Spatial scale and sampling size affect the concordance between remotely sensed information and plant community discrimination in restoration monitoring

Remote sensing cartography and GIS are part of ordinary practice in restoration ecology in discriminating patches of habitats, defining objectives, and planning the monitoring phase, but derived information is not always consistent with field survey. We assessed the mapping process efficiency in discriminating different communities, relying on plant composition data, and considering the effect of sample size and plot dimension (grain), in a heterogeneous environment in Tuscany (central Italy). We identified four land cover classes on a land cover map produced with object-oriented technique; hence we conducted a sampling of 64 plots (4 zones × 4 classes × 4 plots), estimating vascular plant cover using a point-quadrant method. Plots were nested squares with side lengths of 0.50 m, 1 m and, limited to a sub-sample, 2 m. We evaluated the effect of sample size and grain using permutational multivariate analysis of variance (PERMANOVA), testing the simultaneous response of species composition compared to land cover classes. Results demonstrated that for a sample size of 64 plots, grain does not influence the ability of discriminating among the habitat types investigated, while for a smaller sub-sample the effect of grain is significant and communities cannot be distinguished at all plot dimensions. Outcomes corroborate the hypothesis that sampling at a series of scales of observations and an adequate sample size can improve monitoring efficiency in restoration ecology. Nomenclature: Pignatti (1982) and Conti et al (2005) for Festuca.     

经济学思想和方法在行为生态学中的应用

从经济学观点看,动物的任何一种行为都是一种投资,同时又能获得一定的收益。进化和自然选择将趋于使动物行为的净收益增至最大,这种思想也是组建行为生态学最适模型的基础。如果为海滨蟹提供各种大小不同的贻贝任其选食的话,那么它所选食的贻贝大小往往能使它得到最大的能量净收益。为了精确地计算捕食者应当吃多少不同大小的食物,就需要建立一个最适模型。当动物领域行为的收益大于投资时,自然选择就会促进这种行为的产生和发展,而最佳领域大小则可借助于建立经济模型进行预测。将饥饿风险降至最小的原则可应用于动物的觅食决策。绒斑啄木鸟在觅食时可利用它们所收集的信息使其食物摄取率达到最大。     

Wise use of statistical tools in ecological field studies

The currently dominating hypothetico-deductive research paradigm for ecology has statistical hypothesis testing as a basic element. Classic statistical hypothesis testing does, however, present the ecologist with two fundamental dilemmas when field data are to be analyzed: (1) that the statistically motivated demand for a random and representative sample and the ecologically motivated demand for representation of variation in the study area cannot be fully met at the same time; and (2) that the statistically motivated demand for independence of errors calls for sampling distances that exceed the scales of relevant pattern-generating processes, so that samples with statistically desirable properties will be ecologically irrelevant. Reasons for these dilemmas are explained by consideration of the classic statistical Neyman-Pearson test procedure, properties of ecological variables, properties of sampling designs, interactions between properties of the ecological variables and properties of sampling designs, and specific assumptions of the statistical methods. Analytic solutions to problems underlying the dilemmas are briefly reviewed. I conclude that several important research objectives cannot be approached without subjective elements in sampling designs. I argue that a research strategy entirely based on rigorous statistical testing of hypotheses is insufficient for field ecological data and that inductive and deductive approaches are complementary in the process of building ecological knowledge. I recommend that great care is taken when statistical tests are applied to ecological field data. Use of less formal modelling approaches is recommended for cases when formal testing is not strictly needed. Sets of recommendations, “Guidelines for wise use of statistical tools”, are proposed both for testing and for modelling. Important elements of wise-use guidelines are parallel use of methods that preferably belong to different methodologies, selection of methods with few and less rigorous assumptions, conservative interpretation of results, and abandonment of definitive decisions based a predefined significance level.     

