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Range dynamics causes mismatches between a species' geographical distribution and the set of suitable environments in which population growth is positive (the Hutchinsonian niche). This is because source—sink population dynamics cause species to occupy unsuitable environments, and because environmental change creates non-equilibrium situations in which species may be absent from suitable environments (due to migration limitation) or present in unsuitable environments that were previously suitable (due to time-delayed extinction). Because correlative species distribution models do not account for these processes, they are likely to produce biased niche estimates and biased forecasts of future range dynamics. Recently developed dynamic range models (DRMs) overcome this problem: they statistically estimate both range dynamics and the underlying environmental response of demographic rates from species distribution data. This process-based statistical approach qualitatively advances biogeographical analyses. Yet, the application of DRMs to a broad range of species and study systems requires substantial research efforts in statistical modelling, empirical data collection and ecological theory. Here we review current and potential contributions of these fields to a demographic understanding of niches and range dynamics. Our review serves to formulate a demographic research agenda that entails: (1) advances in incorporating process-based models of demographic responses and range dynamics into a statistical framework, (2) systematic collection of data on temporal changes in distribution and abundance and on the response of demographic rates to environmental variation, and (3) improved theoretical understanding of the scaling of demographic rates and the dynamics of spatially coupled populations. This demographic research agenda is challenging but necessary for improved comprehension and quantification of niches and range dynamics. It also forms the basis for understanding how niches and range dynamics are shaped by evolutionary dynamics and biotic interactions. Ultimately, the demographic research agenda should lead to deeper integration of biogeography with empirical and theoretical ecology.

AIM: Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better‐surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. LOCATION: Borneo, Southeast Asia. METHODS: We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range‐restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north‐eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. RESULTS: Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. MAIN CONCLUSIONS: We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

Aim Interest in species distribution models (SDMs) and related niche studies has increased dramatically in recent years, with several books and reviews being prepared since 2000. The earliest SDM studies are dealt with only briefly even in the books. Consequently, many researchers are unaware of when the first SDM software package (bioclim) was developed and how a broad range of applications using the package was explored within the first 8 years following its release. The purpose of this study is to clarify these early developments and initial applications, as well as to highlight bioclim's continuing relevance to current studies. Location Mainly Australia and New Zealand, but also some global applications. Methods We outline the development of the bioclim package, early applications (1984–1991) and its current relevance. Results bioclim was the first SDM package to be widely used. Early applications explored many of the possible uses of SDMs in conservation biogeography, such as quantifying the environmental niche of species, identifying areas where a species might be invasive, assisting conservation planning and assessing the likely impacts of climate change on species distributions. Main conclusions Understanding this pioneering work is worthwhile as bioclim was for many years one of the leading SDM packages and remains widely used. Climate interpolation methods developed for bioclim were used to create the WorldClim database, the most common source of climate data for SDM studies, and bioclim variables are used in about 76% of recent published MaxEnt analyses of terrestrial ecosystems. Also, some of the bioclim studies from the late 1980s, such as measuring niche (both realized and fundamental) and assessing possible impacts of climate change, are still highly relevant to key conservation biogeography issues.

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 presenceonly 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.

Aim: We combined genetic sequence data and ecological niche modelling to resolve the impacts of past climatic fluctuations on the distribution, genetic diversification, and demographic dynamics of an East Asian montane bird, the green-backed tit (Parus monticolus). Location: East Asia. Methods: Phylogenetic analyses were carried out using four mitochondrial fragments and seven nuclear loci from 161 birds sampled from 29 localities spanning the entire geographical range of the green-backed tit. We used BEAST to estimate the species tree and calculate divergence times. Extended Bayesian skyline plots were used to infer potential historical shifts in population size. We used MaxEnt to predict potential distributions during three periods: the present day, the Last Glacial Maximum and the Last Interglacial. Results: The mitochondrial DNA (mtDNA) gene tree showed strong support for three reciprocally monophyletic groups: a south-western clade, a central clade and a Taiwanese clade. Taiwanese and Vietnamese samples had fixed differences at several nuclear loci, but the south-western and central samples shared haplotypes at all nuclear loci. The mtDNA gene tree topology differed from the species tree topology. The species tree suggested sister relationships between Taiwanese and Vietnamese operational taxonomic units (OTUs) and between south-western and central OTUs. Diversification within the green-backed tit was relatively recent, probably within the last 0.9 million years. Extended Bayesian skyline plots suggested rapid population expansion in the south-western and central phylogroups after the Last Interglacial, and this result was consistent with ecological niche models. Main conclusions: Our results suggest that genetic diversification within the green-backed tit was affected by the later Pleistocene climate fluctuations. Ecological niche models indicated that the present-day vegetation distribution was, in many ways, more similar to that of the Last Glacial Maximum than it was to that of the Last Interglacial. Continental populations of the green-backed tit experienced unusual demographic and range expansion that is likely to have occurred during the cooling transition between the Last Interglacial and the Last Glacial Maximum. We found incongruence between the mtDNA gene tree and the species tree, which underscores the importance of using both mitochondrial and nuclear markers when estimating the evolutionary history of populations.

