The quest for trait convergence and divergence in community assembly: are null‐models the magic wand?

The relevance of neutral versus niche‐based community assembly rules (i.e. the processes sorting species present in a larger geographical region into local communities) remains to be demonstrated in ecology and biogeography. To attempt to do this, a number of complex null models are increasingly being used that compare observed community functional diversity (FD, i.e. the extent of trait dissimilarity between coexisting species) with randomly simulated FD. However, little is known about the performance of these null models in detecting non‐neutral community assembly rules such as trait convergence and divergence of communities (supposedly revealing habitat selection and limiting similarity, respectively). Here, using both simulated and field communities, I show that assembly rule detection varies systematically with the magnitude of the observed FD, so that these null models do not really succeed in breaking down the observed functional relationships between species. This is a particular concern, making detection of community assembly dependent on: (1) the pool of samples considered, and (2) the capacity of observed FD to correctly discriminate these rules. Null models should be more thoroughly described and validated before being considered as a magic wand to reveal assembly patterns.     

Niche shift in four non‐native estrildid finches and implications for species distribution models

Non‐native species can have severe impacts on ecosystems. Therefore, predictions of potentially suitable areas that are at risk of the establishment of non‐native populations are desirable. In recent years, species distribution models (SDMs) have been widely applied for this purpose. However, the appropriate selection of species records, whether from the native area alone or also from the introduced range, is still a matter of debate. We combined analyses of native and non‐native realized climate niches to understand differences between models based on all locations, as well as on locations from the native range only. Our approach was applied to four estrildid finch species that have been introduced to many regions around the world. Our results showed that SDMs based on location data from native areas alone may underestimate the potential distribution of a given species. The climatic niches of species in their native ranges differed from those of their non‐native ranges. Niche comparisons resulted in low overlap values, indicating considerable niche shifts, at least in the realized niches of these species. All four species have high potential to spread over many tropical and subtropical areas. However, transferring these results to temperate areas has a high degree of uncertainty, and we urge caution when assessing the potential spread of tropical species that have been introduced to higher latitudes.     

Understanding species distribution in dynamic populations: a new approach using spatio‐temporal point process models

Understanding and predicting a species’ distribution across a landscape is of central importance in ecology, biogeography and conservation biology. However, it presents daunting challenges when populations are highly dynamic (i.e. increasing or decreasing their ranges), particularly for small populations where information about ecology and life history traits is lacking. Currently, many modelling approaches fail to distinguish whether a site is unoccupied because the available habitat is unsuitable or because a species expanding its range has not arrived at the site yet. As a result, habitat that is indeed suitable may appear unsuitable. To overcome some of these limitations, we use a statistical modelling approach based on spatio‐temporal log‐Gaussian Cox processes. These model the spatial distribution of the species across available habitat and how this distribution changes over time, relative to covariates. In addition, the model explicitly accounts for spatio‐temporal dynamics that are unaccounted for by covariates through a spatio‐temporal stochastic process. We illustrate the approach by predicting the distribution of a recently established population of Eurasian cranes Grus grus in England, UK, and estimate the effect of a reintroduction in the range expansion of the population. Our models show that wetland extent and perimeter‐to‐area ratio have a positive and negative effect, respectively, in crane colonisation probability. Moreover, we find that cranes are more likely to colonise areas near already occupied wetlands and that the colonisation process is progressing at a low rate. Finally, the reintroduction of cranes in SW England can be considered a human‐assisted long‐distance dispersal event that has increased the dispersal potential of the species along a longitudinal axis in S England. Spatio‐temporal log‐Gaussian Cox process models offer an excellent opportunity for the study of species where information on life history traits is lacking, since these are represented through the spatio‐temporal dynamics reflected in the model.     