Effects of scale on interpreting life-history characteristics of ungulates and carnivores

Many life-history characteristics of large mammals are scale sensitive. We provide examples where varying temporal and spatial scales can affect interpretation of data concerning life-history characteristics in large herbivores and carnivores and offer recommendations for selecting the most appropriate sampling scale or scales. We also document that some animals make decisions concerning their spatial distribution at scales well beyond the size of the home range. Conversely, other decisions involving sexual segregation of sexes, or where to give birth, may be made at scales below the level of the habitat patch. Such differences in behaviour affect our understanding of habitat selection in large herbivores, and interpreting tradeoffs between acquiring essential resources and avoiding predators. Moreover, some landscape attributes may be selected at one scale, whereas other characteristics of the environment may be selected at another. We argue that even sophisticated models for explaining the ecology and behaviour of mammals benefit from framing specific hypotheses that are related to the to the life-history characteristics of those animals. We also believe that the failure to consider and select the most appropriate scale, or suite of scales, may lead to the mismanagement of critical natural resources. We forge relationships among scale, life-history characteristics of mammals, and biodiversity. Finally, we synthesize the literature on scale for large mammals and make recommendations for future research.     

Selecting Species for Passive and Active Riparian Restoration in Southern Mexico

In revegetation projects, distinguishing species that can be passively restored by natural regeneration from those requiring active restoration is not a trivial decision. We quantified tree species dominance (measured by an importance value index, IVI_i) and used abundance–size correlations to select those species suitable for passive and/or active restoration of disturbed riparian vegetation in the Lacandonia region, Southern Mexico. We sampled riparian vegetation in a 50 × 10–m transect in each of six reference (RE) and five disturbed (DE) riparian ecosystems. Those species representing more than 50% of total IVI in each ecosystem were selected, and Spearman rank correlation between abundance and diameter classes was calculated. For eight species, it was determined that passive restoration could be sufficient for their establishment. Another eight species could be transplanted by means of active restoration. Five species regenerate well in only one ecosystem type, suggesting that both restoration strategies could be used depending on the degree of degradation. Finally, two species were determined to not be suitable for restoration in the RE (based on the above selection criteria) and were not selected during this initial stage of our restoration project. The high number of tree species found in the RE suggests that the species pool for ecological restoration is large. However, sampling in both ecosystem types helped us reduce the number of species that requires active restoration. Restoration objectives must guide the selection of which methods to implement; in different conditions, other criteria such as dispersal syndrome or social value could be considered in the species selection.     

Census data aggregation decisions can affect population‐level inference in heterogeneous populations

1. Conservation and population management decisions often rely on population models parameterized using census data. However, the sampling regime, precision, sample size, and methods used to collect census data are usually heterogeneous in time and space. Decisions about how to derive population‐wide estimates from this patchwork of data are complicated and may bias estimated population dynamics, with important implications for subsequent management decisions.
2. Here, we explore the impact of site selection and data aggregation decisions on pup survival estimates, and downstream estimates derived from parameterized matrix population models (MPMs), using a long‐term dataset on grey seal (Halichoerus grypus) pup survival from southwestern Wales. The spatiotemporal and methodological heterogeneity of the data are fairly typical for ecological census data and it is, therefore, a good model to address this topic.
3. Data were collected from 46 sampling locations (sites) over 25 years, and we explore the impact of data handling decisions by varying how years and sampling locations are combined to parameterize pup survival in population‐level MPMs. We focus on pup survival because abundant high‐quality data are available on this developmental stage.
4. We found that survival probability was highly variable with most variation being at the site level, and poorly correlated among sampling sites. This variation could generate marked differences in predicted population dynamics depending on sampling strategy. The sample size required for a confident survival estimate also varied markedly geographically.
5. We conclude that for populations with highly variable vital rates among sub‐populations, site selection and data aggregation methods are important. In particular, including peripheral or less frequently used areas can introduce substantial variation into population estimates. This is likely to be context‐dependent, but these choices, including the use of appropriate weights when summarizing across sampling areas, should be explored to ensure that management actions are successful.

