperature: feedback mechanisms are able to account for all observations

Stomata respond to increasing leaf-to-air vapour pressure difference (LAVPD) ( D ) by closing. The mechanism by which this occurs is debated. A role for feedback and peristomatal transpiration has been proposed. In this paper, we apply a recent mechanistic model of stomatal behaviour, and compare model and experimental data for the influence of increasing D on stomatal conductance.
We manipulated cuticular conductance ( g _c) by three independent methods. First, we increased g _c by using a solvent mixture applied to both leaf surfaces prior to determining stomatal responses to D ; second, we increased g _c by increasing leaf temperature at constant D ; and third, we coated a small area of leaf with a light oil to decrease g _c. In all three experiments, experimental data and model outputs showed very close agreement.
We conclude, from the close agreement between model and experimental data and the fact that manipulations of g _c, and hence cuticular transpiration, influenced g _s in ways consistent with a feedback mechanism, that feedback is central in determining stomatal responses to D .     

A new stochastic dynamic tool to improve the accuracy of mortality estimates for bats killed at wind farms

Although generally considered environmentally friendly, wind power has been associated with extensive mortality of birds and bats. In this perspective, there is a need for reliable estimates of fatalities at wind farms, where the heterogeneity of the basic information, used among environmental assessment studies, is unlikely to support an accurate universal estimation method. We tested the applicability of the Stochastic Dynamic Methodology (StDM) to estimate bat fatalities, based on multifactorial cause–effect relationships (by integrating multi-model inference statistical analysis and dynamic modelling) between mortality estimates, detected fatalities and the selected key-components of the reality, such as the real number of bat mortalities simulated, the rate of carcasses removal, the searcher efficiency, the monitoring periodicity and the number of turbines for different realistic scenarios associated with particular wind farm conditions. Although some existing mortality estimators are considered accurate, the choice of a given universal formula for all mortality assessments, based on deterministic parameters and assumptions, may originate unsuspected errors. Therefore, we propose a flexible dynamic modelling framework, the StDM estimator, where the obtained algorithms are adaptable to the universe of application intended. The StDM estimator takes into account random, non-constant and scenario dependent parameters, providing bias-corrected estimates. The StDM estimator was applied for the European wind farm context and validated in the most cases tested, through the confrontation with independent data. Overall, this approach is considered a valuable tool to improve the quality of mortality estimates at onshore wind facilities, within the local, environmental and methodological gradients (including the cases where no mortality is detected), namely in the scope of environmental impact assessments and general ecological monitoring programmes.     

多水平贝叶斯模型预测森林土壤全氮

多水平贝叶斯方法阐明了预测中观测值、模型和参数的不确定性,被越来越多的生态学家所使用.应用多水平贝叶斯方法建立了北京八达岭地区森林土壤全氮模型,分析了模型参数及其不确定性,并对该区不同土壤层(A、B、C)全氮含量进行了预测.得到如下结论:(1)该区森林土壤全氮多水平贝叶斯模型为yi～N(β0j[i],k[j]+β1j[i],k[j]xi,σ2y).(2)对模型参数和其曲线不确定性分析表明,该模型能够很好的预测该区土壤全氮含量.(3)模型预测表明:土壤A层,随着海拔的增加,全氮含量递增.土壤B层,随着海拔的升高,植被类型0、1、2、3土壤全氮含量递增,而植被类型4土壤全氮含量出现递减现象.土壤C层,随着海拔的增加,植被类型0土壤全氮含量递增,而植被类型1、2、3、4土壤全氮含量均表现为递减.各植被类型土壤全氮含量都随着土层的深度而减少.     

Precision dating of the Palaeolithic: a new radiocarbon chronology for the Abri Pataud (France), a key Aurignacian sequence

This paper presents a new series of AMS dates on ultrafiltered bone gelatin extracted from identified cutmarked or humanly-modified bones and teeth from the site of Abri Pataud, in the French Dordogne. The sequence of 32 new determinations provides a coherent and reliable chronology from the site’s early Upper Palaeolithic levels 5–14, excavated by Hallam Movius. The results show that there were some problems with the previous series of dates, with many underestimating the real age. The new results, when calibrated and modelled using a Bayesian statistical method, allow detailed understanding of the pace of cultural changes within the Aurignacian I and II levels of the site, something not achievable before. In the future, the sequence of dates will allow wider comparison to similarly dated contexts elsewhere in Europe. High precision dating is only possible by using large suites of AMS dates from humanly-modified material within well understood archaeological sequences modelled using a Bayesian statistical method.     

SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level

In the archaea, some tRNA precursors contain intron(s) not only in the anticodon loop region but also in diverse sites of the gene (intron-containing tRNA or cis-spliced tRNA). The parasite Nanoarchaeum equitans, a member of the Nanoarchaeota kingdom, creates functional tRNA from separate genes, one encoding the 5'-half and the other the 3'-half (split tRNA or trans-spliced tRNA). Although recent genome projects have revealed a huge amount of nucleotide sequence data in the archaea, a comprehensive methodology for intron-containing and split tRNA searching is yet to be established. We therefore developed SPLITS, which is aimed at searching for any type of tRNA gene and is especially focused on intron-containing tRNAs or split tRNAs at the genome level. SPLITS initially predicts the bulge-helix-bulge splicing motif (a well-known, required structure in archaeal pre-tRNA introns) to determine and remove the intronic regions of tRNA genes. The intron-removed DNA sequences are automatically queried to tRNAscan-SE. SPLITS can predict known tRNAs with single introns located at unconventional sites on the genes (100%), tRNAs with double introns (85.7%), and known split tRNAs (100%). Our program will be very useful for identifying novel tRNA genes after completion of genome projects. The SPLITS source code is freely downloadable at http://splits.iab.keio.ac.jp/.     

FATE‐HD: a spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale

During the last decade, despite strenuous efforts to develop new models and compare different approaches, few conclusions have been drawn on their ability to provide robust biodiversity projections in an environmental change context. The recurring suggestions are that models should explicitly (i) include spatiotemporal dynamics; (ii) consider multiple species in interactions and (iii) account for the processes shaping biodiversity distribution. This article presents a biodiversity model (FATE‐HD) that meets this challenge at regional scale by combining phenomenological and process‐based approaches and using well‐defined plant functional groups. FATE‐HD has been tested and validated in a French National Park, demonstrating its ability to simulate vegetation dynamics, structure and diversity in response to disturbances and climate change. The analysis demonstrated the importance of considering biotic interactions, spatio‐temporal dynamics and disturbances in addition to abiotic drivers to simulate vegetation dynamics. The distribution of pioneer trees was particularly improved, as were all undergrowth functional groups.