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One of the aims of island biogeography theory is to explain the number of species in an archipelago. Traditionally, the variables used to explain the species richness on an island are its area and distance to the mainland. However, increasing evidence suggests that accounting for other variables is essential for better estimates. In particular, the distance between islands should play a role in determining species richness. This work uses a Bayesian framework using Gaussian processes to assess whether distance to neighbouring islands (spatial autocorrelation) can better explain arthropod species richness patterns in the Azores Archipelago and in the Canary Islands. This method is flexible and allows the inclusion of other variables, such as maximum altitude above sea level (elevation). The results show that accounting for spatial autocorrelation provides the best results for both archipelagos, but overall, spatial autocorrelation seems to be more important in the Canary archipelago. Similarly, elevation plays a more important role in determining species richness in the Canary Islands. We recommend that spatial autocorrelation should always be considered when modelling an archipelago’s species richness.

Ecological communities change because of both natural and human factors. Distinguishing between the two is critical to ecology and conservation science. One of the most common approaches for modelling species composition changes is calculating beta diversity indices and then relating index changes to environmental changes. The main difficulty with these analyses is that beta diversity indices are paired comparisons, which means indices calculated with the same community are not independent. Mantel tests and generalised dissimilarity modelling (GDM) are two of the most commonly used statistical procedures for analysing such data, employing randomisation tests to consider the data’s dependence. Here, we introduce a Bayesian model-based approach called BetaBayes that explicitly incorporates the data dependence. This approach is based on the Bradley– Terry model, which is a widely used approach for modelling paired comparisons that involves building a standard regression model containing two varying intercepts, one for each community involved in the beta diversity index, that capture their respective contributions. We used BetaBayes to analyse a famous dataset collected in Panama that contains information on multiple 1 ha plots from the rain forests of Panama. We calculated the Bray–Curtis index between all pairs of plots, analysed the relationship between the index and two covariates (geographic distance and elevation), and compared the results of BetaBayes with those from the Mantel test and GDM. BetaBayes has two distinctive features. The first is its flexibility, which allows the user to quickly change it to fit the data structure; namely, by adding varying effects, incorporating spatial autocorrelation, and modelling complex nonlinear relationships. The second is that it provides a clear path for performing model validation and model improvement. BetaBayes avoids hypothesis testing, instead focusing on recreating the data generating process and quantifying all the model configurations that are consistent with the observed data info:eu-repo/semantics/publishedVersion

Credible estimates suggest that a large number of the nearly 7000 languages in the world could go extinct this century, a prospect with profound cultural, socioeconomic, and political ramifications. Despite its importance, we still have little predictive theory for language dynamics and richness. Critical to the language extinction problem, however, is to understand the dynamics of the number of speakers of languages, the dynamics of language abundance distributions (LADs). Many regional LADs are very similar to the bell-shaped distributions of relative species abundance predicted by neutral theory in ecology. Using the tenets of neutral theory, here we show that LADs can be understood as an equilibrium or disequilibrium between stochastic rates of origination and extinction of languages. However, neutral theory does not fit some regional LADs, which can be explained if the number of speakers has grown systematically faster in some languages than others, due to cultural factors and other non-neutral processes. Only the LADs of Australia and the United States, deviate from a bell-shaped pattern. These deviations are due to the documented higher, non-equilibrium extinction rates of low-abundance languages in these countries.

Ecology, biogeography and conservation biology, among other disciplines, often rely on species identity, distribution and abundance to perceive and explain patterns in space and time. Yet, species are not independent units in the way they interact with their environment. Species often perform similar roles in networks and their ecosystems, and at least partial redundancy or difference of roles might explain co-existence, competitive exclusion or other patterns reflected at the community level. Therefore, considering species traits, that is, the organisms’ functional properties that interact with the environment, might be of utmost importance in the study of species relative abundances. Several descriptive measures of diversity, such as the species-area relationship (SAR) and the species abundance distribution (SAD), have been used extensively to characterize the communities and as a possible window to gain insight into underlying processes shaping and maintaining biodiversity. However, if the role of species in a community is better assessed by their functional attributes, then one should also study the SAR and the SAD by using trait-based approaches, and not only taxonomic species. Here we merged species according to their similarity in a number of traits, creating functional units, and used these new units to study the equivalent patterns of the SAR and of the SAD (functional units abundance distributions - FUADs), with emphasis on their spatial scaling characteristics. This idea was tested using data on arthropods collected in Terceira island, in the Azorean archipelago. Our results showed that diversity scales differently depending on whether we use species or functional units. If what determines species communities’ dynamics is their functional diversity, then our results suggest that we may need to revaluate the commonly assumed patterns of species diversity and, concomitantly, the role of the underlying processes. SA was financed by the Fundacao para a Ciencia e a Tecnologia project PTDC/BIA-BIC/5558/2014. LB-A was financed by the Portuguese national funds through FCT-Fundacao para a Ciencia e a Tecnologia, I.P., under the Norma Transitoria-DL57/2016/CP1440/CT0022. info:eu-repo/semantics/publishedVersion

