Estimating growth charts via nonparametric quantile regression: a practical framework with application in ecology

We discuss a practical and effective framework to estimate reference growth charts via regression quantiles. Inequality constraints are used to ensure both monotonicity and non-crossing of the estimated quantile curves and penalized splines are employed to model the nonlinear growth patterns with respect to age. A companion R package is presented and relevant code discussed to favour spreading and application of the proposed methods.     

Application of the quadratic entropy indices for diversity studies of drosophilid assemblages

Most diversity indices widely used in ecology (e.g. the Shannon-Wiener index and the Gini-Simpson index) do not reflect taxonomic or other differences among species. Quadratic entropy, proposed by C.R. Rao (1982), takes these differences into account. The aim of this paper is to demonstrate the application of this diversity index in investigations of drosophilid species diversity. Quadratic entropy and Simpson index values are also compared. The elements of the difference matrix in the quadratic form are taxonomic differences (distances) among the species. The difference is defined by the position of the lowest-ranking taxon containing both species. According to the results, the Gini-Simpson index and the taxonomic quadratic entropy are positively correlated. The observed differences are due to the fact that assemblages with greater taxonomic distances produce greater quadratic entropy. Drosophilid species can be assigned to specific life habit classes, more specifically to resource types. After postulating differences between the types, we used the quadratic entropy measure to analyse resource diversity. These kinds of examinations approximate to an operative association of species diversity and environmental diversity.     

New parameterization scheme for effective indices for emissions from road transport

The local to regional processes of chemical transformations, washout and dry deposition cannot be directly resolved in global scale models, they rather need to be parameterized. A suitable way to account for the non-linearity, e.g., in chemical transformation processes, is the use of effective emission indices (EEIs). EEI translate the actual (small scale) emissions into input for global scale models, partially accounting for unresolved processes occurring shortly after the release of the emissions.The emissions from the road traffic have some specifics, because of which the concept of deriving EEI from the interaction of an instantaneous plume with the ambient air is perhaps not so convenient. A new parameterization scheme for the EEI from the road transport is suggested in the present paper, based on few simplifying assumptions and introducing the adjoin equations approach, which makes it possible to achieve unified, not depending on the specific emission pattern, procedure for calculating the EEI from road traffic.     

Assessing landscape values: a proposal for a multidimensional conceptual model

To evaluate a specific form of resource management, for example, the maintenance of valuable cultural landscapes, the contributions of many different viewpoints must be considered. In this paper, a model for assessing and integrating the different aspects contributing to landscape evaluation is proposed. Some results of its use in landscape assessment in the Madrid region (central Spain) are discussed.The model takes into account five assessment dimensions which are considered to be independent—the ecological, productive, economic, social and cultural evaluative systems and it recognises and assumes conflicts and trade-offs between these components. The inclusion of the production system as an independent assessment dimension is original and is justified because it is the link that connects the ecological and economic systems. Since this dimension acts most directly on the ecosystem, the production system includes the attribute of ecological or strong (in the sense of [For the Common Good, Beacon Press, Boston, 1994]) sustainability.The evaluation method places special emphasis on defining a conceptual framework, and from this defines scenarios in comparison with which particular development models (landscape planning, resources management) can be evaluated. Seven scenarios, coming from a hypothetical, traditional sustainable scenario of resources management, are defined. One of these, the sound sustainable scenario, is defended as the only one viable in the long term, particularly in developing countries.This method was employed to evaluate the agricultural and natural landscape of the Madrid region municipalities. The multivariate approach adopted was based on the selection of indicator sets for each evaluative dimension. The structure of relationships among indicators was then analysed separately for each dimension and values assigned to the municipalities according to their position on the main axes of the multivariate analyses. Each municipality was assigned to one of the seven development scenarios by means of discriminant analysis. The approach’s greatest assets are its flexibility in the selection of the indicators and the efficacy in its monitoring and comparison of the different analysed cases once a rigorous conceptual framework was established.The paper discusses the conditions for the sustainability of the human activities and provides a method for evaluating and comparing scenarios of resources management.     

