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Aim: Spatial and temporal biases in species-occurrence data can compromise broad-scale biogeographical research and conservation planning. Although spatial biases have been frequently scrutinized, temporal biases and the overall quality of species-occurrence data have received far less attention. This study aims to answer three questions: (1) How reliable are species-occurrence data for flowering plants in Africa? (2) Where and when did botanical sampling occur in the past 300 years? (3) How complete are plant inventories for Africa? Location: Africa. Methods: By filtering a publicly available dataset containing 3.5 million records of flowering plants, we obtained 934,676 herbarium specimens with complete information regarding species name, date and location of collection. Based on these specimens, we estimated inventory completeness for sampling units (SUs) of 25 km × 25 km. We then tested whether the spatial distribution of well-sampled SUs was correlated with temporal parameters of botanical sampling. Finally, we determined whether inventory completeness in individual countries was related to old or recently collected specimens. Results: Thirty-one per cent of SUs contained at least one specimen, whereas only 2.4% of SUs contained a sufficient number of specimens to reliably estimate inventory completeness. We found that the location of poorly sampled areas remained almost unchanged for half a century. Moreover, there was pronounced temporal bias towards old specimens in South Africa, the country that holds half of the available data for the continent. There, high inventory completeness stems from specimens collected several decades ago. Main conclusions: Despite the increasing availability of species occurrence data for Africa, broad-scale biogeographical research is still compromised by the uncertain quality and spatial and temporal biases of such data. To avoid erroneous inferences, the quality and biases in species-occurrence data should be critically evaluated and quantified prior to use. To this end, we propose a quantification method based on inventory completeness using easily accessible species-occurrence data.

Whether cities are more or less diverse than surrounding environments, and the extent to which non‐native species in cities impact regional species pools, remain two fundamental yet unanswered questions in urban ecology. Here we offer a unifying framework for understanding the mechanisms that generate biodiversity patterns across taxonomic groups and spatial scales in urban systems. One commonality between existing frameworks is the collective recognition that species co‐occurrence locally is not simply a function of natural colonization and extinction processes. Instead, it is largely a consequence of human actions that are governed by a myriad of social processes occurring across groups, institutions, and stakeholders. Rather than challenging these frameworks, we expand upon them to explicitly consider how human and non‐human mechanisms interact to control urban biodiversity and influence species composition over space and time. We present a comprehensive theory of the processes that drive biodiversity within cities, between cities and surrounding non‐urbanized areas and across cities, using the general perspective of metacommunity ecology. Armed with this approach, we embrace the fact that humans substantially influence β‐diversity by creating a variety of different habitats in urban areas, and by influencing dispersal processes and rates, and suggest ways how these influences can be accommodated to existing metacommunity paradigms. Since patterns in urban biodiversity have been extensively described at the local or regional scale, we argue that the basic premises of the theory can be validated by studying the β‐diversity across spatial scales within and across urban areas. By explicitly integrating the myriad of processes that drive native and non‐native urban species co‐occurrence, the proposed theory not only helps reconcile contrasting views on whether urban ecosystems are biodiversity hotspots or biodiversity sinks, but also provides a mechanistic understanding to better predict when and why alternative biodiversity patterns might emerge.

Aim: Spatial analysis of the distribution and density of species is of continuing interest within theoretical and applied ecology. Species distribution models (SDMs) are being increasingly used to analyse count, presence-absence and presence-only data sets. There is a growing literature on dynamic SDMs (which incorporate temporal variation in species distribution), joint SDMs (which simultaneously analyse the correlated distribution of multiple species) and geostatistical models (which account for similarity between nearby sites caused by unobserved covariates). However, no previous study has combined all three attributes within a single framework. Innovation: We develop spatial dynamic factor analysis for use as a 'joint, dynamic SDM' (JDSDM), which uses geostatistical methods to account for spatial similarity when estimating one or more 'factors'. Each factor evolves over time following a density-dependent (Gompertz) process, and the logdensity of each species is approximated as a linear combination of different factors. We demonstrate a JDSDM using two multispecies case studies (an annual survey of bottom-associated species in the Bering Sea and a seasonal survey of butterfly density in the continental USA), and also provide our code publicly as an R package. Main conclusions: Case study applications show that that JDSDMs can be used for species ordination, i.e. showing that dynamics for butterfly species within the same genus are significantly more correlated than for species from different genera. We also demonstrate how JDSDMs can rapidly identify dominant patterns in community dynamics, including the decline and recovery of several Bering Sea fishes since 2008, and the 'flight curves' typical of early or late-emerging butterflies. We conclude by suggesting future research that could incorporate phylogenetic relatedness or functional similarity, and propose that our approach could be used to monitor community dynamics at large spatial and temporal scales.