Original Research Biological collections, including herbarium specimens, are unique sources of biodiversity data presenting a window on the history of the development and accumulation of knowledge of a specific geographical region. Understanding how the process of discovery impacts that knowledge is particularly important for oceanic islands which are often characterized by both high levels of endemic diversity and high proportions of threatened taxa. The archipelagos of the Macaronesian region (i.e. Azores, Canaries, Savages, Madeira, and Cabo Verde) have been the focus of attention for scientific expeditions since the end of the 17th century. However, there is no integrated study describing the historical process of collecting, discovery and description of its flora. Using as a case study the Cabo Verde endemic angiosperm flora, we review the history of collecting in the flora and apply a Bayesian approach to assess the accumulation of species discovery, through time and space across the nine islands of the archipelago. Our results highlight the central role not only of natural characteristics (e.g. area, age, maximum altitude and average value of the terrain ruggedness index) but also historical factors (i.e. the location of major harbors) for the development of knowledge of the flora. The main factors that have determined the process of species description in the archipelago and how this impact our understanding of diversity patterns across archipelagos are discussed info:eu-repo/semantics/publishedVersion

Aim Land-use change is a major threat to biodiversity globally. Roads cause direct mortality and limitation of individual movements, which may isolate populations and affect their viability in the long term. Here we provide the first comprehensive global assessment of the exposure of terrestrial mammalian carnivores to roads using an integrated modelling framework. Location Global. Methods We estimated critical road densities and critical patch sizes for each species based on a spatially explicit model and life-history traits. We calculated the distribution of landscape fragment sizes for each carnivore species by intersecting global road density with each species range. The proportion of a species’ geographical range with fragments below the critical patch size is used as an index of the vulnerability to roads. Results We found that the carnivores expected to be most exposed to roads belong to families Felidae, Ursidae, Mustelidae, Canidae and Procyonidae. Approximately one-third of the species most affected have not been identified by the IUCN as threatened by roads. Our model projects time to extinction that may be as low as one century for some species, such as the endangered Iberian lynx. Species are expected to be more exposed in areas with medium to high road density but, surprisingly, also in areas where road density is relatively low. Hotspots of the number of species locally endangered by roads occur in North America and Asia. Main conclusions Our results suggest the need to reassess the status and threats of those species that have not been previously recognized as strongly affected by roads. Our framework can be applied at different spatial scales, to assess the effects of the development of the road network and inform prioritization schemes for road building, and to identify areas for conservation, and species requiring particular mitigation and restoration measures.

Railway ecology is an emerging discipline. In this review, we focus on what is known today regarding the impacts of railways on wildlife, and on the methods to identify, monitor, and mitigate these impacts. Wildlife-train collisions are the most often reported impact, although railway lines can also represent barriers to animal movement, bisecting populations or reducing wildlife access to resources. Little is known on the impact of habitat loss and fragmentation due to railways alone, or on their disturbance effects, including pollution (noise, chemical, light), and on the potential to provide habitat connectivity or surrogate habitats for native species in degraded landscapes. Molecular techniques are one of the most promising methods to study the impacts of railways, as genetic analyses are useful to identify both population sub-structuring, and to assess the potential restoration of functional connectivity by mitigation measures like wildlife passes, or to estimate effective population sizes. Field work is necessary to provide credible mortality rates, which, combined with computer simulations, can allow for estimations of the impact of mortality on population viability. Studies should ideally have Before-After-Control-Impact designs and be long-term. We need to improve mortality estimates, and to understand how impacts threaten population dynamics. We need to go from local-scale studies (e.g., animals use the underpasses) to landscape-scale (i.e., where to place these underpasses to maximize the connectivity at regional/populational levels). Finally, we need to expand our knowledge on less studied, less charismatic species, and to explore the potential environmental benefits of green practices on railway corridors.

