不同底质和透明度下马来眼子菜的表型可塑性研究

马来眼子菜(Potamogeton malaianusMiq.)是目前太湖沉水植物优势种之一。文章比较分析了3种不同底质和透明度情况下马来眼子菜的生长特征,探索其在太湖不断扩展的原因及其适应性。分别选取粘土质粉砂、粉砂和下蜀黄土底质上生长的马来眼子菜进行观察试验。结果表明,这3种底质在粒度组成、营养盐和分布特征上具有显著差异。在太湖粘土质粉砂和粉砂底质上马来眼子菜的生物量比下蜀黄土底质上的马来眼子菜高,其生物量随着底质营养盐的增加而增加。马来眼子菜与觅光相关的形态指标,如高度、节间距、节数、叶数、叶长及叶面积均随着底质营养盐的增加而显著增加。马来眼子菜的冠层高度与水体的透明度呈显著负相关,表明其对剧烈变化的湖泊光环境具有很强的适应能力。马来眼子菜在不同底质上的形态可塑性是其优先占据湖泊资源成为优势种的重要原因。     

Analysis of annual fluctuations of C. nodosa in the Venice lagoon: Modeling approach

A simple simulation model was developed to describe the growth trends of Cymodocea nodosa (Ucria) Ascherson based on data sets from the Venice lagoon. The model reproduces the seasonal fluctuations in the above and belowground biomass and in shoot density. The modeling results are in good agreement with data on net production, growth rates and chemical–physical parameters of water. It was assumed that light and temperature are the most important factors controlling C. nodosa development, and that the growth was not limited by nutrient availability. The aim was to simulate biomass production as a function of external forcing variables (light, water temperature) and internal control (plant density). A series of simulation experiments were performed with the basic model showing that among the most important phenomena affecting C. nodosa growth are: (1) inhibition of production and recruitment of new shoots by high temperature and (2) light attenuation due to seasonal fluctuation.     

Epidemiological risk assessment using linked network and grid based modelling: Phytophthora ramorum and Phytophthora kernoviae in the UK

We developed a stochastic simulation model incorporating most processes likely to be important in the spread of Phytophthora ramorum and similar diseases across the British landscape (covering Rhododendron ponticum in woodland and nurseries, and Vaccinium myrtillus in heathland). The simulation allows for movements of diseased plants within a realistically modelled trade network and long-distance natural dispersal. A series of simulation experiments were run with the model, representing an experiment varying the epidemic pressure and linkage between natural vegetation and horticultural trade, with or without disease spread in commercial trade, and with or without inspections-with-eradication, to give a 2 × 2 × 2 × 2 factorial started at 10 arbitrary locations spread across England. Fifty replicate simulations were made at each set of parameter values. Individual epidemics varied dramatically in size due to stochastic effects throughout the model. Across a range of epidemic pressures, the size of the epidemic was 5–13 times larger when commercial movement of plants was included. A key unknown factor in the system is the area of susceptible habitat outside the nursery system. Inspections, with a probability of detection and efficiency of infected-plant removal of 80% and made at 90-day intervals, reduced the size of epidemics by about 60% across the three sectors with a density of 1% susceptible plants in broadleaf woodland and heathland. Reducing this density to 0.1% largely isolated the trade network, so that inspections reduced the final epidemic size by over 90%, and most epidemics ended without escape into nature. Even in this case, however, major wild epidemics developed in a few percent of cases. Provided the number of new introductions remains low, the current inspection policy will control most epidemics. However, as the rate of introduction increases, it can overwhelm any reasonable inspection regime, largely due to spread prior to detection.     

Simulating the temporal pattern of waste production in farmed gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and Atlantic bluefin tuna (Thunnus thynnus)

Most fish farming waste output models provide gross waste rates as a function of stocked or produced biomass for a year or total culture cycle, but without contemplating the temporality of the discharges. This work aims to ascertain the temporal pattern of waste loads by coupling available growth and waste production models and developing simulation under real production rearing conditions, considering the overlapping of batches and management of stocks for three widely cultured species in the Mediterranean Sea: gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and Atlantic bluefin tuna (Thunnus thynnus). For a similar annual biomass production, the simulations showed that waste output and temporal dumping patterns differ between the three species as a result of the disparities in growth velocity, nutrient digestibility, maintenance metabolic budget and husbandry. The simulations allowed the temporal patterns including the periods of maximum discharge and the dissolved and particulate nitrogen and phosphorus content in the wastes released to be determined, both of which were seen to be species-specific.     

