Experimental verification of ecological niche modeling in a heterogeneous environment

The current range of ecological habitats occupied by a species reflects a combination of the ecological tolerance of the species, dispersal limitation, and competition. Whether the current distribution of a species accurately reflects its niche has important consequences for the role of ecological niche modeling in predicting changes in species ranges as the result of biological invasions and climate change. We employed a detailed data set of species occurrence and spatial variation in biotic and abiotic attributes to model the niche of a native California annual plant, Collinsia sparsiflora. We tested the robustness of our model for both the realized and fundamental niche by planting seeds collected from four populations, representing two ecotypes, into plots that fully represented the five-dimensional niche space described by our model. The model successfully predicted which habitats allowed for C. sparsiflora persistence, but only for one of the two source ecotypes. Our results show that substantial niche divergence has occurred in our sample of four study populations, illustrating the importance of adequately sampling and describing within-species variation in niche modeling.     

Climatic niche divergence or conservatism? Environmental niches and range limits in ecologically similar damselflies

The factors that determine species' range limits are of central interest to biologists. One particularly interesting group comprises odonates (dragonflies and damselflies), which show large differences in secondary sexual traits and respond quickly to climatic factors, but often have minor interspecific niche differences, challenging models of niche-based species coexistence. We quantified the environmental niches at two geographic scales to understand the ecological causes of northern range limits and the coexistence of two congeneric damselflies (Calopteryx splendens and C. virgo). Using environmental niche modeling, we quantified niche divergence first across the whole geographic range in Fennoscandia, and second only in the sympatric part of this range. We found evidence for interspecific divergence along the environmental axes of temperature and precipitation across the northern range in Fennoscandia, suggesting that adaptation to colder and wetter climate might have allowed C. virgo to expand farther north than C. splendens. However, in the sympatric zone in southern Fennoscandia we found only negligible and nonsignificant niche differences. Minor niche differences in sympatry lead to frequent encounters and intense interspecific sexual interactions at the local scale of populations. Nevertheless, niche differences across Fennoscandia suggest that species differences in physiological tolerances limit range expansions northward, and that current and future climate could have large effects on the distributional ranges of these and ecologically similar insects.     

生态修复后九曲湾水库浮游动物优势种演替及生态位特征分析

探究生态修复后九曲湾水库浮游动物优势种生态位特征及主要影响因素,为九曲湾水库及相关饮用水源地水库生态系统的保护、修复提供理论和技术支撑.于生态修复前2014年4月(平稳期)、2014年7月(爆发期),2015—2016年生态修复后12月(枯水期)、4月(平水期)、7月(丰水期)进行数据采集,采用优势度、Levins生态...     

Coexistence of the niche and neutral perspectives in community ecology

The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.     

外来红树植物无瓣海桑的入侵生态特征

无瓣海桑因其具有速生性的特点而被广泛的用于滩涂海岸造林和控制外来杂草互花米草。但是同样作为外来种,无瓣海桑其自身的入侵性及生态风险已经成为近年来研究的一大热点。依据外来种风险评估的侧重点,分别从定居特性、传播特性及其影响等方面总结了国内外无瓣海桑的入侵生态特征的相关研究,表明无瓣海桑具有速生、高生产力、对低温和土壤具有一定的适应性、已在澳门等地出现扩散入侵现象等利于入侵的特点;但是同时它生态位宽度中等,繁殖率较低,并且它的种植会改善红树林生态系统土壤养分,有利于乡土红树植物的生长。现有对无瓣海桑入侵生态特征的定性研究并不能完全确定其入侵性和生态风险。因此今后需采用风险评估模型等手段对无瓣海桑入侵性进行更为深入地评估。     

Forecasting New Zealand Mudsnail invasion range: model comparisons using native and invaded ranges.