     

Individual‐based ecology of coastal birds

Conservation objectives for non‐breeding coastal birds (shorebirds and wildfowl) are determined from their population size at coastal sites. To advise coastal managers, models must predict quantitatively the effects of environmental change on population size or the demographic rates (mortality and reproduction) that determine it. As habitat association models and depletion models are not able to do this, we developed an approach that has produced such predictions thereby enabling policy makers to make evidence‐based decisions. Our conceptual framework is individual‐based ecology, in which populations are viewed as having properties (e.g. size) that arise from the traits (e.g. behaviour, physiology) and interactions of their constituent individuals. The link between individuals and populations is made through individual‐based models (IBMs) that follow the fitness‐maximising decisions of individuals and predict population‐level consequences (e.g. mortality rate) from the fates of these individuals. Our first IBM was for oystercatchers Haematopus ostralegus and accurately predicted their density‐dependent mortality. Subsequently, IBMs were developed for several shorebird and wildfowl species at several European sites, and were shown to predict accurately overwinter mortality, and the foraging behaviour from which predictions are derived. They have been used to predict the effect on survival in coastal birds of sea level rise, habitat loss, wind farm development, shellfishing and human disturbance. This review emphasises the wider applicability of the approach, and identifies other systems to which it could be applied. We view the IBM approach as a very useful contribution to the general problem of how to advance ecology to the point where we can routinely make meaningful predictions of how populations respond to environmental change.     

Making decisions about the optimal selection environment using Gibbs sampling

The use of Gibbs sampling in making decisions about the optimal selection environment was demonstrated. Marginal posterior distributions of the efficiency of selection across sites were obtained using the Gibbs sampler, a Bayesian method, from which the probability that the efficiency of selection lay between specified values and the variance of the distribution were computed, providing a lot of information on which to make decisions regarding the location of genetic tests. The heritability, genetic correlations and efficiencies of selection estimated using REML and Gibbs sampling were similar. However, the latter approach showed that the point estimates of the efficiencies of selection were subject to substantial error. The decision regarding selection at maturity was consistent with that obtained using point estimates from REML, but Gibbs sampling allowed the efficiencies of selection to be interpreted with more confidence. The decision regarding early selection differed from that based on REML point estimates. Generally, the decisions to make early selections at site B for planting at both site B and A, and to make selections at maturity at each individual site, were robust to different priors in the Gibbs sampling. Received: 19 June 2000 / Accepted: 18 October 2000     

On the estimation of species richness based on the accumulation of previously unrecorded species

Estimation of species richness of local communities has become an important topic in community ecology and monitoring. Investigators can seldom enumerate all the species present in the area of interest during sampling sessions. If the location of interest is sampled repeatedly within a short time period, the number of new species recorded is typically largest in the initial sample and decreases as sampling proceeds, but new species may be detected if sampling sessions are added. The question is how to estimate the total number of species. The data collected by sampling the area of interest repeatedly can be used to build species accumulation curves: the cumulative number of species recorded as a function of the number of sampling sessions (which we refer to as “species accumulation data”). A classic approach used to compute total species richness is to fit curves to the data on species accumulation with sampling effort. This approach does not rest on direct estimation of the probability of detecting species during sampling sessions and has no underlying basis regarding the sampling process that gave rise to the data. Here we recommend a probabilistic, nonparametric estimator for species richness for use with species accumulation data. We use estimators of population size that were developed for capture‐recapture data, but that can be used to estimate the size of species assemblages using species accumulation data. Models of detection probability account for the underlying sampling process. They permit variation in detection probability among species. We illustrate this approach using data from the North American Breeding Bird Survey (BBS). We describe other situations where species accumulation data are collected under different designs (e.g., over longer periods of time, or over spatial replicates) and that lend themselves to of use capture‐recapture models for estimating the size of the community of interest. We discuss the assumptions and interpretations corresponding to each situation.     