Aim To analyse the occurrence and abundance of native versus alien fish species in relation to climate, land use, hydrologic alteration and habitat fragmentation in a heavily invaded and human‐impacted riverine ecosystem. To test whether co‐occurrence patterns of native versus alien species are structured by environmental filtering or biotic associations. Location Mediterranean, Iberian Peninsula, Ebro River catchment. Methods We modelled freshwater fish distributions and their association with environmental conditions using a hurdle model‐like approach involving boosted regression trees. Additionally, we applied a joint species distribution model to quantify the co‐occurrence of native versus alien fish species that can be attributed to shared environmental responses or potentially to biotic interactions. Results Our results point to environmental factors, rather than biotic associations, as major correlates of the increase of alien and the decline of native fishes in the Ebro River. We observed contrasting patterns of native versus alien species along the upstream‐downstream gradient. Alien species dominated in the lower reaches associated with warmer temperatures, higher shares of intensive land use and appeared facilitated by dams and river regulation. Native species richness was highest in the larger tributaries followed by a strong decline in the main stem which was related to the river network position and land use type. Fragmentation played a subordinate role in explaining fish richness and abundance patterns. Main conclusions Given the strong association with temperature, a further range expansion of alien fishes in the Ebro with future climate change may be expected. More local‐scale factors related to habitat degradation and hydrologic alteration will further exacerbate the invasion success of many alien fishes. Further multiple, independent species introductions might mask isolation and fragmentation effects of dams on the future spread and distribution of alien fish.

Linking diversity to biological processes is central for developing informed and effective conservation decisions. Unfortunately, observable patterns provide only a proportion of the information necessary for fully understanding the mechanisms and processes acting on a particular population or community. We suggest conservation managers use the often overlooked information relative to species absences and pay particular attention to dark diversity (i.e., a set of species that are absent from a site but that could disperse to and establish there, in other words, the absent portion of a habitat-specific species pool). Together with existing ecological metrics, concepts, and conservation tools, dark diversity can be used to complement and further develop conservation prioritization and management decisions through an understanding of biodiversity relativized by its potential (i.e., its species pool). Furthermore, through a detailed understanding of the population, community, and functional dark diversity, the restoration potential of degraded habitats can be more rigorously assessed and so to the likelihood of successful species invasions. We suggest the application of the dark diversity concept is currently an underappreciated source of information that is valuable for conservation applications ranging from macroscale conservation prioritization to more locally scaled restoration ecology and the management of invasive species. Enlazar la diversidad con los procesos biológicos es esencial para el desarrollo de decisiones informadas y efectivas de conservación. Desafortunadamente, los patrones observables brindan sólo una proporción de la información necesaria para entender por completo los mecanismos y los procesos que actúan sobre una población o comunidad en particular. Le sugerimos a los administradores de la conservación que usen la información que es ignorada continuamente en relación a la ausencia de especies y que le presentar particular atención a la diversidad oscura (es decir, un conjunto de especies que está ausente de un sitio pero que podría dispersarse a y establecerse ahí, en otras palabras, la porción ausente de un acervo de especies específicas de habitat). Junto con las medidas y conceptos ecológicos y las herramientas de conservación, la diversidad oscura puede utilizarse para complementary desarrollar afondo lapriorización de la conservación y las decisiones administrativas por medio del entendimiento de la biodiversidad relativizada por su potencial (es decir, su acervo de especies). Más allá, a través del entendimiento detallado de la población, la comunidad y la diversidad oscura funcional, el potencial de restauración de los habitats degradados puede ser valorado a fondo de manera más rigurosa, así como la probabilidad de invasiones exitosas de especies. Sugerimos que la aplicación del concepto de diversidad oscura actualmente es una fuente de información poco valorada que es valiosa para las aplicaciones de la conservación, que van desde la priorización de la conservación a macroescala hasta la ecología de restauración con escalas más locales y el manejo de especies invasoras.

The study of community spatial structure is central to understanding diversity patterns over space and species co-occurrence at local scales. Although most analytical approaches consider horizontal and vertical dimensions separately, in this study we introduce a three-dimensional spatial analysis that simultaneously includes horizontal and vertical species associations. Using tree census data (2000–2016) and allometries from the Luquillo forest plot in Puerto Rico, we show that spatial organization becomes less random over time as the forest recovered from land-use legacy effects and hurricane disturbance. Tree species vertical segregation is predominant in the forest with almost all species that co-occur in the horizontal plane avoiding each other in the vertical dimension. Horizontal segregation is less common than vertical, whereas three-dimensional aggregation (a proxy for direct tree competition) is the least frequent type of spatial association. Furthermore, dominant species are involved in more non-random spatial associations, implying that species co-occurrence is facilitated by species segregation in space. This novel three-dimensional analysis allowed us to identify and quantify tree species spatial distributions, how interspecific competition was reduced through forest structure, and how it changed over time after disturbance, in ways not detectable from two-dimensional analyses alone.

