Modelling the abundance of three key plant species in New Zealand hill-pasture using a decision tree approach

Decision tree models were developed to investigate and predict the relative abundance of three key pasture plants [ryegrass (Lolium perenne), browntop (Agrostis capillaris), and white clover (Trifolium repens)] with integration of a geographical information system (GIS) in a naturalised hill-pasture in the North Island, New Zealand, and were compared with regression models with respect to model fit and predictive accuracy. The results indicated that the decision tree models had a better model fit in terms of average squared error (ASE) and a higher percentage of adequately predicted cases in model validation than the corresponding regression models. These decision tree models clearly revealed the relative importance of environmental and management variables in influencing the abundance of these three species. Hill slope was the most significant environmental factor influencing the abundance of ryegrass while soil Olsen P and annual P fertilizer input were the most significant factors influencing the abundance of browntop, and white clover, respectively. Soil Olsen P of approximately 10 μg/g, or a slope of about 10.5° was critical points where the competition between ryegrass and browntop tended to come to an equilibrium. Integrating the decision tree models with a GIS in this study not only facilitated the model development and analyses, but also provided a useful decision support tool in pasture management such as in assisting precision fertilizer placement. The insights obtained from the decision tree models also have important implications for pasture management, for example, it is important to maintain a soil Olsen P higher than 10 μg/g in order to keep the dominance of ryegrass in the hill-pasture.     

Relevant scales of variability of the benthic allochthonous microalga Chrysophaeum taylorii

Chrysophaeum taylorii (Pelagophyceae) is an allochthonous benthic microalga recently recorded in the Mediterranean Sea. During summer, the occurrence of C. taylorii is usually visible to the naked eye due to the large amount of mucilage this species produces. Information on the spatio-temporal variability of this species and on the predictability of massive mucilage events is still scarce and requires to define ad hoc managing strategies of major bloom events. The aim of this work was to identify the relevant scales of variation in the abundance of C. taylorii abundance and to estimate the relative recurrence of its blooms, testing the hypothesis that mucilage was dependent on the cell density. The first approach was the identification of the most appropriate sampling procedure to estimate benthic cell abundance of C. taylorii. The second one was the estimation of the magnitude of variation in C. taylorii cell abundance attributable to each of several spatial (areas, sites, zones and replicates) and temporal scales (fortnights and years) in the Marine Protected Area of Tavolara Punta Coda Cavallo (Western Mediterranean Sea). The results indicate fortnight and year as the most relevant scales of variability in the cell abundance of C. taylorii and highlight the unimportance of small spatial scales (zone and replicates) to the species variability. The collected data also evidence the absence of a direct relationship between the cell density of C. taylorii and the production of mucilage. In conclusion, these results indicate that patterns in the cell abundance of C. taylorii vary notably depending on the considered scale and that future investigations on processes affecting its performance will need to consider the relevant scales of variation evidenced.     

Spatially distributed modeling of the long-term carbon balance of a boreal landscape

Spatially and temporally distributed information on the sizes of biomass carbon (C) pools (BCPs) and soil C pools (SCPs) is vital for improving our understanding of biosphere-atmosphere C fluxes. Because the sizes of C pools result from the integrated effects of primary production, age-effects, changes in climate, atmospheric CO₂ concentration, N deposition, and disturbances, a modeling scheme that interactively considers these processes is important. We used the InTEC model, driven by various spatio-temporal datasets to simulate the long-term C-balance in a boreal landscape in eastern Canada. Our results suggested that in this boreal landscape, mature coniferous stands had stabilized their productivity and fluctuated as a weak C-sink or C-source depending on the interannual variations in hydrometeorological factors. Disturbed deciduous stands were larger C-sinks (NEP₂₀₀₄ = 150 gC m⁻² yr⁻¹) than undisturbed coniferous stands (e.g. NEP₂₀₀₄ = 8 gC m⁻² yr⁻¹). Wetlands had lower NPP but showed temporally consistent C accumulation patterns. The simulated spatio-temporal patterns of BCPs and SCPs were unique and reflected the integrated effects of climate, plant growth and atmospheric chemistry besides the inherent properties of the C pool themselves. The simulated BCPs and SCPs generally compared well with the biometric estimates (BCPs: r = 0.86, SCPs: r = 0.84). The largest BCP biases were found in recently disturbed stands and the largest SCP biases were seen in locations where moss necro-masses were abundant. Reconstructing C pools and C fluxes in the ecosystem in such a spatio-temporal manner could help reduce the uncertainties in our understanding of terrestrial C-cycle.     