Evaluations of the potential distribution of invasive species can increase the efficiency of their management by focusing prevention measures. Generally, ecological models are built using occurrence data from a species' native range to predict the distribution in areas that the species may invade. However, historical and geographical constraints can limit a species' native distribution. Genetic Algorithm for Rule-set Production (GARP), an ecological niche modeling program, was used to predict the potential distribution of the invasive, freshwater New Zealand mudsnail, Potamopyrgus antipodarum, in Australia and North America. We compared the strength of the predictions made by models built with data from the snail's native range in New Zealand to models built with data from the locations invaded by the species. A time-series analysis of the Australian models demonstrated that range-of-invasion data can make better predictions about the potential distribution of invasive species than models built with native range data. Large differences among the model forecasts indicate that uncritical choice of the data set used in training the GARP models can result in misleading predictions. The models predict a large expansion in the range of P. antipodarum in both Australia and North America unless prevention measures are implemented rapidly.     

Rethinking receiver operating characteristic analysis applications in ecological niche modeling

The area under the curve (AUC) of the receiver operating characteristic (ROC) has become a dominant tool in evaluating the accuracy of models predicting distributions of species. ROC has the advantage of being threshold-independent, and as such does not require decisions regarding thresholds of what constitutes a prediction of presence versus a prediction of absence. However, we show that, comparing two ROCs, using the AUC systematically undervalues models that do not provide predictions across the entire spectrum of proportional areas in the study area. Current ROC approaches in ecological niche modeling applications are also inappropriate because the two error components are weighted equally. We recommend a modification of ROC that remedies these problems, using partial-area ROC approaches to provide a firmer foundation for evaluation of predictions from ecological niche models. A worked example demonstrates that models that are evaluated favorably by traditional ROC AUCs are not necessarily the best when niche modeling considerations are incorporated into the design of the test.     

滹沱河流域湿地植被优势种群生态位研究

采用Shannon-Wiener生态位宽度指数和Petraitis生态位重叠指数测定了滹沱河流域湿地植被20个优势种群的生态位宽度和生态位重叠.结果表明,浮叶眼子菜、莎草、藨草等占据较窄的生态位,生态位发生明显特化.苔草、海乳草、黄花蒿、赖草等占据较宽的生态位,生态位泛化比较明显.根据生态位宽度指数将湿地植物分为4个生态类群.在20个优势种群构成的380个种对中,有71个种对间表现出生态位重叠,占整个种对的18.68%.说明优势种群间生态位重叠现象并不普遍,各种群间生态位明显分离,因此不同种群利用资源的方式具有较为显著的差异性.图1表3参15     

Geography and Recovery under the U.S. Endangered Species Act

Abstract: The U.S. Endangered Species Act (ESA) defines an endangered species as one “at risk of extinction throughout all or a significant portion of its range.” The prevailing interpretation of this phrase, which focuses exclusively on the overall viability of listed species without regard to their geographic distribution, has led to development of listing and recovery criteria with fundamental conceptual, legal, and practical shortcomings. The ESA's concept of endangerment is broader than the biological concept of extinction risk in that the “esthetic, ecological, educational, historical, recreational, and scientific” values provided by species are not necessarily furthered by a species mere existence, but rather by a species presence across much of its former range. The concept of “significant portion of range” thus implies an additional geographic component to recovery that may enhance viability, but also offers independent benefits that Congress intended the act to achieve. Although the ESA differs from other major endangered‐species protection laws because it acknowledges the distinct contribution of geography to recovery, it resembles the “representation, resiliency, and redundancy” conservation‐planning framework commonly referenced in recovery plans. To address representation, listing and recovery standards should consider not only what proportion of its former range a species inhabits, but the types of habitats a species occupies and the ecological role it plays there. Recovery planning for formerly widely distributed species (e.g., the gray wolf [Canis lupus]) exemplifies how the geographic component implicit in the ESA's definition of endangerment should be considered in determining recovery goals through identification of ecologically significant types or niche variation within the extent of listed species, subspecies, or “distinct population segments.” By linking listing and recovery standards to niche and ecosystem concepts, the concept of ecologically significant type offers a scientific framework that promotes more coherent dialogue concerning the societal decisions surrounding recovery of endangered species.     