Invasive species distribution models – how violating the equilibrium assumption can create new insights

Aim Two core assumptions of species distribution models (SDMs) do not hold when modelling invasive species. Invasives are not in equilibrium with their environment and niche quantification and transferability in space and time are limited. Here, we test whether combining global‐ and regional‐scale data in a novel framework can overcome these limitations. Beyond simply improving regional niche modelling of non‐native species, the framework also makes use of the violation of regional equilibrium assumptions, and aims at estimating the stage of invasion, range filling and risk of spread in the near future for 27 invasive species in the French Alps. Innovation For each invader we built three sets of SDMs using a committee averaging method: one global model and two regional models (a conventional model and one using the global model output to weight pseudo‐absences). Model performances were compared using the area under the receiver operating characteristic curve, the true skill statistic, sensitivity and specificity scores. Then, we extracted the predictions for observed presences and compared them to global and regional models. This comparison made it possible to identify whether invasive species were observed within or outside of their regional and global niches. Main conclusions This study provides a novel methodological framework for improving the regional modelling of invasive species, where the use of a global model output to weight pseudo‐absences in a regional model significantly improved the predictive performance of regional SDMs. Additionally, the comparison of the global and regional model outputs revealed distinct patterns of niche estimates and range filling among the species. These differences allowed us to draw conclusions about the stage of invasion and the risk of spread in the near future, which both correspond to experts' expectations. This framework can be easily applied to a large number of species and is therefore useful for control of biological invasions and eradication planning.     

PSDS 2.0: 一个基于GIS和多个模型的生物潜在分布地预测系统

根据对生物分布地预测模型和软件发展现状的分析和总结, 本研究在PSDS 1.0的基础上提出并实现一个基于GIS且具有多个代表性模型的生物分布地预测系统(PSDS 2.0)。PSDS 2.0系统继承了1.0的环境包络和聚类包络模型, 进一步引入了限制因子包络、马氏距离、支持向量机等新模型, 并针对本领域中模型比较与选择的难点增加了迭代交叉验证的多模型选择功能。系统还实现了灵活定制和评估伪负样本的功能, 通过用只需要正样本的I类模型预测的结果对随机产生的伪负样本进行评估, 减小其落入适宜地区的概率, 进一步提高需要正负样本的II类模型的准确率。GIS功能在PSDS 2.0中也得到加强, 被应用于数据准备及结果分析等重要环节。文章最后以白冠长尾雉(Syrmaticus reevesii)为例, 运用PSDS 2.0系统预测其在中国范围内的潜在分布地, 并对各种模型的预测结果进行评估和比较。     

Phylogenetic and ecological structure of Mediterranean caddisfly communities at various spatio‐temporal scales

Aim The evolutionary processes structuring the composition of communities remain unclear due to the complexity of factors active at various spatial and temporal scales. Here, we conducted ecological and evolutionary analyses of communities of caddisflies in the genus Hydropsyche (Insecta: Trichoptera) composed of ecomorphologically differentiated species. Location River ecosystems in the Iberian Peninsula and northern Morocco. Methods Nineteen environmental variables were assessed at 180 local study sites and species presence/absence at these sites was used to determine their ecological niche. The evolutionary framework for all 19 species of Hydropsyche encountered was generated by phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I gene and three nuclear genes: wingless, elongation factor 1‐alpha and 28S RNA. The phylogenetic tree was used: (1) to assess evolutionary niche conservatism by ecological trait correlation with the tree; and (2) to analyse the phylogenetic relatedness of community member species, at three spatial scales (local stream reaches, drainage basins, biogeographical regions). Results Ecological measurements grouped most species into either headwater, mid‐stream or lowland specialists, and traits presumably relevant to river zonation were found to be phylogenetically conservative. Species assemblages at local stream reaches were mostly mono‐ or dispecific. Species diversity increased at larger spatial scales, by adding species with non‐overlapping ecological niches at the level of river basins and by turnover of anciently differentiated lineages at the level of biogeographical regions. This indicates the effects of competition and niche filtering on community structure locally, and ancient ecological diversification and allopatric speciation, respectively, in building up the species pool at basin and biogeographical scales. Main conclusions The study demonstrates the importance of scale (grain size) in studying what determines community composition. Current ecological factors (i.e. competitive exclusion) in Hydropsyche were evident only when studying narrow local sites, while studies of assemblages at larger spatial scales instead demonstrated the roles of ecological niche differentiation, phylogenetic history of trait diversification and allopatric speciation. Increasing the grain size of investigation reveals different portions of correlated spatial and evolutionary processes.     

Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model's performance and that the spatial variations of species presence-absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution.     

Bio‐ORACLE: a global environmental dataset for marine species distribution modelling

Aim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user‐friendly, high‐resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high‐resolution and readily usable package of global environmental rasters. Location Global, marine. Methods We compiled global coverage data, e.g. satellite‐based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile. Results We present Bio‐ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user‐friendly data package for marine species distribution modelling is available for download at http://www.bio‐oracle.ugent.be . The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow‐water marine organisms. Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence‐only model of a notorious invasive seaweed shows that the information contained in Bio‐ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.     

The difficulty of using species distribution modelling for the conservation of refugee species – the example of European bison

Refugee species have been confined to suboptimal habitat through historic anthropogenic factors. If this is unknown, management might actively conserve these species in suboptimal habitat assuming it represents optimal habitat. Similarly, species distribution modelling (SDM) might misguide conservation management of refugee species by only using presence data from suboptimal habitats. We illustrate this by commenting on a recent SDM for European bison that reconstructed the historic distribution of the species. We challenge the interpretation of this model by suggesting an alternative historic biogeography based on the refugee species concept. We argue that, in the case of refugee species, historic reconstructions using SDM cannot be used as a template for conservation management. Rather, experimental re‐introduction programmes should provide us with population performance and life history data from a range of suboptimal to optimal habitats. Such data could be used in mechanistic niche modelling to predict potential distribution of refugee species.     

A problem with variable selection in a comparison of correlative and process‐based species distribution models: Comments on Higgins et al., 2020

Comments are presented on an article published in October 2020 in Ecology and Evolution (“Predictive ability of a process‐based versus a correlative species distribution model”) by Higgins et al. This analyzed natural distributions of Australian eucalypt and acacia species and assessed the adventive range of selected species outside Australia. Unfortunately, inappropriate variables were used with the MaxEnt species distribution model outside Australia, so that large climatically suitable areas in the Northern Hemisphere were not identified. Examples from a previous analysis and from the use of the freely available spatial portal of the Atlas of Living Australia are provided to illustrate how the problem can be overcome. The comparison of methods described in the Higgins et al. paper is worthwhile, and it is hoped that the authors will be able to repeat their analyses using appropriate variables with the correlative model.     

Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta‐diversity: a meta‐analysis

A major challenge in ecology, conservation and global‐change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β‐diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null‐models and meta‐analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β‐diversity through neutral‐sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change.     

Community‐based native seed production for restoration in Brazil – the role of science and policy

• Large‐scale restoration programmes in the tropics require large volumes of high quality, genetically diverse and locally adapted seeds from a large number of species. However, scarcity of native seeds is a critical restriction to achieve restoration targets.
• In this paper, we analyse three successful community‐based networks that supply native seeds and seedlings for Brazilian Amazon and Cerrado restoration projects. In addition, we propose directions to promote local participation, legal, technical and commercialisation issues for up‐scaling the market of native seeds for restoration with high quality and social justice.
• We argue that effective community‐based restoration arrangements should follow some principles: (i) seed production must be based on real market demand; (ii) non‐governmental and governmental organisations have a key role in supporting local organisation, legal requirements and selling processes; (iii) local ecological knowledge and labour should be valued, enabling local communities to promote large‐scale seed production; (iv) applied research can help develop appropriate techniques and solve technical issues.
• The case studies from Brazil and principles presented here can be useful for the up‐scaling restoration ecology efforts in many other parts of the world and especially in tropical countries where improving rural community income is a strategy for biodiversity conservation and restoration.