The continental and marine territories of Uruguay are characterised by a rich convergence of multiple biogeographic ecoregions of the Neotropics, making this country a peculiar biodiversity spot. However, despite the biological significance of Uruguay for the South American subcontinent, the distribution of biodiversity patterns in this country remain poorly understood, given the severe gaps in available records of geographic species distributions. Currently, national biodiversity datasets are not openly available and, thus, a dominant proportion of the primary biodiversity data produced by researchers and institutions across Uruguay remains highly dispersed and difficult to access for the wider scientific and environmental community. In this paper, we aim to fill this gap by developing the first comprehensive, open-access database of biodiversity records for Uruguay (Biodiversidata), which is the result of a large-scale collaboration involving experts working across the entire range of taxonomic diversity found in the country. As part of the first phase of Biodiversidata, we here present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates. The database provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country. The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https://doi.org/10.5281/zenodo.2650169. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date and it represents the first open repository for the country.

Aim Ecological communities are composed of both species and the biotic relationships (interactions or spatial associations) among them. Biotic homogenization in species composition (i.e., increased site‐to‐site similarity) is recognized as a common consequence of global change, but less is known about how the similarity of species relationships changes over space and time. Does homogenization of species composition lead to homogenization of species relationships or are the dynamics of species relationships decoupled from changes in species composition? Location Wisconsin, USA. Time period 1950–2012. Major taxa studied Vascular plants. Methods We used long‐term resurvey data to analyse changes in plant species association patterns between the 1950s and 2000s at 266 sites distributed among three community types in Wisconsin, USA. We used species associations (quantified via local co‐occurrence patterns) to represent one type of relationship among species. Species pairs that co‐occur more or less than expected by chance have positive or negative associations, respectively. We then measured beta diversity in both species composition and species association networks over time and space. Results Shifts in species associations consistently exceeded the shifts observed in species composition. Less disturbed forests of northern Wisconsin have converged somewhat in species composition but little in species associations. In contrast, forests in central Wisconsin succeeding from pine barrens to closed‐canopy forests have strongly homogenized in both species composition and species associations. More fragmented forests in southern Wisconsin also tended to converge in species composition and in the species’ negative associations, but their positive associations diverged over the last half century. Species composition and associations are generally affected by a similar set of environmental variables. Their relative importance, however, has changed over time. Main conclusions Long‐term shifts in species relationships appear to be decoupled from shifts in species composition despite being affected by similar environmental variables.

Protected areas are designed to shield populations from harmful human impacts. However, in the face of global climate change, a static approach to conservation within these areas is neither feasible nor desirable. One key measure of ecological change at this scale is the arrival of new species and the local extinction of others. Despite strong interest from both scientists and land managers, reliably tracking these dynamics for diverse groups has remained out of reach – until now. The rise of large‐scale data collection by citizen scientists within protected areas presents a powerful new opportunity to revisit and redefine conservation goals. By integrating citizen science observations with herbarium collections, we developed dynamic plant species lists for two of the oldest and most thoroughly documented national parks: Royal National Park (Australia) and Yosemite National Park (USA). While these parks are exceptionally data rich, the framework we present will be increasingly applicable to other protected areas as citizen science efforts continue to expand globally.

Aim Climate change is driving species to migrate to novel areas as current environments become unsuitable. As a result, species distributions have shifted uphill in montane ecosystems globally. Heterogeneous dispersal rates among shifting species could result in complex changes to community assemblages. For example, interspecific differences in dispersal ability could lead to the disruption, or creation, of species interactions and processes within communities, likely amplifying the impact of climate change on ecosystems. Here, we studied the dispersal success of vertebrate species in a tropical montane ecosystem under a climate‐induced uphill shift and assessed the derived impacts on community structures. Location The Australian Wet Tropics bioregion. Method We simulated the uphill shift of 7613 community assemblages across the elevational gradient using thermal resistance layers for movement analyses. Dispersal success was calculated as the probability of shifting given species’ dispersal ability and landscape composition. We then used dissimilarity indices to measure the potential changes in community structures resulting from the heterogeneous dispersal success among migrating species. Results Dispersal success was strongly influenced by species’ dispersal ability, landscape composition and climate change. The heterogeneous dispersal success among migrating species induced marked temporal changes between community assemblages along the elevational gradient. The local extinction rate (i.e. the proportion of species unable to shift) was especially remarkable at high elevations, suggesting potential mass local extinctions of upland species. Furthermore, the increasing local extinction rate with elevation resulted in substantial declines in species co‐occurrence in high‐altitude ecosystems. Main conclusions Our study highlights the escalating impact of climate change on community assemblages in response to climate‐induced elevational shifts, providing a classic example of the \"escalator to extinction.\" Future predictions of the impacts of climate change on ecosystems will benefit from improvements in understanding species interactions, population dynamics and species potential to adapt to a changing environment.