Model selection and model averaging in behavioural ecology: the utility of the IT-AIC framework

Behavioural ecologists often study complex systems in which multiple hypotheses could be proposed to explain observed phenomena. For some systems, simple controlled experiments can be employed to reveal part of the complexity; often, however, observational studies that incorporate a multitude of causal factors may be the only (or preferred) avenue of study. We assess the value of recently advocated approaches to inference in both contexts. Specifically, we examine the use of information theoretic (IT) model selection using Akaike’s information criterion (AIC). We find that, for simple analyses, the advantages of switching to an IT-AIC approach are likely to be slight, especially given recent emphasis on biological rather than statistical significance. By contrast, the model selection approach embodied by IT approaches offers significant advantages when applied to problems of more complex causality. Model averaging is an intuitively appealing extension to model selection. However, we were unable to demonstrate consistent improvements in prediction accuracy when using model averaging with IT-AIC; our equivocal results suggest that more research is needed on its utility. We illustrate our arguments with worked examples from behavioural experiments.     

指数施肥对杉木苗期基质中微生物功能多样性的影响

为向轻型基质容器苗合理施肥,实现苗木养分精准调控提供理论依据,以杉木优良无性系"洋061"轻型基质容器苗为研究对象,设置7个施氮处理[对照(CK,0 mg/株)、常规集中施肥处理(CF1,40 mg/株)、常规分次施肥处理(CF,240 mg/株)、指数施肥(EF1,40 mg/株;EF2,80 mg/株;EF3,12...     

玉米免耕秸秆覆盖对土壤微生物群落功能多样性的影响

为了研究免耕对土壤微生物功能多样性的影响,本项试验运用Biolog-ECO检测手段,对连续2年的玉米（Zea mays L.）保护性耕作试验全部秸秆覆盖免耕和常规耕作2种耕作处理的土样进行了土壤微生物功能多样性研究。试验表明：（1）免耕土壤微生物对碳源利用率以及不同碳源利用率高于常规耕作,免耕对总体碳源利用率平均值比常规耕作高53.1%;（2）免耕土壤微生物丰富度指数、多样性指数显著高于常规耕作,免耕微生物群落丰富度指数22.33±0.57,多样性指数3.02±0.04,常规耕作微生物群路丰富度指数14.33±1.15,多样性指数2.56±0.12。免耕秸秆覆盖耕作措施促进了土壤微生物活性、增加土壤微生物数量。     

Random forests for classification in ecology

Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature.     

Landscape constraints on functional diversity of birds and insects in tropical agroecosystems

In this paper, we analyzeatabases on birds and insects to assess patterns of functional diversity in human-dominated landscapes in the tropics. A perspective from developed landscapes is essential for understanding remnant natural ecosystems, because most species experience their surroundings at spatial scales beyond the plot level, and spillover between natural and managed ecosystems is common. Agricultural bird species have greater habitat and diet breadth than forest species. Based on a global data base, bird assemblages in tropical agroforest ecosystems were composed of disproportionately more frugivorous and nectarivorous, but fewer insectivorous bird species compared with forest. Similarly, insect predators of plant-feeding arthropods were more diverse in Ecuadorian agroforest and forest compared with rice and pasture, while, in Indonesia, bee diversity was also higher in forested habitats. Hence, diversity of insectivorous birds and insect predators as well as bee pollinators declined with agricultural transformation. In contrast, with increasing agricultural intensification, avian pollinators and seed dispersers initially increase then decrease in proportion. It is well established that the proximity of agricultural habitats to forests has a strong influence on the functional diversity of agroecosystems. Community similarity is higher among agricultural systems than in natural habitats and higher in simple than in complex landscapes for both birds and insects, so natural communities, low-intensity agriculture, and heterogeneous landscapes appear to be critical in the preservation of beta diversity. We require a better understanding of the relative role of landscape composition and the spatial configuration of landscape elements in affecting spillover of functionally important species across managed and natural habitats. This is important for data-based management of tropical human-dominated landscapes sustaining the capacity of communities to reorganize after disturbance and to ensure ecological functioning.     

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.     