A class of models of selectively neutral alleles

Using exchangeability as a statistical analog of neutrality, we derive a generalized sampling distribution for neutral alleles. The distribution depends upon a parameter that determines the underlying marginal distribution of the number of copies of a neutral allele and that can range from zero to infinity. The sampling model of Ewens (1972) is a special case characterized by an extreme value (0) of this parameter. Two other special cases are considered, one of which seems to be applicable to populations with a structure like that of the Yanomama Indians of South America. We then investigate the expected frequency spectra under these three special cases and discover that all three models yield a broad range of possible spectra with overlap between the special cases. We finally show that Ewens' sampling model cannot be used to construct tests of neutrality versus selection tending to maintain polymorphisms, but it can be used to construct tests of directional selection versus neutrality plus selection tending to yield polymorphic states.     

Population consequences of reproductive decisions

Behaviour can be a key component of animal population ecology yet the population consequences of behavioural decisions are poorly understood. We conducted a behavioural and demographic study of the bitterling Rhodeus sericeus, a freshwater fish that spawns in live unionid mussels. We used a population model incorporating game theory decisions and measurements of demographic parameters in order to provide predictions of population size among 13 populations of this fish. Our model predicted that the observed behavioural spawning decisions, while maximizing individual fitness, cause a significant 6% reduction in population size compared with randomly distributed spawnings. We discuss our findings in the context of the population consequences of adaptive behaviour.     

Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long‐term studies. Non‐invasive marking techniques are especially important in fishes of the Family Syngnathidae (pipefishes, seahorses and seadragons), as many of these taxa are of conservation concern or used extensively in studies of sexual selection. Here, we assessed the reliability of natural markings as a character for individual identification in a wild population of Nerophis lumbriciformis by comparing results from natural markings to individual genetic assignments based on eight novel microsatellite loci. We also established a minimally invasive method based on epithelial cell swabbing to sample DNA. All pipefish used in the validation of natural markings, independently of sex or time between recaptures, were individually recognized through facial colouration patterns. Their identities were verified by the observation of the same multilocus genotype at every sampling event for each individual that was identified on the basis of natural markings. Successful recaptures of previously swabbed pipefish indicated that this process probably did not induce an elevated rate of mortality. Also, the recapture of newly pregnant males showed that swabbing did not affect reproductive behaviour.     

Comparison of two methods for sampling invertebrates: vacuum and sweep‐net sampling

ABSTRACT With numerous invertebrate sampling techniques available, deciding which technique to use under certain circumstances may be difficult. Many researchers interested in invertebrate abundance and availability relative to the foraging ecology of birds may use a technique (e.g., vacuum sampling or sweep‐netting) without understanding the impacts their choice may have on the samples collected and the ability of the method to meet research objectives. We compared the characteristics, including overall biomass, morphospecies richness, average size, diversity, and body length categories, of invertebrates collected using a sweep‐net and a Dietrick vacuum sampler along paired transects in Woodward County, Oklahoma, from May to July 2007 and 2008. These sampling techniques differed in the taxa collected, with the orders Diptera, Homoptera, and Hymenoptera dominating vacuum samples and the orders Homoptera, Orthoptera, and Araneae dominating sweep‐net samples. Although morphospecies richness was similar for the two techniques, the mean size of invertebrates collected and overall invertebrate biomass were greater for sweep‐netting than vacuum sampling. Vacuum sampling was more effective at collecting small (e.g., <5 cm) invertebrates, whereas sweep‐netting captured large (>5 cm) Orthopteran and Lepidopteran larvae at higher rates. Thus, our results indicate that neither sampling method effectively sampled all invertebrate families and investigators should be aware of the potential biases of different sampling techniques and be certain that the technique selected will allow study objectives to be met.     