Demography and interannual variability of salp swarms (Thalia democratica)

Swarms of the pelagic tunicate, Thalia democratica, form during spring, but the causes of the large interannual variability in the magnitude of salp swarms are unclear. Changes in asexual reproduction (buds per chain) of T. democratica populations in the coastal waters of south-east Australia (32–35°S) were observed in three austral springs (October 2008–2010). T. democratica abundance was significantly higher in 2008 (1,312 individuals m^?3) than 2009 and 2010 (210 and 92 individuals m^?3, respectively). There was a significant negative relationship (linear regression, r ² = 0.61, F _1,22 = 33.83, P < 0.001) between abundance and asexual reproduction. Similarly, relative growth rates declined with decreasing abundance. Generalised additive mixed modelling showed that T. democratica abundance was significantly positively related to preferred food >2 μm in size (P < 0.05) and negatively related to the proportion of non-salp zooplankton (P < 0.001). Salp swarm magnitude, growth, and asexual reproduction may depend on the abundance of larger phytoplankton (prymnesiophytes and diatoms) and competition with other zooplankton.     

Spatio-temporal modelling of ground vegetation development in mountain spruce forests

More complex models of forest ecosystems are required to understand how land-cover changes can impact vegetation dynamics and spatial pattern. In order to document spatio-temporal modelling abilities, the observations conducted in the declined climax mountain Norway spruce forest during the recovery period (1995-2006) are used for simulation and spatial analysis in the GIS environment. The developed spatio-temporal model is used for simulation of forest vegetation dynamics in a mountain spruce forest in the framework of regeneration processes after stress from air pollution. In order to explore the spatial and temporal phenomena of regeneration processes, the spatio-temporal model is based on a large set of ordinary differential equations that solve dynamic processes in sets of microsites arranged in grids for each ground vegetation species and each age group of Norway spruce seedlings. The spatial extent of the explored site is composed of a set of 50 × 50 microsites. Each microsite is represented by a square with dimensions of 1 m × 1 m. The presented simulation studies are mainly focused on seedlings from the seed year 1992, in order to explore the longest monitored time series of survival. It is based on exponential growth models that are related to the environmental conditions for each microsite. The canopy gaps based on estimates of the local crown projected area, the soil type layer, and the dominant grass density are used to provide case simulation studies. The first case study simulates the influence of microsite positions in relation to the local tree crown projections on the survival of spruce seedlings. It is assumed that the density of the trees is the main factor that determines the light and heat supply to the ground level of the Norway spruce seedlings. The second case study extends the previous study to include terms that determine the growth ratio in dependence on the crown projection area. The third case study provides further extensions in order to simulate growth ratio relations to the local soil type. The fourth case study demonstrates the local influence of the dominant grasses, such as Avenella flexuosa and Calamagrostis villosa, on the natural regeneration of Norway spruce. Starting from the conditions at the sites before the recovery period, the case simulation studies are able to project the short-term succession for a regeneration decade and the approximate long-term development. In addition to the standard simulation procedures based on solution of ordinary differential equations, spatio-temporal modelling in the GIS environment is able to provide spatial data management, analysis and visualization of the data.     