Data-directed modelling of Daphnia dynamics in a long-term micro-ecosystem experiment

The micro-ecosystem under consideration consists of three compartments forming a closed chain in which water circulates. Three trophic levels are represented in different compartments: autotrophs (algae, mainly Chlorella vulgaris), herbivores (Daphnia magna) and microbial decomposers. From a 20 years experiment with this system, data has been selected for this study. The dynamics of algae and Daphnia magna in only one of the compartments were modeled by different systems of differential and difference equations. We describe the successive steps in the process of model development, and the fitting of parameters using a Nelder-Mead simplex calibration method. Identification problems were overcome by taking values for physiological parameters in agreement with the literature. It turned out that a logistic type of model gives the best result for the structured Daphnia population because of the set up of the experiment: algae grow and reproduce in the upstream compartment. For this reason well-known plant–herbivore models did not comply with the data. The results of the parameter estimation procedure are discussed. The estimated grazing rate by Daphnia was smaller than expected. Possibly the Daphnia fed also on detritus and decomposing algae which were not measured.     

Design of a Domain Specific Language for modelling processes in landscapes

The modelling of processes that occur in landscapes is often confronted to issues related to the representation of space and the difficulty of properly handling time and multiple scales. In order to investigate these issues, a flexible modelling environment is required. We propose to develop such a tool based on a Domain Specific Language (DSL) that capitalises on the service-oriented architecture (SOA) paradigm. The modelling framework around the DSL is composed of a model building environment, a code generator and compiler, and a program execution platform. The DSL introduces five language elements (entity, service, relation, scenario and datafacer) that can be combined to offer a wide range of possibilities for modelling in space and time at different scales. When developing a model, model parts are either built using the DSL or taken from libraries of previously built ones, and adapted to the specific model. The practical usage of the DSL is illustrated first with the Lotka–Volterra model, and then with a landscape modelling experiment on the spread of a mosquito-borne disease in the Sahelian region of West Africa. An interesting characteristic of this approach is the possibility of adding new elements into an existing model, and replacing others with more appropriate ones, thus allowing potentially complex models to be built from simpler parts.     

Effect of streambed bacteria release on E. coli concentrations: Monitoring and modeling with the modified SWAT

Streambed sediment has been attracting attention as a reservoir for bacteria, including pathogenic strains. Soil and Water Assessment Tool (SWAT) has been augmented with a bacteria transport subroutine in SWAT2005 in which bacteria die-off is the only in-stream process. The purpose of this study was to develop the partial model of sediment-associated bacteria transport in stream and to evaluate the potential significance of streambed Escherichia coli (E. coli) release and deposition within the SWAT microbial water quality simulations. Streambed E. coli release and deposition were simulated based on the sediment resuspension and deposition modules in SWAT. The modified SWAT was applied to the Little Cove Creek watershed, Pennsylvania, which has forestry and dairy pasture landuses. Temporal changes in sediment E. coli concentrations were derived from monitoring data rather than from a streambed bacteria population model. Sensitivity analyses and calibrations were separately conducted for both hydrologic and bacteria parameters. Hydrologic calibration characterized soils in the watershed as pervious and thus the surface runoff was only moderately contributing to the streamflow. However, the surface runoff carried large numbers of E. coli to the stream, and sediment resuspension contributed to the persistent concentration of E. coli in stream water. Although the uncertainty of E. coli concentrations in streambed sediments and from wildlife probably affected the performance of the modified SWAT model, this study qualitatively confirmed the significance of modeling E. coli release from streambed and deposition for the SWAT microbial water quality simulations. Further developments should include modeling dynamics of bacteria populations within streambeds.     