High evolutionary constraints limited adaptive responses to past climate changes in toad skulls

Interactions among traits that build a complex structure may be represented as genetic covariation and correlation. Genetic correlations may act as constraints, deflecting the evolutionary response from the direction of natural selection. We investigated the relative importance of drift, selection, and constraints in driving skull divergence in a group of related toad species. The distributional range of these species encompasses very distinct habitats with important climatic differences and the species are primarily distinguished by differences in their skulls. Some parts of the toad skull, such as the snout, may have functional relevance in reproductive ecology, detecting water cues. Thus, we hypothesized that the species skull divergence was driven by natural selection associated with climatic variation. However, given that all species present high correlations among skull traits, our second prediction was of high constraints deflecting the response to selection. We first extracted the main morphological direction that is expected to be subjected to selection by using within- and between-species covariance matrices. We then used evolutionary regressions to investigate whether divergence along this direction is explained by climatic variation between species. We also used quantitative genetics models to test for a role of random drift versus natural selection in skull divergence and to reconstruct selection gradients along species phylogeny. Climatic variables explained high proportions of between-species variation in the most selected axis. However, most evolutionary responses were not in the direction of selection, but aligned with the direction of allometric size, the dimension of highest phenotypic variance in the ancestral population. We conclude that toad species have responded to selection related to climate in their skulls, yet high evolutionary constraints dominated species divergence and may limit species responses to future climate change.     

Habitat specificity and home-range size as attributes of species vulnerability to extinction: a case study using sympatric rattlesnakes

Large home-range size and habitat specificity are two commonly cited ecological attributes that are believed to contribute to species vulnerability. The eastern diamondback rattlesnake Crotalus adamanteus is a declining species that occurs sympatrically with the more abundant canebrake rattlesnake Crotalus horridus in a portion of the south-eastern Coastal Plain, USA. In this study, we use the ecological similarities of the two species as experimental controls to test the role of home-range size and habitat specificity in the imperilment of the eastern diamondback rattlesnake. We used analysis of variance to investigate differences in home-range size between the two species, and home-range selection was modeled as habitat use versus availability with a case control sampling design using logistic regression. We failed to detect differences in home-range size between the two species; therefore, we could not identify home-range size as an attribute contributing to the imperilment of eastern diamondback rattlesnakes. Eastern diamondback rattlesnakes selected pine savannas to a degree that suggests that the species is a habitat specialist. Of the two factors examined, habitat specificity to the imperiled longleaf pine ecosystem may be a significant contributor to the decline of the eastern diamondback rattlesnake.     

Emergent properties of conspecific attraction in fragmented landscapes

Attraction to conspecifics may have wide-ranging implications for habitat selection and metapopulation theory, yet little is known about the process of attraction and its effects relative to other habitat selection strategies. Using individual-based simulations, I investigated the emergent properties of conspecific attraction during habitat selection on survival, fecundity, short-term fitness (survival x fecundity), and distributions in fragmented landscapes. I simulated conspecific attraction during searching and settlement decisions and compared attraction with random, habitat-based (searching for the presence of habitat), and habitat quality sampling strategies (searching for and settling in high-quality habitat). Conspecific attraction during searching or settlement decisions had different consequences for animals: attraction while searching increased survival by decreasing time spent in nonsuitable habitat, whereas attraction during settlement increased fecundity by aggregating animals in high-quality habitats. Habitat-based sampling did not improve fitness over attraction, but directly sampling habitat quality resulted in the highest short-term fitness among strategies. These results suggest that attraction can improve fitness when animals cannot directly assess habitat quality. Interestingly, conspecific attraction influenced distributions by generating patch size effects and weak edge effects, highlighting that attraction is one potential, yet previously unappreciated, mechanism to explain the widespread patterns of animal sensitivity to habitat fragmentation.     