Towards a co-evolutionary framework for implementing sustainable development

SUMMARY

A quantitative method which can be used to gauge the sustainability of existing socio-cultural, economic and environmental constructs is proposed. An underlying assumption of the approach is that a co-evolutionary relationship exists between social, cultural, economic and environmental systems and that these cannot be addressed in a reductionist and deterministic manner. The method focuses on both broad trends and patterns of variance in a multivariate data matrix, it allows the identification of dominant trends as well as underlying tensions, does not treat socio-cultural, economic and environmental heterogeneity as statistical noise and can be applied at different administrative scales. Furthermore, it may be used to identify potential sources of human insecurity, factors that may affect the probability of positive human survival, developmental patterns at odds with the established values system of civil society that can be targeted for political action, and to inform public debate. In addition, the method can be used to identify unexpected synergies between variables and may serve as an early warning system for regional planners.     

Using information theory as a substitute for stepwise regression in ecology and behavior

In ecological and behavioral research, drawing reliable conclusions from statistical models with multiple predictors is usually difficult if all predictors are simultaneously in the model. The traditional way of handling multiple predictors has been the use of threshold-based removal-introduction algorithms, that is, stepwise regression, which currently receives considerable criticism. A more recent and increasingly propagated modelling method for multiple predictors is the information theoretic (IT) approach that quantifies the relative suitability of multiple, potentially non-nested models based on a balance of model fit and the accuracy of estimates. Here, we examine three shortcomings of stepwise regression, subjective critical values, model uncertainty, and parameter estimation bias, which have been suggested to be avoided by applying information theory. We argue that, in certain circumstances, the IT approach may be sensitive to these issues as well. We point to areas where further testing and development could enhance the performance of IT methods and ultimately lead to robust inferences in behavioral ecology.     

Oxygen microoptodes: a new tool for oxygen measurements in aquatic animal ecology

We describe two applications of a recently introduced system for very precise, continuous measurement of water oxygen saturation. Oxygen microoptodes (based on the dynamic fluorescence quenching principle) with a tip diameter of ~50 µm, an eight-channel optode array, an intermittent flow system, and online data registration were used to perform two types of experiments. The metabolic activity of Antarctic invertebrates (sponges and scallops) was estimated in respiration experiments, and, secondly, oxygen saturation inside living sponge tissue was determined in different flow regimes. Even in long-term experiments (several days) no drift was detectable in between calibrations. Data obtained were in excellent correspondence with control measurements performed with a modified Winkler method. Antarctic invertebrates in our study showed low oxygen consumption rates, ranging from 0.03-0.19 cm³ O₂ h^-1 ind.^-1. Oxygen saturation inside living sponge specimens was affected by flow regime and culturing conditions of sponges. Our results suggest that oxygen optodes are a reliable tool for oxygen measurements beyond the methodological limits of traditional methods.     

Towards a common Mediterranean framework for beach nourishment projects

Integrated Coastal Zone Management as a strategy for achieving conservation and sustainable multiple use of the coastal zone includes various types of management initiatives. Due to natural phenomena such as tides and winds and to social and economic activities, coastal areas undergo transformation. Coastal erosion and the disappearance of beaches as a result of wrong planning decisions and lack of effective legislation are among the most damaging effects and to reverse them requires application of a series of engineering techniques. Beach nourishment projects as a way towards shore protection and utilization through recreational purposes in the Spanish and Italian coasts are noteworthy in this respect. In beach nourishment projects, the roles of various entities, both public and private, should be clearly indicated and in the evaluation and execution stage a series of questions should be answered for the successful completion of any nourishment project. Past projects in the Mediterranean and experiences from recent Italian projects in Anzio and Nettuno confirm this. For example, dredging of the entrance channel of the port of Anzio enabled middle-sized ferryboats once again to enter the port (which had not been possible before). This will in turn increase the tourism potential of the town. Nourishment of two beaches at these sites prevented further erosion and provided more area for recreational purposes. Expected economic contribution of beach nourishments to the regional authority was estimated for Nettuno and Anzio; the resulting theoretical payback period was found to be 3 yr for the former and 15 yr for the latter.     

Estimation methods for nonlinear state-space models in ecology

The use of nonlinear state-space models for analyzing ecological systems is increasing. A wide range of estimation methods for such models are available to ecologists, however it is not always clear, which is the appropriate method to choose. To this end, three approaches to estimation in the theta logistic model for population dynamics were benchmarked by Wang (2007). Similarly, we examine and compare the estimation performance of three alternative methods using simulated data. The first approach is to partition the state-space into a finite number of states and formulate the problem as a hidden Markov model (HMM). The second method uses the mixed effects modeling and fast numerical integration framework of the AD Model Builder (ADMB) open-source software. The third alternative is to use the popular Bayesian framework of BUGS. The study showed that state and parameter estimation performance for all three methods was largely identical, however with BUGS providing overall wider credible intervals for parameters than HMM and ADMB confidence intervals.     