Development and validation of an individual based Daphnia magna population model: The influence of crowding on population dynamics

An individual-based model was developed to predict the population dynamics of Daphnia magna at laboratory conditions from individual life-history traits observed in experiments with different feeding conditions. Within the model, each daphnid passes its individual life cycle including feeding on algae, aging, growing, developing and – when maturity is reached – reproducing. The modelled life cycle is driven by the amount of ingested algae and the density of the Daphnia population. At low algae densities the population dynamics is mainly driven by food supply, when the densities of algae are high, the limiting factor is “crowding” (a density-dependent mechanism due to chemical substances released by the organisms or physical contact, but independent of food competition).     

GIS-based modeling of the geographic distribution of Quercus emoryi Torr. (Fagaceae) in México and identification of significant environmental factors influencing the species’ distribution

The greatest concentration of oak species in the world is believed to be found in Mexico. These species are potentially useful for reforestation because of their capacity to adapt to diverse environments. Knowledge of their geographic distribution and of species–environment relations is essential for decision-making in the management and conservation of natural resources. The objectives of this study were to develop a model of the distribution of Quercus emoryi Torr. in Mexico, using geographic information systems and data layers of climatic and other variables, and to determine the variables that significantly influence the distribution of the species. The study consisted of the following steps: (A) selection of the target species from a botanical scientific collection, (B) characterization of the collecting sites using images with values or categories of the variables, (C) model building with the overlay of images that meet the habitat conditions determined from the characterization of sites, (D) model validation with independent data in order to determine the precision of the model, (E) model calibration through adjustment of the intervals of some variables, and (F) sensitivity analysis using precision and concordance non-parametric statistics applied to pairs of images. Results show that the intervals of the variables that best describe the species’ habitat are the following: altitude from 1650 to 2750 amsl, slope from 0 to 66°; average minimum temperature of January from −12 to −3 °C; mean temperature of June from 11 to 25 °C; mean annual precipitation from 218 to 1225 mm; soil units: lithosol, eutric cambisol, haplic phaeozem, chromic luvisol, rendzina, luvic xerosol, mollic planosol, pellic vertisol, eutric regosol; type of vegetation: oak forest, oak–pine forest, pine forest, pine–oak forest, juniperus forest, low open forest, natural grassland and chaparral. The resulting model of the geographic distribution of Quercus emoryi in Mexico had the following values for non-parametric statistics of precision and agreement: Kappa index of 0.613 and 0.788, overall accuracy of 0.806 and 0.894, sensitivity of 0.650 and 0.825, specificity of 0.963, positive predictive value of 0.945 and 0.957 and negative predictive value of 0.733 and 0.846. Results indicate that the variable average minimum temperature of January, with a maximum value of −3 °C, is an important factor in limiting the species’ distribution.     

Application of a temperature-dependent von Bertalanffy growth model to bullhead (Cottus gobio)

The most studied and commonly applied model of fish growth is the von Bertalanffy model. However, this model does not take water temperature into account, which is one of the most important environmental factors affecting the life cycle of fish, as many physiological processes that determine growth, e.g. metabolic rate and oxygen supply, are directly influenced by temperature. In the present study we propose a version of the von Bertalanffy growth model that includes mean annual water temperatures by correlating the growth coefficient, k, explicitly and the asymptotic length, L_∞, implicitly to water temperature. All relationships include parameters with an obvious biological relevance that makes them easier to identify. The model is used to fit growth data of bullhead (Cottus gobio) at different locations in the Bez River network (Drme, France). We show that temperature explains much of the growth variability at the different sampling sites of the network.     

