种间作用对物种分布模拟的影响及建模方法

物种分布模型(SDMs)通过量化物种分布和环境变量之间的关系,并将其外推到未知的景观单元,模拟、预测地理空间中生物的潜在分布,是生态学、生物地理学、保护生物学等研究领域的重要工具.然而,目前物种分布模型主要采用非生物因素作为预测变量,由于数据量化和建模表达困难,生物因素特别是种间作用在物种分布模型中常被忽略,将种间作用...     

物种分布模型在海洋潜在生境预测的应用研究进展

海洋生物的栖息分布与环境要素的关联性一直是海洋生态学研究的热点之一.近年来,物种分布模型被广泛应用于预测海洋物种分布、潜在适宜性生境评价等研究,为保护海洋生物多样性、防治外来物种入侵及制定渔业管理措施等提供了一条有效途径.物种分布模型主要包括生境适宜性指数模型、机理模型和统计模型.本文对物种分布模型的理论基础进行了归纳和总结,回顾了物种分布模型在预测海洋物种潜在地理分布研究中的开发与应用,重点介绍了不同类型统计模型在海洋物种潜在分布预测中的研究实例.比较各种选取变量和模型验证方法,认为赤池信息准则对于选取模型变量具有优势,Kappa系数和受试者操作特征曲线下面积在验证模型精度中应用最广泛.阐述了物种分布模型存在的问题及未来发展趋势,随着海洋生物生理机制研究的进一步深入,机理模型将是今后物种分布模型发展的重点.     

Common species have lower taxonomic diversity Evidence from the urban floras of Brussels and Rome

The species pool hypothesis claims that the large‐scale regional species pool is the chief parameter in determining small‐scale species richness through filtering of species that can persist within a community on the basis of their tolerance of the abiotic environment. Accordingly, different environmental conditions give rise to different species assemblages. From a taxonomic perspective, under the assumption of trait conservatism, co‐occurring species that experience similar environmental conditions are likely to be more taxonomically similar than ecologically distant species. The next step consists in understanding how commonness and rarity of individual species produce the observed taxonomic diversity. In this paper, the importance of environmental filtering in regulating the taxonomic structure of rare and common plant species in the urban floras of Brussels (Belgium) and Rome (Italy) is tested. First, we computed the taxonomic diversity of the rare and common species of Brussels and Rome based on the branching topology of the Linnaean taxonomic trees. Next, using a randomization procedure, we determined whether the taxonomic diversity of the rare species was significantly higher than the diversity of the common species. Results show that, for both urban floras, common species that shape the community matrix and experience similar environmental conditions have a taxonomic diversity that is significantly lower than that of the rare species that represent a relatively incidental set of species of more ‘disperse’ origin. Finally, from a conservation/management perspective our results imply that, given their high taxonomic heterogeneity, the protection of rare species is a central issue for preserving high levels of diversity in urban areas.     

What spatial data do we need to develop global mammal conservation strategies?

Spatial data on species distributions are available in two main forms, point locations and distribution maps (polygon ranges and grids). The first are often temporally and spatially biased, and too discontinuous, to be useful (untransformed) in spatial analyses. A variety of modelling approaches are used to transform point locations into maps. We discuss the attributes that point location data and distribution maps must satisfy in order to be useful in conservation planning. We recommend that before point location data are used to produce and/or evaluate distribution models, the dataset should be assessed under a set of criteria, including sample size, age of data, environmental/geographical coverage, independence, accuracy, time relevance and (often forgotten) representation of areas of permanent and natural presence of the species. Distribution maps must satisfy additional attributes if used for conservation analyses and strategies, including minimizing commission and omission errors, credibility of the source/assessors and availability for public screening. We review currently available databases for mammals globally and show that they are highly variable in complying with these attributes. The heterogeneity and weakness of spatial data seriously constrain their utility to global and also sub-global scale conservation analyses.     

The effect of sample size on the accuracy of species distribution models: considering both presences and pseudo‐absences or background sites

Most high‐performing species distribution modelling techniques require both presences, and either absences or pseudo‐absences or background points. In this paper, we explore the effect of sample size, towards developing improved strategies for modelling. We generated 1800 virtual species with three levels of prevalence using ten modelling techniques, while varying the number of training presences (NTP) and the number of random points (NRP representing pseudo‐absences or background sites). For five of the ten modelling techniques we built two versions of models: one with an equal total weight (ETW) setting where the total weight for pseudo‐absence is equivalent to the total weight for presence, and another with an unequal total weight (UTW) setting where the total weight for pseudo‐absence is not required to be equal to the total weight for presence. We compared two strategies for NRP: a small multiplier strategy (i.e. setting NRP at a few times as large as NTP), and a large number strategy (i.e. using numerous random points). We produced ensemble models (by averaging the predictions from 30 models built with the same set of training presences and different sets of random points in equivalent numbers) for three NTP magnitudes and two NRP strategies. We found that model accuracy altered as NRP increased with four distinct patterns of performance: increasing, decreasing, arch‐shaped and horizontal. In most cases ETW improved model performance. Ensemble models had higher accuracy than the corresponding single models, and this improvement was pronounced when NTP was low. We conclude that a large NRP is not always an appropriate strategy. The best choice for NRP will depend on the modelling techniques used, species prevalence and NTP. We recommend building ensemble models instead of single models, using the small multiplier strategy for NRP with ETW, especially when only a small number of species presence records are available.     