Reliability of Indicators of Decline in Abundance

Abstract: Although there are many indicators of endangerment (i.e., whether populations or species meet criteria that justify conservation action), their reliability has rarely been tested. Such indicators may fail to identify that a population or species meets criteria for conservation action (false negative) or may incorrectly show that such criteria have been met (false positive). To quantify the rate of both types of error for 20 commonly used indicators of declining abundance (threat indicators), we used receiver operating characteristic curves derived from historical (1938–2007) data for 18 sockeye salmon (Oncorhynchus nerka) populations in the Fraser River, British Columbia, Canada. We retrospectively determined each population's yearly status (reflected by change in abundance over time) on the basis of each indicator. We then compared that population's status in a given year with the status in subsequent years (determined by the magnitude of decline in abundance across those years). For each sockeye population, we calculated how often each indicator of past status matched subsequent status. No single threat indicator provided error‐free estimates of status, but indicators that reflected the extent (i.e., magnitude) of past decline in abundance (through comparison of current abundance with some historical baseline abundance) tended to better reflect status in subsequent years than the rate of decline over the previous 3 generations (a widely used indicator). We recommend that when possible, the reliability of various threat indicators be evaluated with empirical analyses before such indicators are used to determine the need for conservation action. These indicators should include estimates from the entire data set to take into account a historical baseline.     

Determining Decision Thresholds and Evaluating Indicators when Conservation Status is Measured as a Continuum

Categorization of the status of populations, species, and ecosystems underpins most conservation activities. Status is often based on how a system's current indicator value (e.g., change in abundance) relates to some threshold of conservation concern. Receiver operating characteristic (ROC) curves can be used to quantify the statistical reliability of indicators of conservation status and evaluate trade‐offs between correct (true positive) and incorrect (false positive) classifications across a range of decision thresholds. However, ROC curves assume a discrete, binary relationship between an indicator and the conservation status it is meant to track, which is a simplification of the more realistic continuum of conservation status, and may limit the applicability of ROC curves in conservation science. We describe a modified ROC curve that treats conservation status as a continuum rather than a discrete state. We explored the influence of this continuum and typical sources of variation in abundance that can lead to classification errors (i.e., random variation and measurement error) on the true and false positive rates corresponding to varying decision thresholds and the reliability of change in abundance as an indicator of conservation status, respectively. We applied our modified ROC approach to an indicator of endangerment in Pacific salmon (Oncorhynchus nerka) (i.e., percent decline in geometric mean abundance) and an indicator of marine ecosystem structure and function (i.e., detritivore biomass). Failure to treat conservation status as a continuum when choosing thresholds for indicators resulted in the misidentification of trade‐offs between true and false positive rates and the overestimation of an indicator's reliability. We argue for treating conservation status as a continuum when ROC curves are used to evaluate decision thresholds in indicators for the assessment of conservation status. Determinación de Umbrales de Decisiones y Evaluación delos Indicadores cuando se Mide el Estado de de Conservación como un Continuo     

Hierarchical Bayesian Modelling of plant colonisation by winged aphids: Inferring dispersal processes by linking aerial and field count data

Understanding and modelling insect pest dispersal is an important prerequisite for designing integrated pest management programs. Nevertheless, studies investigating the dispersal of small insects in natural conditions remain scarce mainly because of the difficulty of tracking the movements of these organisms. Here we propose to use Hierarchical Bayesian Modelling (HBM) framework to gain knowledge on hidden processes that cannot be observed directly in natura, such as insect landing and insect mortality, through the definition of latent variables. An HBM describing crop colonization by winged aphids was fitted to a large dataset of field observations issued from a long term survey at a wide scale of both aerial and field densities of the bird cherry-oat aphid Rhopalosiphum padi. This study provides the first evidence that suction trap data are reliable proxies of aphid colonizing rates in cereal fields in autumn and can be a nice alternative to the very time-consuming crop sampling. The proportion of winged aphids landing in cereal fields is shown to vary between regions according to the degree of investment of local R. padi population in sexual reproduction. Results also indicate that under autumnal field conditions, less than 5% of winged aphids survive more than 10 days after landing. This HBM provides the basis of a predictive model for aphid crop colonization that fully accounts for all sources of uncertainty. It should be of great value to improve the trust of users in any decision making systems.     