Comparative feeding ecology of felids in a neotropical rainforest

Summary Diet and habitat use of jaguar, puma, and ocelot, and populations of their mammalian prey, were studied in an undisturbed rainforest in southeastern Peru. Analysis of scats (feces) showed terrestrial mammals to be the chief prey of all three felids, but reptiles and birds were also numerically important in the diets of ocelot and jaguar. Prey diversity is high and the cats evidently take any readily captured vertebrate. For major terrestrial mammal prey of felids, density, biomass, prey/predator ratios, and annual offtake from the study area are estimated. All three cat species seem to hunt by opportunistic encounter of prey. Most mammalian prey species were taken in about the ratios of occurrence, but peccaries were taken by jaguar more often than expected. Most prey of jaguar have a body weight of >1 kg, those of ocelot, 1 kg. Jaguar often used waterside habitats, where they captured caiman and river turtles. Puma did not use these habitats or resources, although the puma prey sample was too small for much inference. The possible effects of felids on study area prey populations are discussed. Large and small cats partition prey at the body weight region where prey switches from low to high reproductive rates.     

The ecology,discharge diversity and predatory behaviour of gymnotiforme electric fish in the coastal streams of French Guiana

Summary 1. A survey of the species distribution, discharge characteristics, ecology and behaviour of South American Gymnotiforme electric fish was carried out during two field trips to sites in the vicinity of Kourou, French Guiana, in 1983 and 1985. 2. Measurements of water conditions, collected over a twelve month period, highlight the strong ecological pressure on species exploiting the rapidly fluctuating and often temporary coastal streams. Adaptation of the reproductive cycle to the rainy seasons is particularly marked and the possible zeitgebers are considered. Given the almost invariant water conductivity, its suggested use as an environmental trigger is rejected in favour of acoustic or mechanical cues. 3. The two main study areas were inhabited principally by pulse gymnotoids of the genera Gymnotus and Hypopomus. A new Hypopomus species was discovered as well as specimens of G. pantherinus, previously undescribed in French Guiana. Larvae of H. beevei were found prior to the start of the 1985 rainy season. Developmental data for this species are presented which support the view that, as in other weakly electric gymnotoids, a primitive larval electric organ probably precedes the adult structure. The larval discharge also strongly resembles that of the adult electric eel, lending weight to published theories of an Electrophorus-like ancestor to the wekly electric fish. 4. The predatory behaviour of the strongly electric eel was recorded in detail. The field results indicated that this species preyed on weakly electric fish whose responses to the foraging eel are also reported. The probable use of electrical cues by hunting eels was further investigated in a laboratory experiment in which predatory responses were compared in the presence of non-electric and electric live prey, and models mimicking electric prey. It is concluded that electrical cues are probably of paramount importance in the eel's normal prey capture behaviour.     

Nonparametric conditional density estimation in a deep learning framework for short-term forecasting

Environmental and Ecological Statistics - Short-term forecasting is an important tool in understanding environmental processes. In this paper, we incorporate machine learning algorithms into a...     

Connectivity for conservation: a framework to classify network measures

Graph theory, network theory, and circuit theory are increasingly being used to quantify multiple aspects of habitat connectivity and protected areas. There has been an explosive proliferation of network (connectivity) measures, resulting in over 60 measures for ecologists to now choose from. Conceptual clarification on the ecological meaning of these network measures and their interrelationships is overdue. We present a framework that categorizes network measures based on the connectivity property that they quantify (i.e., route-specific flux, route redundancy, route vulnerability, and connected habitat area) and the structural level of the habitat network to which they apply. The framework reveals a lack of network measures in the categories of "route-specific flux among neighboring habitat patches" and "route redundancy at the level of network components." We propose that network motif and path redundancy measures can be developed to fill the gaps in these categories. The value of this framework lies in its ability to inform the selection and application of network measures. Ultimately, it will allow a better comparison among graph, network, and circuit analyses, which will improve the design and management of connected landscapes.