中国生物入侵的生态分布

生物入侵已被列为当今世界最为棘手的三大环境难题(生物入侵、全球气候变化和生境破坏)之一。文章阐述了我国生物入侵的现状，以时间和地理区域为尺度，初步探讨了生物入侵的生态分布特征。指出其特征是：生物入侵对生物多样性造成重大影响，入侵生物的数量逐年增加，具有时间动态性；生物入侵的分布具有纬度地带性规律，纬度越低生物入侵的现象越严重；入侵生物的数量具有地理区域性。     

Native ecotypic variation and the role of host identity in the spread of an invasive herbivore, Cactoblastis cactorum

Environmental niche models (ENMs) have gained enormous popularity as tools to investigate potential changes in species distributions resulting from climate change and species introductions. Despite recognition that species interactions can influence the dynamics of invasion spread, most implementations of ENMs focus on abiotic factors as the sole predictors of potential range limits. Implicit in this approach is the assumption that biotic interactions are relatively unimportant, either because of scaling issues, or because fundamental and realized niches are equivalent in a species' native range. When species are introduced into exotic landscapes, changes in biotic interactions relative to the native range can lead to occupation of different regions of niche space and apparent shifts in physiological tolerances. We use an escaped biological control organism, Cactoblastis cactorum (Berg.), to assess the role of the environmental envelope as compared with patterns of host-herbivore associations based on collections made in the native range. Because all nonnative populations are derived from a single C. cactorum ecotype, we hypothesize that biotic interactions associated with this ecotype are driving the species' invasion dynamics. Environmental niche models constructed from known native populations perform poorly in predicting nonnative distributions of this species, except where there is an overlap in niche space. In contrast, genetic isolation in the native range is concordant with the observed pattern of host use, and strong host association has been noted in nonnative landscapes. Our results support the hypothesis that the apparent shift in niche space from the native to the exotic ranges results from a shift in biotic interactions, and demonstrate the importance of considering biotic interactions in assessing the risk of future spread for species whose native range is highly constrained by biotic interactions.     

Building statistical models to analyze species distributions.

Models of the geographic distributions of species have wide application in ecology. But the nonspatial, single-level, regression models that ecologists have often employed do not deal with problems of irregular sampling intensity or spatial dependence, and do not adequately quantify uncertainty. We show here how to build statistical models that can handle these features of spatial prediction and provide richer, more powerful inference about species niche relations, distributions, and the effects of human disturbance. We begin with a familiar generalized linear model and build in additional features, including spatial random effects and hierarchical levels. Since these models are fully specified statistical models, we show that it is possible to add complexity without sacrificing interpretability. This step-by-step approach, together with attached code that implements a simple, spatially explicit, regression model, is structured to facilitate self-teaching. All models are developed in a Bayesian framework. We assess the performance of the models by using them to predict the distributions of two plant species (Proteaceae) from South Africa's Cape Floristic Region. We demonstrate that making distribution models spatially explicit can be essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results. Adding hierarchical levels to the models has further advantages in allowing human transformation of the landscape to be taken into account, as well as additional features of the sampling process.     

Stakeholder participation in management of invasive vertebrates

Stakeholders are increasingly involved in species conservation. We sought to understand what features of a participatory conservation program are associated with its ecological and social outcomes. We conducted a case study of the management of invasive vertebrates in Australia. Invasive vertebrates are a substantial threat to Australia's native species, and stakeholder participation in their management is often necessary for their control. First, we identified potential influences on the ecological and social outcomes of species conservation programs from the literature. We used this information to devise an interview questionnaire, which we administered to managers of 34 participatory invasive-vertebrate programs. Effects of invasive species were related to program initiator (agency or citizen), reasons for use of a participatory approach, and stakeholder composition. Program initiator was also related to the participation methods used, level of governance (i.e., governed by an agency or citizens), changes in stakeholder interactions, and changes in abundance of invasive species. Ecological and social outcomes were related to changes in abundance of invasive species and stakeholder satisfaction. We identified relations between changes in the number of participants, stakeholder satisfaction, and occurrence of conflict. Potential ways to achieve ecological and social goals include provision of governmental support (e.g., funding) to stakeholders and minimization of gaps in representation of stakeholder groups or individuals to, for example, increase conflict mitigation. Our findings provide guidance for increasing the probability of achieving ecological and social objectives in management of invasive vertebrates and may be applicable to other participatory conservation programs.     