River network structure shapes interannual feedbacks between adult sea lamprey migration and larval habitation

Adult sea lampreys (Petromyzon marinus) migrating upstream to spawn follow a pheromone released by instream larvae. The size (i.e. flow) of a tributary dilutes the concentration of this pheromone, such that the downstream propagation pattern of larval pheromone must be influenced by patterns in the relative sizes and numbers of confluent tributaries. We developed an individual-based model to explicitly test the resulting hypothesis that river network structure influences the migration decisions of adult lampreys following the larval pheromone, and in turn the distribution of larvae. First, we initialized the model using randomly generated river networks, and found a strong positive relationship between network diameter and larval aggregation. Larvae aggregated over time, and the degree and rate of this aggregation depended on network diameter. Second, we initialized the model using a river network based on the Muskegon River, Michigan, and compared model-generated larval distribution to available field survey data. We found a significant correlation between model-generated larval abundance and field-measured larval densities (r₂ = 0.54; p < 0.0001). We also found an inverse relationship between subwatershed area and the degree to which path-dependent effects influenced larval abundance in that subwatershed. Our results overall suggest that larval distribution across a watershed results from a system of context-dependent interannual feedbacks shaped by network structure and the past migratory and spawning behavior of adults.     

Estimation of annual potential evapotranspiration at regional scale based on the effect of moisture on soil respiration

Potential evapotranspiration (PET) is an important component of water cycle. For traditional models derived from the principle of aerodynamics and the surface energy balance, its calculation always includes many parameters, such as net radiation, water vapor pressure, air temperature and wind speed. We found that it can be acquired in an easier way in specific regions. In this study, a new PET model (PETP model) derived from two empirical models of soil respiration was evaluated using the Penman-Monteith equation as a standard method. The results indicate that the PETP model estimation concur with the Penman-Monteith equation in sites where annual precipitation ranges from 717.71 mm to 1727.37 mm (R² = 0.68, p = 0.0002), but show large discrepancies in all sites (R² = 0.07, p = 0.1280). Then we applied our PETP model at the global scale to the regions with precipitation higher than 700 mm using 2.5° CMAP data to obtain the annual PET for 2006. As expected, the spatial pattern is satisfactory overall, with the highest PET values distributed in the lower latitudes or coastal regions, and with an average of 1292.60 ± 540.15 mm year⁻¹. This PETP model provides a convenient approach to estimate PET at regional scales.     

Mechanisms of moisture stress in a mid-latitude temperate forest: Implications for feedforward and feedback controls from an irrigation experiment

While it is well established that stomata close during moisture stress, strong correlations among environmental (e.g., vapor pressure deficit, soil moisture, air temperature, radiation) and internal (e.g., leaf water potential, sap flow, root-shoot signaling) variables obscure the identification of causal mechanisms from field experiments. Models of stomatal control fitted to field data therefore suffer from ambiguous parameter identification, with multiple acceptable (i.e., nearly optimal) model structures emphasizing different moisture status indicators and different processes. In an effort to minimize these correlations and improve parameter and process identification, we conducted an irrigation experiment on red maples (Acer rubrum L.) at Harvard Forest (summers of 2005 and 2006). Control and irrigated trees experienced similar radiative and boundary layer forcings, but different soil moisture status, and thus presumably different diurnal cycles of internal leaf water potential. Measured soil moisture and atmospheric forcing were used to drive a transient tree hydraulic model that incorporated a Jarvis-type leaf conductance in a Penman–Monteith framework with a Cowan-type (resistance and capacitance) tree hydraulic representation. The leaf conductance model included dependence on both leaf matric potential, Ψ_L (so-called feedback control) and on vapor pressure deficit, D (so-called feedforward control). Model parameters were estimated by minimizing the error between predicted and measured sap flow. The whole-tree irrigation treatment had the effect of elevating measured transpiration during summer dry-downs, demonstrating the limiting effect that subsurface resistance may have on transpiration during these times of moisture stress. From the best fitted model, we infer that during dry downs, moisture stress manifests itself in an increase of soil resistance with a resulting decrease in Ψ_L, leading to both feedforward and feedback controls in the control trees, but only feedforward control for the irrigated set. Increases in the sum-of-squares error when individual model components were disabled allow us to reject the following three null hypotheses: (1) the f(D) stress is statistically insignificant (p = 0.01); (2) the f(Ψ_L) stress is statistically insignificant (p = 0.07); and (3) plant storage capacitance is independent of moisture status (p = 0.07).     