栖息地毁坏与动物物种灭绝关系的模拟研究

利用多个物种共存模式模拟了不同情况下的不同动物种群演化的动力学特性,研究结果表明：（1）由于栖息地的毁坏所导致的动手的种灭绝是依赖于对物种死亡率和有关平衡态的假设的,不同的假设下,既使栖息地的破坏率相同,灭绝的物种可能是竞争能力最强的若干物种,也可能是竞争能力相对较弱的若干物种,既不象传统的物种进化理论所认为的必是弱的物种先灭绝,也不象Tilman等人所认为的一定是最强的若干物种先灭绝;（2）如果弱的物种具有较高的平均死亡率,则当栖息地受到一定的毁坏时,将有较多强的物种灭绝,而且物种灭绝时间将大大缩短;（3）在物种死亡率不变的情形下,物种在未受毁坏栖息地上的平衡态和大占有率pl^0,将有利于物种的生存。     

Confronting species distribution model predictions with species functional traits

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day⁻¹. Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = −0.26, 95% CI (−0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.     

An ecoregion assessment of projected tree species vulnerabilities in western North America through the 21st century

Forest ecosystems across western North America will likely see shifts in both tree species dominance and composition over the rest of this century in response to climate change. Our objective in this study was to identify which ecological regions might expect the greatest changes to occur. We used the process‐based growth model 3‐PG, to provide estimates of tree species responses to changes in environmental conditions and to evaluate the extent that species are resilient to shifts in climate over the rest of this century. We assessed the vulnerability of 20 tree species in western North America using the Canadian global circulation model under three different emission scenarios. We provided detailed projections of species shifts by including soil maps that account for the spatial variation in soil water availability and soil fertility as well as by utilizing annual climate projections of monthly changes in air temperature, precipitation, solar radiation, vapor pressure deficit and frost at a spatial resolution of one km. Projected suitable areas for tree species were compared to their current ranges based on observations at >40 000 field survey plots. Tree species were classified as vulnerable if environmental conditions projected in the future appear outside that of their current distribution ≥70% of the time. We added a migration constraint that limits species dispersal to <200 m yr^?1 to provide more realistic projections on species distributions. Based on these combinations of constraints, we predicted the greatest changes in the distribution of dominant tree species to occur within the Northwest Forested Mountains and the highest number of tree species stressed will likely be in the North American Deserts. Projected climatic changes appear especially unfavorable for species in the subalpine zone, where major shifts in composition may lead to the emergence of new forest types.     

物种分布模型理论研究进展

利用物种分布模型估计物种的真实和潜在分布区,已成为区域生态学与生物地理学中非常活跃的研究领域。然而,到目前为止,这项技术的理论基础仍然存在不足之处,一些关键的生态过程未能被有效纳入到物种分布模型的理论框架中,从而为解释物种分布模型预测的结果带来了诸多困惑。鉴于此,总结了物种分布模型的理论基础;系统探讨了物种分布模型与物种分布区的关系;特别指出了物种分布模型研究中存在的理论问题;重点阐述了物种分布模型未来的发展方向。研究认为,物种分布模型与生态位理论、源-库理论、种群动态理论、集合种群理论、进化理论等具有重要的联系;正确理解物种分布模型的预测结果与物种分布区的关系,有赖于对影响物种分布的3个主要因素(环境条件、物种相互作用与物种迁移能力)做出定量的分离;目前物种分布模型主要存在的问题是未能将物种的相互作用和物种的迁移能力有效纳入到模型的构建过程中;未来物种分布模型的发展应该加强模型背后理论框架的研究,并进一步加强整合物种相互作用过程、种群动态过程、迁移过程和物种进化过程等内容。研究还认为,从更高的理论层次模拟功能群和群落结构将是未来物种分布模型的重要发展方向。     

Using a species distribution model to guide NSW surveys of the long‐footed potoroo (Potorous longipes)