E‐commerce trade in invasive plants

Biological invasions are a major concern in conservation, especially because global transport of species is still increasing rapidly. Conservationists hope to anticipate and thus prevent future invasions by identifying and regulating potentially invasive species through species risk assessments and international trade regulations. Among many introduction pathways of non‐native species, horticulture is a particularly important driver of plant invasions. In recent decades, the horticultural industry expanded globally and changed structurally through the emergence of new distribution channels, including internet trade (e‐commerce). Using an automated search algorithm, we surveyed, on a daily basis, e‐commerce trade on 10 major online auction sites (including eBay) of approximately three‐fifths of the world's spermatophyte flora. Many recognized invasive plant species (>500 species) (i.e., species associated with ecological or socio‐economic problems) were traded daily worldwide on the internet. A markedly higher proportion of invasive than non‐invasive species were available online. Typically, for a particular plant family, 30–80% of recognized invasive species were detected on an auction site, but only a few percentages of all species in the plant family were detected on a site. Families that were more traded had a higher proportion of invasive species than families that were less traded. For woody species, there was a significant positive relationship between the number of regions where a species was sold and the number of regions where it was invasive. Our results indicate that biosecurity is not effectively regulating online plant trade. In the future, automated monitoring of e‐commerce may help prevent the spread of invasive species, provide information on emerging trade connectivity across national borders, and be used in horizon scanning exercises for early detection of new species and their geographic source areas in international trade.     

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.     

Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation

Customary medicinal plant species used by Australian Aborigines are disappearing rapidly with its associated knowledge, due to the loss of habitats. Conservation and protection of these species is important as they represent sources of novel therapeutic phytochemical compounds and are culturally valuable. Information on the spatial distribution and use of customary medicinal plants is often inadequate and fragmented, posing limitations on the identification and conservation of species-rich areas and culturally valuable habitats.In this study, the habitat suitability modeling program, MaxEnt, was used to predict the potential ecological niches of 431 customary medicinal plant species, based on bioclimatic variables. Specimen locality records were obtained from the Global Biodiversity Information Facility (GBIF) data portal and from Australia's Virtual Herbarium (AVH).Ecological niche models of 414 predicted species, which had 30 or more occurrence points, were used to produce maps indicating areas that were ecologically suitable for multiple species (concordance of high predicted ecological suitability) and having cultural values. For the concordance map, individual species niche models were thresholded and summed. To derive a map of culturally valuable areas, customary medicinal uses from Customary Medicinal Knowledgebase (CMKb) (www.biolinfo.org/cmkb) were used to weight individual species models, resulting in a value within each grid cell reflecting its cultural worth.Even though the available information is scarce and fragmented, our approach provides an opportunity to infer areas predicted to be suitable for multiple species (i.e. concordance hotspots) and to estimate the cultural value of a particular geographical area. Our results also indicate that to conserve bio-cultural diversity, comprehensive information and active participation of Aboriginal communities is indispensable.     

Species-specific tuning increases robustness to sampling bias in models of species distributions: An implementation with Maxent