Integrating soil carbon cycling with that of nitrogen and phosphorus in the watershed model SWAT: Theory and model testing

In this paper we describe and test a sub-model that integrates the cycling of carbon (C), nitrogen (N) and phosphorus (P) in the Soil Water Assessment Tool (SWAT) watershed model. The core of the sub-model is a multi-layer, one-pool soil organic carbon (S_C) algorithm, in which the decomposition rate of S_C and input rate to S_C (through decomposition and humification of residues) depend on the current size of S_C. The organic N and P fluxes are coupled to that of C and depend on the available mineral N and P, and the C:N and N:P ratios of the decomposing pools. Tillage explicitly affects the soil organic matter turnover rate through tool-specific coefficients. Unlike most models, the turnover of soil organic matter does not follow first order kinetics. Each soil layer has a specific maximum capacity to accumulate C or C saturation (S_x) that depends on texture and controls the turnover rate. It is shown in an analytical solution that S_x is a parameter with major influence in the model C dynamics. Testing with a 65-yr data set from the dryland wheat growing region in Oregon shows that the model adequately simulates the S_C dynamics in the topsoil (top 0.3 m) for three different treatments. Three key model parameters, the optimal decomposition and humification rates and a factor controlling the effect of soil moisture and temperature on the decomposition rate, showed low uncertainty as determined by generalized likelihood uncertainty estimation. Nonetheless, the parameter set that provided accurate simulations in the topsoil tended to overestimate S_C in the subsoil, suggesting that a mechanism that expresses at depth might not be represented in the current sub-model structure. The explicit integration of C, N, and P fluxes allows for a more cohesive simulation of nutrient cycling in the SWAT model. The sub-model has to be tested in forestland and rangeland in addition to agricultural land, and in diverse soils with extreme properties such high or low pH, an organic horizon, or volcanic soils.     

Modeling amphibian energetics, habitat suitability, and movements of western toads, Anaxyrus (=Bufo) boreas, across present and future landscapes

Effective conservation of amphibian populations requires the prediction of how amphibians use and move through a landscape. Amphibians are closely coupled to their physical environment. Thus an approach that uses the physiological attributes of amphibians, together with knowledge of their natural history, should be helpful. We used Niche Mapper™ to model the known movements and habitat use patterns of a population of Western toads (Anaxyrus (=Bufo) boreas) occupying forested habitats in southeastern Idaho. Niche Mapper uses first principles of environmental biophysics to combine features of topography, climate, land cover, and animal features to model microclimates and animal physiology and behavior across landscapes. Niche Mapper reproduced core body temperatures (T_c) and evaporation rates of live toads with average errors of 1.6 ± 0.4 °C and 0.8 ± 0.2 g/h, respectively. For four different habitat types, it reproduced similar mid-summer daily temperature patterns as those measured in the field and calculated evaporation rates (g/h) with an average error rate of 7.2 ± 5.5%. Sensitivity analyses indicate these errors do not significantly affect estimates of food consumption or activity. Using Niche Mapper we predicted the daily habitats used by free-ranging toads; our accuracy for female toads was greater than for male toads (74.2 ± 6.8% and 53.6 ± 15.8%, respectively), reflecting the stronger patterns of habitat selection among females. Using these changing to construct a cost surface, we also reconstructed movement paths that were consistent with field observations. The effect of climate warming on toads depends on the interaction of temperature and atmospheric moisture. If climate change occurs as predicted, results from Niche Mapper suggests that climate warming will increase the physiological cost of landscapes thereby limiting the activity for toads in different habitats.     

Mathematical analysis of change in forest carbon use efficiency with stand development: A case study on Abies veitchii Lindl.

Changes in carbon use efficiency (CUE), which is defined as the ratio of net primary production (NPP) to gross primary production (GPP), were analyzed for Abies veitchii Lindl. forests with respect to stand development by developing a simple mathematical model incorporating data on physiological variables and leaf mass ratio. A decrease in CUE with stand development was successfully expressed as a function of stand biomass (y) based on the following three assumptions: (1) a power-law relationship between mean respiration and mean individual tree mass, (2) a power-functional relationship between mean gross primary production and mean individual tree mass, and (3) self-thinning relationship between stand biomass and density. Based on this model, a parameter of CUE–y relationship was defined, and it was clarified that CUE decrease with stand development is caused not by the ratio of specific respiration rate to specific gross photosynthetic rate, but by leaf mass ratio. Since CUE is high in young forests, helpful information on selecting woody species when planting seedlings was provided from the viewpoints of reducing CO₂ in the atmosphere and global warming.     