Knowledge of threatened species’ distributions is essential for effective conservation decision‐making. Species distribution models (SDMs) are widely used to map species’ geographic ranges, identify new areas of suitable habitat and guide field surveys. In New South Wales (NSW), Australia, there are grave doubts about whether populations of the critically endangered long‐footed potoroo (Potorous longipes) remain extant, and identification of occupied sites is a high priority for its conservation. We used an SDM (Maxent) to identify regions in NSW that may have suitable habitat for the potoroo. The SDM was built with seven climate layers and had strong predictive performance (cross‐validated AUC = 0.94). We then combined this information on habitat suitability with vegetation and topography, to identify 58 survey sites across NSW. From April 2016 to May 2017, we undertook six field trips deploying six to eight cameras at each site for 52–63 days, resulting in 25 120 camera trap nights. A total of 215 759 images captured 43 native and feral animal species, but no long‐footed potoroos. Following the survey, newly available, independent presence and absence data were used to validate our model. A Kruskal–Wallis H test indicated that habitat suitability values were significantly higher at presence locations than absence locations (H = 58.66, d.f. = 1, P < 0.001). Finally, we refitted the Maxent model with the new data and identified additional regions that future surveys could explore. We conclude, however, that if the long‐footed potoroo remains extant in NSW, it is extremely rare.     

五鹿山国家级自然保护区森林群落演替分析

植物群落演替分析对植被恢复,森林管理等有重要的意义。以空间代替时间的方法,搜集数据,运用TWINSPAN和DCA进行分析。结果表明:五鹿山植物群落的演替系列:酸枣灌丛→荆条灌丛→黄刺玫灌丛→白皮松+侧柏林→白皮松林→油松林→辽东栎林;虎榛子灌丛→茶条槭灌丛→华北落叶松林→白桦林。这可以作为五鹿山植物群落演替的模型。在演替进程中物种的结构、组成以及生活型变化显著。使用六个指数来分析演替过程中物种的异质性、均匀度和丰富度变化。随着演替的进行,物种异质性、丰富度均有所增加,均匀度逐渐降低。     

Predicting the distribution of a rare species of moss: The case of Buxbaumia viridis (Bryopsida,Buxbaumiaceae)

Buxbaumia viridis is a rare policy species restricted to decaying woods in forests. Although Member States of EU are required to monitor its conservation status, specific models able to predict species distribution are still lacking. However, the availability of such models would strongly improve the efficiency in collection additional data and consequently lead to a better knowledge of its ecology. Aims of this work were (i) to provide a model for species distribution assessing the importance of different environmental variables thought to be important in setting the occurrence of Buxbaumia viridis and (ii) to test the effect of imperfect detection in defining the environmental space where the species occur. With this work, records of B. viridis increased twofold in the Alpine region of Italy, passing from 13 records to 26. We showed that on the Alps, occurrence of Buxbaumia viridis was best predicted by northness, rainfall, canopy closure and necromass. Necromass was the single most important variable. A volume of 48–61 m³/ha of necromass was identified as the threshold value determining the high probability of species occurrence. The imperfect detection probability of the species (p = 0.25), biased towards zero the importance of the environmental variables.     

Species interactions weakly modify climate‐induced tree co‐occurrence patterns

Aims

Species distributions are hypothesized to be underlain by a complex association of processes that span multiple spatial scales including biotic interactions, dispersal limitation, fine‐scale resource gradients and climate. Species disequilibrium with climate may reflect the effects of non‐climatic processes on species distributions, yet distribution models have rarely directly considered non‐climatic processes. Here, we use a Joint Species Distribution Model (JSDM) to investigate the influence of non‐climatic factors on species co‐occurrence patterns and to directly quantify the relative influences of climate and alternative processes that may generate correlated responses in species distributions, such as species interactions, on tree co‐occurrence patterns.

Location

US Rocky Mountains.

Methods

We apply a Bayesian JSDM to simultaneously model the co‐occurrence patterns of ten dominant tree species across the Rocky Mountains, and evaluate climatic and residual correlations from the fitted model to determine the relative contribution of each component to observed co‐occurrence patterns. We also evaluate predictions generated from the fitted model relative to a single‐species modelling approach.

Results

For most species, correlation due to climate covariates exceeded residual correlation, indicating an overriding influence of broad‐scale climate on co‐occurrence patterns. Accounting for covariance among species did not significantly improve predictions relative to a single‐species approach, providing limited evidence for a strong independent influence of species interactions on distribution patterns.

Conclusions

Overall, our findings indicate that climate is an important driver of regional biodiversity patterns and that interactions between dominant tree species contribute little to explain species co‐occurrence patterns among Rocky Mountain trees.     

Assessing habitat loss and fragmentation and their effects on population viability of forest specialist birds: Linking biogeographical and population approaches

Aim

Biogeographic approaches usually have been developed apart from population ecology, resulting in predictive models without key parameters needed to account for reproductive and behavioural limitations on dispersal. Our aim was to incorporate fully spatially explicit population traits into a classic species distribution model (SDM) using Geographic Information Systems (GIS), aiming at conservation purposes.