A population model for the peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae), in a Korean orchard system

A population model for the peach fruit moth, Carposina sasakii Matsumura, was constructed to understand the population dynamics of this pest species and to develop an effective management strategy for various orchard (apple, peach, apple + peach) systems. The model was structured by the five developmental stages of C. sasakii: egg, larva, pupa, larval-cocoon (overwintering larva), and adult. The model consisted of a series of component models: (1) a bimodal spring adult emergence model, (2) an adult oviposition model, (3) stage emergence models of eggs, larvae, and pupae, (4) a larval survival rate model in fruits, (5) a larval-cocoon formation model, and (6) an insecticide effect model. Simulations using the model described the typical patterns of C. sasakii adult abundance in various orchard systems well, and was specific to the composition of host plants: three adult abundance peaks (first peak, mid-season peak, and last peak) a year with decreased peaks after the first peak in monoculture orchards of late apple, two adult peaks a year with a much higher last peak in monoculture orchards of early peach, and three adult peaks a year with much higher later peaks in mixed orchards of late apple and early peach. The average deviation between model outputs and actual records for first and second adult peak dates was 2.8 and 3.9 d, respectively, in simulations without an insecticide effect. The deviation decreased when insecticide effects were incorporated into the model. We also performed a sensitivity analysis of our model, and suggest possible applications of the model.     

Batrachochytrium dendrobatidis and the Collapse of Anuran Species Richness and Abundance in the Upper Manu National Park,Southeastern Peru

Abstract: Amphibians are declining worldwide, but these declines have been particularly dramatic in tropical mountains, where high endemism and vulnerability to an introduced fungal pathogen, Batrachochytrium dendrobatidis (Bd), is associated with amphibian extinctions. We surveyed frogs in the Peruvian Andes in montane forests along a steep elevational gradient (1200–3700 m). We used visual encounter surveys to sample stream‐dwelling and arboreal species and leaf‐litter plots to sample terrestrial‐breeding species. We compared species richness and abundance among the wet seasons of 1999, 2008, and 2009. Despite similar sampling effort among years, the number of species (46 in 1999) declined by 47% between 1999 and 2008 and by 38% between 1999 and 2009. When we combined the number of species we found in 2008 and 2009, the decline from 1999 was 36%. Declines of stream‐dwelling and arboreal species (a reduction in species richness of 55%) were much greater than declines of terrestrial‐breeding species (reduction of 20% in 2008 and 24% in 2009). Similarly, abundances of stream‐dwelling and arboreal frogs were lower in the combined 2008–2009 period than in 1999, whereas densities of frogs in leaf‐litter plots did not differ among survey years. These declines may be associated with the infection of frogs with Bd. B. dendrobatidis prevalence correlated significantly with the proportion of species that were absent from the 2008 and 2009 surveys along the elevational gradient. Our results suggest Bd may have arrived at the site between 1999 and 2007, which is consistent with the hypothesis that this pathogen is spreading in epidemic waves along the Andean cordilleras. Our results also indicate a rapid decline of frog species richness and abundance in our study area, a national park that contains many endemic amphibian species and is high in amphibian species richness.     