Various methods exist to model a species’ niche and geographic distribution using environmental data for the study region and occurrence localities documenting the species’ presence (typically from museums and herbaria). In presence-only modelling, geographic sampling bias and small sample sizes represent challenges for many species. Overfitting to the bias and/or noise characteristic of such datasets can seriously compromise model generality and transferability, which are critical to many current applications - including studies of invasive species, the effects of climatic change, and niche evolution. Even when transferability is not necessary, applications to many areas, including conservation biology, macroecology, and zoonotic diseases, require models that are not overfit. We evaluated these issues using a maximum entropy approach (Maxent) for the shrew Cryptotis meridensis, which is endemic to the Cordillera de Mérida in Venezuela. To simulate strong sampling bias, we divided localities into two datasets: those from a portion of the species’ range that has seen high sampling effort (for model calibration) and those from other areas of the species’ range, where less sampling has occurred (for model evaluation). Before modelling, we assessed the climatic values of localities in the two datasets to determine whether any environmental bias accompanies the geographic bias. Then, to identify optimal levels of model complexity (and minimize overfitting), we made models and tuned model settings, comparing performance with that achieved using default settings. We randomly selected localities for model calibration (sets of 5, 10, 15, and 20 localities) and varied the level of model complexity considered (linear versus both linear and quadratic features) and two aspects of the strength of protection against overfitting (regularization). Environmental bias indeed corresponded to the geographic bias between datasets, with differences in median and observed range (minima and/or maxima) for some variables. Model performance varied greatly according to the level of regularization. Intermediate regularization consistently led to the best models, with decreased performance at low and generally at high regularization. Optimal levels of regularization differed between sample-size-dependent and sample-size-independent approaches, but both reached similar levels of maximal performance. In several cases, the optimal regularization value was different from (usually higher than) the default one. Models calibrated with both linear and quadratic features outperformed those made with just linear features. Results were remarkably consistent across the examined sample sizes. Models made with few and biased localities achieved high predictive ability when appropriate regularization was employed and optimal model complexity was identified. Species-specific tuning of model settings can have great benefits over the use of default settings.     

Managing Invasive Aquatic Plants in a Changing System: Strategic Consideration of Ecosystem Services

Abstract:  Climate change is projected to increase stress for many coastal plant communities. Along large portions of the North American coast, habitat degradation from anthropogenic changes to the environment already threaten the community structure of tidal marshes and submerged aquatic grass beds. The potential loss of ecological services historically provided by these communities has been a long-standing rationale for aggressive control of invading plants such as Phragmites australis and Hydrilla verticillata . Increasing evidence of ecological services provided by invasive species such as P. australis and H. verticillata suggest that, in the face of increasing stress, it may be prudent to take a more pragmatic approach regarding the effect of these species on coastal ecosystems. The notable resilience of these species to control efforts and their competitive success and comparative vigor in stressed systems and capacity to provide at least some beneficial services combine to suggest some invasive species may have a useful role in managed coastal ecosystems.     

Species distribution modelling: Does one size fit all? A phytogeographic analysis of Salix in Ontario

Empirical models for predicting the distribution of organisms from environmental data have often focused on principles of ecological niche theory. However, even at large scales, there is little agreement over how to represent the dimensions of a species’ niche. The performance of such models is greatly affected by the nature of species distributional and environmental data. Regional scale distribution models were developed for 30 willow species in Ontario to examine (i) the predictive ability of logistic regression analysis, and (ii) the effects of using different distributional and environmental data sets. Two original measures of model accuracy and over-prediction were employed and evaluated using independent data. Models based on unique combinations of monthly climate data predicted distributions most accurately for all species. Models based on a fixed set of variables, while generating the highest average probabilities of occurrence for certain species with limited ranges, resulted in the greatest under- and over-estimates of willow distributions. Comparisons of models demonstrated climatic patterns among willows of differing habit and habitat. The distribution of dwarf willow species, present only in the Ontario arctic, followed gradients of summer maximum temperatures. The distribution of the tree species in the southerly portions of the province followed gradients of fall and winter minimum temperatures. Regardless of distributional and environmental data input, no algorithm maximized model performance for all species. Individual species models require individual approaches; i.e., the variable selection technique, the set of environmental factors used as predictors, and the nature of species distributional data must be carefully matched to the intended application. An understanding of evolutionary processes enhances the meaningful interpretation of individual species models. Unless sampling bias and species prevalence can be accounted for, models based on collection point data are best used to guide field surveys. While inferred range data may be better suited to determine potential ecological niches, overestimation of species prevalence and environmental tolerance must be recognized. A combination of available distributional data types is recommended to best determine species niches, an important step in developing conservation strategies.