Location

Southern South America.

Methods

Our analysis incorporates the effects of habitat loss and fragmentation on population viability and therefore provides insights into how much spatially explicit population traits can improve the SDM prediction of habitable habitat. We utilized a well‐studied focal endemic bird of South American temperate rainforests (Scelorchilus rubecula). First, at a large scale, we assessed the historical extent habitat based on climate envelopes in an SDM. Second, we used a land cover change analysis at a regional scale to account for recent habitat loss and fragmentation. Third, we used empirically derived criteria to predict population responses to fragmented forest landscapes to identify actual losses of habitat and population. Then we selected three sites of high conservation value in southern Chile and applied our population model. Finally, we discuss the degree to which spatially explicit population traits can improve the SDM output without intervening in the modelling process itself.

Results

We found a historical habitat loss of 39.12% and an additional forest cover loss of 3.03% during 2000–2014; the latter occurred with a high degree of fragmentation, reducing the overall estimation of (1) carrying capacity by ?82.4%, ?33.1% and ?45.1% and (2) estimated number of pairs on viable populations by ?84.1%, ?33.0% and ?54.6% on the three selected sites.

Main conclusion

We conclude that our approach sharpened the SDM prediction on environmental suitability by 54.4%, adjusting the habitable area by adding population parameters through GIS, and allowing to incorporate other phenomena as fragmentation and habitat loss.

     

Challenges in the application of geometric constraint models

Discerning the processes influencing geographical patterns of species richness remains one of the central goals of modern ecology. Traditional approaches to exploring these patterns have focused on environmental and ecological correlates of observed species richness. Recently, some have suggested these approaches suffer from the lack of an appropriate null model that accounts for species ranges being constrained to occur within a bounded domain. Proponents of these null geometric constraint models (GCMs), and the mid-domain effect these models produce, argue their utility in identifying meaningful gradients in species richness. This idea has generated substantial debate. Here we discuss what we believe are the three major challenges in the application of GCMs. First, we argue that there are actually two equally valid null models for the random placement of species ranges within a domain, one of which actually predicts a uniform distribution of species richness. Second, we highlight the numerous decisions that must be made to implement a GCM that lead to marked differences in the predictions of the null model. Finally, we discuss challenges in evaluating the importance of GCMs once they have been implemented.     

Global habitat suitability models of terrestrial mammals

Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals.     

中国北方5种栎属树木多度分布及其对未来气候变化的响应

植物分布与气候之间的关系是预估未来气候变化对生态系统影响的实现基础。以往的物种分布模型通常以物种的分布区或者分布点的物种存在数据作为物种分布的响应变量。相较于物种存在数据, 多度反映了一个物种占用资源并把资源分配给个体的能力, 更能衡量物种对区域生态系统的影响。该研究通过野外调查获取了华北及周边地区1 045个样方的栎属树木多度, 利用广义线性模型、广义加性模型和随机森林模型模拟栓皮栎(Quercus variabilis)、麻栎(Q. acutissima)、槲栎(Q. aliena)、锐齿槲栎(Q. aliena var. acuteserrata)和蒙古栎(Q. mongolica) 5个树种多度的地理分布及未来2个不同时期(2050年和2070年)的潜在分布。结果表明: 随机森林模型对5个栎属树种的多度的拟合结果要优于广义线性模型和广义加性模型; 典型浓度路径(RCP) 8.5下的5个栎属树种在未来两个时期的多度变化幅度都要大于RCP 2.6下的变化, 在超过一半面积的区域中麻栎、槲栎、锐齿槲栎和蒙古栎的多度减少, 其中内蒙古东北部和黑龙江北部地区是5种栎属植物多度减少的集中分布地区。未来气候变化背景下, 需要加强对这几个区域的监测与物种保护。     

An evolutionary modelling approach to understanding the factors behind plant invasiveness and community susceptibility to invasion

Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionarily younger communities. The main findings were that species that had previously been the most abundant in their original communities have significantly higher rates of establishment than did species that had previously occurred at low abundance in their original community. However, if establishment did occur, previously abundant and previously low-abundant species were equally likely to become dominant and were equally likely to exclude other species from their new community. There was a suggestion that the species that were most likely to establish and exclude others were 'genetically' different. When species that had evolved in different simulations (but with identical environmental conditions) were transplanted into communities that had also evolved in different simulations of the same conditions, the outcomes were difficult to predict. Observed rates of establishment and subsequent competitive dominance were observed to be species- and community combination-specific. This evolutionary study represents a novel in silico attempt to tackle invasiveness in an experimental framework and may provide a new methodology for tackling these issues.