Relationships between simulated water stress and mortality and growth rates in underplanted Toona ciliata Roem. in subtropical Argentinean plantations

Toona ciliata Roem. (Australian red cedar) requires a nurse-tree overstory to prevent damage from drought and irradiation in some regions of north-eastern Argentina. T. ciliata was planted in the understory of Pinus taeda L. (625 stems/ha), Pinus elliottii Engelm. × Pinus caribaea Morelet (625 stems/ha), and Grevillea robusta A. Cunn. (833 stems/ha) nurse trees, which were thinned to 0, 25, 50, 75 and 100% of the initial densities. We measured initial T. ciliata mortality and growth as well as Leaf Area Index (LAI) based on light transmission. T. ciliata soil water availability and its effect on early growth and mortality were examined by modelling drought stress using the two-dimensional forest hydrology model ForWaDy. Simulated patterns in T. ciliata water stress for the different overstory treatments were consistent with observed patterns of mortality. Early mortality was lowest with a G. robusta overstory, with corresponding lowest drought stress values and high modelled soil water contents in the top soil layer in intermediate and high overstory densities. Mortality was highest with a P. elliottii × P. caribaea overstory in treatments with the highest modelled drought stress values in the most open treatments. The model supported our field observations by indicating that water stress was an important limitation to T. ciliata survival and growth on our study sites. The linkage between T. ciliata establishment success, early growth and soil water availability as indicated by ForWaDy, leads us to conclude that the model is a suitable stand management tool for guiding establishment of T. ciliata plantations.     

Modelling the effects of extreme events on the dynamics of the amphipod Corophium orientale

The brackish water amphipod Corophium orientale is the dominant macroinvertebrate species in the upper Mira estuary, a small mesotidal system located in the southwest coast of Portugal. As climate changes will increase the frequency and intensity of extreme events such as floods and droughts, these will have a negative effect on benthic estuarine invertebrates, namely C. orientale. In order to understand the effects of these events on C. orientale, a dynamic model, based on published information and calibrated with field data, was developed and different scenarios were tested.For model construction, the annual development of three cohorts of C. orientale, their growth rates, and the establishment of the timing of each cohort rise and extinction are introduced. This structure can be repeated indefinitely, for years, and few parameters are required. The model simulations highlight the need for refuge areas that enable a fast recovery of the amphipod population after an extreme event and the recolozination of the affected areas.     

Computer simulation applied to the biological control of the insect Aphis gossypii for the parasitoid Lysiphlebus testaceipes

In integrated pest management (IPM), biological control is one of the possible options for the prevention or remediation of an unacceptable pest activity or damage. The success of forecast models in IPM depends, among other factors, on the knowledge of temperature effect over pests and its natural enemies. In this work, we simulated the effects of parasitism of Lysiphlebus testaceipes (Cresson, 1880) (Hymenoptera: Aphidiidae) on Aphis gossypii (Glover, 1877) (Hemiptera: Aphididae), a pest that is associated to crops of great economic importance in several parts of the world. We made use of experimental data relative to the host and its parasitoid at different temperatures. Age structure was incorporated into the dynamics through the Penna model. The results obtained showed that simulation, as a forecast model, can be a useful tool for biological control programs.     

COSMOS,a spatially explicit model to simulate the epidemiology of Cosmopolites sordidus in banana fields

A stochastic individual-based model called COSMOS was developed to simulate the epidemiology of banana weevil Cosmopolites sordidus, a major pest of banana fields. The model is based on simple rules of local movement of adults, egg laying of females, development and mortality, and infestation of larvae inside the banana plants. The biological parameters were estimated from the literature, and the model was validated at the small-plot scale. Simulated and observed distributions of attacks were similar except for five plots out of 18, using a Kolmogorov–Smirnov test. These exceptions may be explained by variation in predation of eggs and measurement error. An exhaustive sensitivity analysis using the Morris method showed that predation rate of eggs, demographic parameters of adults and mortality rate of larvae were the most influential parameters. COSMOS was therefore used to test different spatial arrangements of banana plants on the epidemiology of C. sordidus. Planting bananas in groups increased the time required to colonise plots but also the percentage of banana plants with severe attacks. Spatial heterogeneity of banana stages had no effect on time required to colonise plots but increased the mean level of attacks. Our model helps explain key factors of population dynamics and the epidemiology of this tropical pest.     