Drought survival and reproduction impose contrasting selection pressures on maximum body size and sexual size dimorphism in a snake, Seminatrix pygaea

The causes and consequences of body size and sexual size dimorphism (SSD) have been central questions in evolutionary ecology. Two, often opposing selective forces are suspected to act on body size in animals: survival selection and reproductive (fecundity and sexual) selection. We have recently identified a system where a small aquatic snake species (Seminatrix pygaea) is capable of surviving severe droughts by aestivating within dried, isolated wetlands. We tested the hypothesis that the lack of aquatic prey during severe droughts would impose significant survivorship pressures on S. pygaea, and that the largest individuals, particularly females, would be most adversely affected by resource limitation. Our findings suggest that both sexes experience selection against large body size during severe drought when prey resources are limited, as nearly all S. pygaea are absent from the largest size classes and maximum body size and SSD are dramatically reduced following drought. Conversely, strong positive correlations between maternal body size and reproductive success in S. pygaea suggest that females experience fecundity selection for large size during non-drought years. Collectively, our study emphasizes the dynamic interplay between selection pressures that act on body size and supports theoretical predictions about the relationship between body size and survivorship in ectotherms under conditions of resource limitation.     

Free and open source geographic information tools for landscape ecology

Geographic Information tools (GI tools) have become an essential component of research in landscape ecology. In this article we review the use of GIS (Geographic Information Systems) and GI tools in landscape ecology, with an emphasis on free and open source software (FOSS) projects. Specifically, we introduce the background and terms related to the free and open source software movement, then compare eight FOSS desktop GIS with proprietary GIS to analyse their utility for landscape ecology research. We also provide a summary of related landscape analysis FOSS applications, and extensions. Our results indicate that (i) all eight GIS provide the basic GIS functionality needed in landscape ecology, (ii) they all facilitate customisation, and (iii) they all provide good support via forums and email lists. Drawbacks that have been identified are related to the fact that most projects are relatively young. This currently affects the size of their user and developer communities, and their ability to include advanced spatial analysis functions and up-to-date documentation. However, we expect these drawbacks to be addressed over time, as systems mature. In general, we see great potential for the use of free and open source desktop GIS in landscape ecology research and advocate concentrated efforts by the landscape ecology community towards a common, customisable and free research platform.     

The ecology of information: an overview on the ecological significance of making informed decisions

Information is characterized as the reduction of uncertainty and by a change in the state of a receiving organism. Thus, organisms can acquire information about their environment that reduces uncertainty and increases their likelihood of choosing a best‐matching strategy. We define the ecology of information as the study of how organisms acquire and use information in decision‐making and its significance for populations, communities, landscapes and ecosystems. As a whole, it encompasses the reception and processing of information, decision‐making, and the ecological consequences of making informed decisions. The first two stages constitute the domains of, e.g. sensory ecology and behavioral ecology. The exploration of the consequences of information use at larger spatial and temporal scales in ecology has lagged behind these other disciplines. In our overview we characterize information, discuss statistical decision theory as a quantitative framework to analyze information and decision‐making, and discuss potential ecological ramifications. Rather than attempt a cursory review of the enormity of the scope of information we highlight information use in development, breeding habitat selection, and interceptive eavesdropping on alarm calls. Through these topics we discuss specific examples of ecological information use and the emerging ecological consequences. We emphasize recurring themes: information is collected from multiple sources, over varying temporal and spatial scales, and in many cases links heterospecifics to one another. We conclude by breaking from specific ecological contexts to explore implications of information as a central organizing principle, including: information webs, information as a component of the niche concept, and information as an ecosystem process. With information having such an enormous reach in ecology we further cast a spotlight on the potential harmful effects of anthropogenic noise and info‐disruption.     

Habitat diversity associated to island size and environmental filtering control the species richness of rock‐savanna plants in neotropical inselbergs

Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island‐like system of 22 French Guianan neotropical inselbergs covered with rock‐savanna. We separated the effects of size (rock‐savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest‐matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small‐scale versus large‐scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock‐savanna vegetation patches, with increasing richness associated with higher rock‐savanna area, while inselberg isolation and forest‐matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial‐habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody‐plant species richness. Inselberg size and environmental filtering both explained the richness of small‐scale and large‐scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large‐scale and negatively for small‐scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.