Coastal areas are at the centre of human–nature relationship, shaped by recreation, tourism and aesthetic values. However, socioeconomic drivers of biodiversity change in coastal areas have received less attention. Soft sediment seafloors support diverse species communities and contribute to ecosystem functionality. One of the main threats is dredging, which sweeps resident organisms. Dredgings are commonly done to deepen waterways, but also for the purposes of private housing. The ecological impacts of these small‐sized dredgings are not well known over broad environmental and geographical gradients. We developed a simple approach for spatial integration of ecological and socioeconomic system, to describe how recreational land use change contributes to the loss of marine biodiversity. It shows how human behaviour, such as preference for a location of second home, can be derived from spatial data and coupled with ecological change. We characterize typical locations of second homes based on accessibility, aesthetics and environment, and with the information identified suitable areas for new second homes. We also quantified typical areas of dredging, based on the depth and substrate of the sea floor, and the extent of the reed beds, influencing the access to properties. We then simulate an annual increase of new second homes and expected land‐use change, namely dredging of shores. Finally, we quantified the realized and projected loss of marine biodiversity from dredged sites, based on species distribution models, relying on extensive ecological data collected from over 170,000 underwater sites. We found that small‐sized dredging can be detrimental to coastal biodiversity, as dredging targets shallow, photic bays and lagoons, with diverse algal and aquatic plant communities, with limited recovery potential. Dredgings also had broad impacts on benthic faunal habitats, which maintain ecosystem processes and functions. Our results reveal a significant ecological change driven by recreational land use. Reversing the trend of biodiversity loss requires a holistic understanding of socioecological systems. Our results highlight the need for integrating land–sea interactions into conservation policies and reforming current land‐use regulation for the benefit of marine biodiversity. Read the free Plain Language Summary for this article on the Journal blog. Read the free Plain Language Summary for this article on the Journal blog.

Aim: Species distribution models (SDMs) have been used to address a wide range of theoretical and applied questions in the terrestrial realm, but marine-based applications remain relatively scarce. In this review, we consider how conceptual and practical issues associated with terrestrial SDMs apply to a range of marine organisms and highlight the challenges relevant to improving marine SDMs. Location: We include studies from both marine and terrestrial systems that encompass many geographic locations around the globe. Methods: We first performed a literature search and analysis of marine and terrestrial SDMs in ISI Web of Science to assess trends and applications. Using knowledge from terrestrial applications, we critically evaluate the application of SDMs in marine systems in the context of ecological factors (dispersal, species interactions, aggregation and ontogenetic shifts) and practical considerations (data quality, alternative modelling approaches and model validation) that facilitate or create difficulties for model application. Results: The relative importance of ecological factors to be considered when applying SDMs varies among terrestrial and marine organisms. Correctly incorporating dispersal is frequently considered an important issue for terrestrial models, but because there is greater potential for dispersal in the ocean, it is often less of a concern in marine SDMs. By contrast, ontogenetic shifts and feeding have received little attention in terrestrial SDM applications, but these factors are important to many marine SDMs. Opportunities also exist for applying more advanced SDM approaches in the marine realm, including mechanistic ecophysiological models, where water balance and heat transfer equations are simpler for some marine organisms relative to their terrestrial counterparts. Main conclusions: SDMs have generally been under-utilized in the marine realm relative to terrestrial applications. Correlative SDM methods should be tested on a range of marine organisms, and we suggest further development of methods that address ontogenetic shifts and feeding interactions. We anticipate developments in, and cross-fertilization between, coupled correlative and process-based SDMs, mechanistic eco-physiological SDMs, and spatial population dynamic models for climate change and species invasion applications in particular. Comparisons of the outputs of different model types will provide insight that is useful for improved spatial management of marine species.