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

Peponapis bees are considered specialized pollinators of Cucurbita flowers, a genus that presents several species of economic value (squashes and pumpkins). Both genera originated in the Americas, and their diversity dispersion center is in Mexico. Ten species of Peponapis and ten species of Cucurbita (only non-domesticated species) were analyzed considering the similarity of their ecological niche characteristics with respect to climatic conditions of their occurrence areas (abiotic variables) and interactions between species (biotic variables). The similarity of climatic conditions (temperature and precipitation) was estimated through cluster analyses. The areas of potential occurrence of the most similar species were obtained through ecological niche modeling and summed with geographic information system tools. Three main clusters were obtained: one with species that shared potential occurrence areas mainly in deserts (P. pruinosa, P. timberlakei, C. digitata, C. palmata, C. foetidissima), another in moist forests (P. limitaris, P. atrata, C. lundelliana, C. o. martinezii) and a third mainly in dry forests (C. a. sororia, C. radicans, C. pedatifolia, P. azteca, P. smithi, P. crassidentata, P. utahensis). Some species with similar ecological niche presented potential shared areas that are also similar to their geographical distribution, like those occurring predominantly on deserts. However, some clustered species presented larger geographical areas, such as P. pruinosa and C. foetidissima suggesting other drivers than climatic conditions to shape their distributions. The domestication of Cucurbita and also the natural history of both genera were considered also as important factors.     

Application of a Random Forest algorithm to predict spatial distribution of the potential yield of Ruditapes philippinarum in the Venice lagoon, Italy

We present a modelling framework that combines machine learning techniques and Geographic Information Systems to support the management of an important aquaculture species, Manila clam (Ruditapes philippinarum). We use the Venice lagoon (Italy), the first site in Europe for the production of R. philippinarum, to illustrate the potential of this modelling approach. To investigate the relationship between the yield of R. philippinarum and a set of environmental factors, we used a Random Forest (RF) algorithm. The RF model was tuned with a large data set (n = 1698) and validated by an independent data set (n = 841). Overall, the model provided good predictions of site-specific yields and the analysis of marginal effect of predictors showed substantial agreement among the modelled responses and available ecological knowledge for R. philippinarum. The most influent environmental factors for yield estimation were percentage of sand in the sediment, salinity, and water depth. Our results agree with findings from other North Adriatic lagoons. The application of the fitted RF model to continuous maps of all the environmental variables allowed estimates of the potential yield for the whole basin. Such a spatial representation enabled site-specific estimates of yield in different farming areas within the lagoon. We present a possible management application of our model by estimating the potential yield under the current farming distribution and comparing it to a proposed re-organization of the farming areas. Our analysis suggests a reduction of total yield is likely to result from the proposed re-organization.     

Integrating farming techniques in an ecological matrix model: Implementation on the primrose (Primula vulgaris)

Several studies have proven the importance of field margins in sustaining biodiversity and other work has been done on the effect of field management on field margin flora. However few models have been built to predict the effects of field management on the flora. Our project addresses this need for a model capable of predicting the effect of cropping techniques and their timing on the flora of field margins. Primula vulgaris is a biodiversity indicator, characteristic of undisturbed flora and found in field margins and woodlands: its population has been declining for several years. We created a temporal matrix model of P. vulgaris populations on field margins, taking into account the effects of field, field margin and roadside management based on literature and expert knowledge. We then analysed its sensitivity to demographic parameters by comparing lambda (growth rate) sensitivity and elasticity. We compared the management parameter effect using the relative growth rate of the population after 6 years of simulation. Sensitivity analysis to biological parameters showed the importance of adult survival and seed production and germination. Results show that P. vulgaris is particularly sensitive to broad-spectrum herbicides and that other management techniques like early mowing, scything and scrub-killer (diluted broad-spectrum herbicide or specific herbicide) are less aggressive. Our simulations show that management of cash crops in Brittany is too aggressive for P. vulgaris populations and that 4-5 years of grassland in the adjacent field are necessary to maintain populations.