Multi-metric evaluation of the models WARM,CropSyst, and WOFOST for rice

WARM (Water Accounting Rice Model) simulates paddy rice (Oryza sativa L.), based on temperature-driven development and radiation-driven crop growth. It also simulates: biomass partitioning, floodwater effect on temperature, spikelet sterility, floodwater and chemicals management, and soil hydrology. Biomass estimates from WARM were evaluated and compared with the ones from two generic crop models (CropSyst, WOFOST). The test-area was the Po Valley (Italy). Data collected at six sites from 1989 to 2004 from rice crops grown under flooded and non-limiting conditions were split into a calibration (to estimate some model parameters) and a validation set. For model evaluation, a fuzzy-logic based multiple-metrics indicator (MQI) was used: 0 (best) ≤ MQI ≤ 1 (worst). WARM estimates compared well with the actual data (mean MQI = 0.037 against 0.167 and 0.173 with CropSyst and WOFOST, respectively). On an average, the three models performed similarly for individual validation metrics such as modelling efficiency (EF > 0.90) and correlation coefficient (R > 0.98). WARM performed best in a weighed measure of the Akaike Information Criterion: (worst) 0<wk<1$0<w_k<1$ (best), considering estimation accuracy and number of parameters required to achieve it (mean wk=0.983$w_k=0.983$ against 0.007 and ∼0.000 with CropSyst and WOFOST, respectively). WARM results were sensitive to 30% of the model parameters (ratio being lower with both CropSyst, <10%, and WOFOST, <20%), but appeared the easiest model to use because of the lowest number of crop parameters required (10 against 15 and 34 with CropSyst and WOFOST, respectively). This study provides a concrete example of the possibilities offered using a range of assessment metrics to evaluate model estimates, predictive capabilities, and complexity.     

Mating effort and space use of an alpine ungulate during the rut

In ungulates, the rut generally leads to increased intra and interpopulation movements for males. Because movements induce energetic costs and missed feeding opportunities, they could be an indication of male mating effort. We studied space use of 44 male mountain goats (Oreamnos americanus) from three neighboring subpopulations in southeast Alaska, during the rut from 2005 to 2008. Using mixed models and an information theoretic approach with AIC, we analyzed the relationships between individual traits of males and their space use. We found no indication of breeding migration between subpopulations. Distances between individual seasonal ranges were not related to any individual trait. Daily movements, home range sizes, and total distance traveled during the rut did not vary with mass or age of individuals. As such, effects of individual traits on male space use during the rut appear weak and observed space use patterns do not support any of the main mating effort hypotheses.     

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.     

Local calibration of coliforms parameters of water quality problem at Igapó I Lake, Londrina, Paraná, Brazil

This article presents results concerning the local calibration of the transport parameters (longitudinal and transversal diffusions and decay coefficient) for a two-dimensional problem of water quality at Igapó I Lake, located in Londrina, Paraná, Brazil, using fecal coliforms as an indicator of water quality. The simulation of fecal coliforms concentrations all over the water body is conducted by means of a structured discretization of the geometry of Igapó I Lake, together with the finite difference and finite element methods. By using the velocity field, modeled by the Navier-Stokes and Poisson equations, the flow of fecal coliforms is described by means of a transport model, which considers advective and diffusive processes, as well as a process of fecal coliforms decay. In the checkpoint, the longitudinal and transversal diffusion coefficients and the coliforms decay coefficient that best fitted the value of the fecal coliforms concentration were D_x = D_y = 0.001 m²/h and k = 0.5 d⁻¹ = 0.02083 h⁻¹. A qualitative and quantitative analysis of the numerical simulations conducted in function of the diffusion coefficients and of the coliforms decay parameter provided a better understanding of the local water quality at Igapó I Lake.     

Equivalence of the realized input and output oriented indirect effects metrics in Ecological Network Analysis

A new understanding of the consequences of how ecosystem elements are interconnected is emerging from the development and application of Ecological Network Analysis. The relative importance of indirect effects is central to this understanding, and the ratio of indirect flow to direct flow (I/D) is one indicator of their importance. Two methods have been proposed for calculating this indicator. The unit approach shows what would happen if each system member had a unit input or output, while the realized technique determines the ratio using the observed system inputs or outputs. When using the unit method, the input oriented and output oriented ratios can be different, potentially leading to conflicting results. However, we show that the input and output oriented I/D ratios are identical using the realized method when the system is at steady state. This work is a step in the maturation of Ecological Network Analysis that will let it be more readily testable empirically and ultimately more useful for environmental assessment and management.