Social-ecological systems (SES) are dynamic systems that continuously change in response to internal or external pressures. A better understanding of the interactions of the social and ecological systems that drive those dynamics is crucial for the development of sustainable management strategies. Dynamic models can serve as tools to explore social-ecological interactions; however, the complexity of the studied systems and the need to integrate knowledge, theories, and approaches from different disciplines pose considerable challenges for their development. We assess the potential of Ostrom’s general SES framework (SESF) to guide a systematic and transparent process of model development in light of these difficulties. We develop a stepwise procedure for applying SESF to identify variables and their relationships relevant for an analysis of the SES. In doing so we demonstrate how the hierarchy of concepts in SESF and the identification of social-ecological processes using the newly introduced process relationships can help to unpack the system in a systematic and transparent way. We test the procedure by applying it to develop a dynamic model of decision making in the management of recreational fisheries. The added value of the common framework lies in the guidance it provides for (1) a structured approach to identifying major variables and the level of detail needed, and (2) a procedure that enhances model transparency by making explicit underlying assumptions and choices made when selecting variables and their interactions as well as the theories or empirical evidence on which they are based. Both aspects are of great relevance when dealing with the complexity of SES and integrating conceptual backgrounds from different disciplines. We discuss the advantages and difficulties of the application of SESF for model development, and contribute to its further refinement.

East Asia's temperate deciduous forests served as sanctuary for Tertiary relict trees, but their ages and response to past climate change remain largely unknown. To address this issue, we elucidated the evolutionary and population demographic history of Cercdiphyllum, comprising species in China/Japan (Cercdiphyllum japonicum) and central Japan (Cercdiphyllum magnificum). Fifty-three populations were genotyped using chloroplast and ribosomal DNA sequences and microsatellite loci to assess molecular structure and diversity in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modelling. Late Tertiary climate cooling was reflected in a relatively recent speciation event, dated at the Mio-/Pliocene boundary. During glacials, the warm-temperate C. japonicum experienced massive habitat losses in some areas (north-central China. north Japan) but increases in others (southwest/-east China, East China Sea landbridge, south Japan). In China, the Sichuan Basin and/or the middle-Yangtze were source areas of postglacial northward recolonization; in Japan, this may have been facilitated through introgressive hybridization with the cool-temperate C. magnificum. Our findings challenge the notion of relative evolutionary and demographic stability of Tertiary relict trees, and may serve as a guideline for assessing the impact of Neogene climate change on the evolution and distribution of East Asian temperate plant.

Heterochrony, the change in the rate or timing of development between ancestors and their descendants, plays a major role in evolution. When heterochrony produces polymorphisms, it offers the possibility to test hypotheses that could explain its success across environments. Amphibians are particularly suitable to exploring these questions because they express complex life cycles (i.e. metamorphosis) that have been disrupted by heterochronic processes (paedomorphosis: retention of larval traits in adults). The large phenotypic variation across populations suggests that more complex processes than expected are operating, but they remain to be investigated through multivariate analyses over a large range of natural populations across time. In this study, we compared the likelihood of multiple potential environmental determinants of heterochrony. We gathered data on the proportion of paedomorphic and metamorphic palmate newts (Lissotriton helveticus) across more than 150 populations during 10 years and used an information‐theoretic approach to compare the support of multiple potential processes. Six environmental processes jointly explained the proportion of paedomorphs in populations: predation, water availability, dispersal limitation, aquatic breathing, terrestrial habitat suitability and antipredator refuges. Analyses of variation across space and time supported models based on the advantage of paedomorphosis in favourable aquatic habitats. Paedomorphs were favoured in deep ponds, in conditions favourable to aquatic breathing (high oxygen content), with lack of fish and surrounded by suitable terrestrial habitat. Metamorphs were favoured by banks allowing easy dispersal. These results indicate that heterochrony relies on complex processes involving multiple ecological variables and exemplifies why heterochronic patterns occur in contrasted environments. On the other hand, the fast selection of alternative morphs shows that metamorphosis and paedomorphosis developmental modes could be easily disrupted in natural populations.