Linear infrastructures (e.g. roads, railways or power lines) promote a myriad of negative impacts on wildlife around the world, of which direct mortality is the most visible one. When high mortality rates are found, mitigation measures are often discussed and applied. On the other hand, the lack of mortality is commonly interpreted as evidence of low impact on wildlife. We argue that the lack of mortality may actually mask two pervasive effects of linear infrastructures on animal populations: past massive mortality, causing local extinctions, or strong barrier effects due to the inability or reluctance of individuals to traverse the infrastructure corridor. In order to obtain a sound impact assessment of the linear infrastructures on wildlife, research is needed that integrates long-term mortality data with information on the abundance of the focal species, their genetic patterns and movement behavior. We discuss the implications of these impacts for both infrastructures and landscape management. Keywords: Barrier effect, Fences, Population depletion, Power lines, Railways, Roadkill, Roads, Transportation networks

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.

Linear infrastructures, one of several forms of land-use, are a major driver of biodiversity loss. Roads impact populations at many levels, with direct road mortality and barrier effect contributing to decreased population abundance, higher isolation and subdivision, and therefore to increased extinction risk. In this paper, we compared the effect of road mortality and of the barrier effect on population isolation, persistence and size, and assessed the interaction of these effects with dispersal. We used a spatially explicit, process-based model of population dynamics in landscapes fragmented by varying levels of road density. We modelled a barrier effect independently from road mortality by varying the probability with which individuals avoid crossing roads. Both road mortality and the barrier effect caused population isolation. While road mortality alone had stronger negative effects than the barrier effect without extra mortality, the latter also resulted in decreased population size. Yet, road avoidance could, in some cases, rescue populations from extinction. Populations with a large dispersal distance were more negatively affected as road mortality increased. However, when there was no road mortality they maintained larger sizes than populations with a short dispersal distance. Our results highlight the much higher relative importance of road mortality than the barrier effect for population size and persistence, and the importance of assessing relevant species traits for effective long-term transportation planning and conservation management. Our model can be used in species-specific situations and with real landscape configurations in applications such as conservation planning info:eu-repo/semantics/publishedVersion

Understanding patterns of community structure and the causes for their variation can be furthered by comparative biogeographic analyses of island biotas. We used woody plant data at the local scale to investigate variations in species rarity, alpha, beta, and gamma diversity within and between three islands from the oceanic archipelagoes of Azores, Canaries and Mascarene. We used standardized protocols to sample ten 50 m × 50 m forest plots in each of the three islands with contrasting climate and regional species pools: Terceira (Azores), Tenerife (Canaries), and Reunion (Mascarene Islands). Occupancy frequency distributions and species abundance distributions were used to investigate rarity. The partitioning of beta diversity in a distance-decay framework was used to test for spatial patterns of community composition. Rarity was much more pronounced in the highly diverse islands of Tenerife and Reunion than in the regionally poorer island of Terceira. The number of species rose faster with increasing sample area in both Tenerife and Reunion. The slope of the species rank abundance curve was steeper in Terceira whereas the richer island assemblages approached a lognormal model. Compositional changes according to spatial distance were mostly due to replacement of species in Terceira and Reunion. Our results point to important differences in the community structure of Terceira, which is the less diverse and temperate region in comparison to Tenerife and Reunion which are highly diverse., This research was supported by the ERA-Net Net -Biome research framework, financed through the: Canary Islands Government ACIISI grants SE-12/02 (PO), SE-12/03 (JCC), SE-12/04 (BE), co-financed by FEDER; Portuguese FCT-NETBIOME grant 0003/2011 (PB); French ANR-NETBIOME grant n°11-EBIM-001-01 (CT); Région Reunion council for research activities (DS), Universitéde La Reunion contract DGADD/PE/20120585 (DS). CR, FR and IRA were supported by grants from Fundação da Ciência e Tecnologia - FCT-SFRH/BPD/91357/2012, FCT-PTDC/BIA-BIC/119255/2010, FCT-SFRH/BPD/102804/2014 respectively. MF has been funded by Direcção Regional da Ciência e Tecnologia, DRCT-M3.1.7/F/002/2011 and the Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq (401045/2014-5), Programa Ciência sem Fronteiras; the current MF’s contract is supported by the Universidad de Alcalá. The work of LBD in this manuscript was performed within the scope of the project MOMENTOS (PTDC/BIA-BIC/5558/2014).

Islands harbour evolutionary and ecologically unique biota, which are currently disproportionately threatened by a multitude of anthropogenic factors, including habitat loss, invasive species and climate change. Native forests on oceanic islands are important refugia for endemic species, many of which are rare and highly threatened. Long-term monitoring schemes for those biota and ecosystems are urgently needed: (i) to provide quantitative baselines for detecting changes within island ecosystems, (ii) to evaluate the effectiveness of conservation and management actions, and (iii) to identify general ecological patterns and processes using multiple island systems as repeated ‘natural experiments’. In this contribution, we call for a Global Island Monitoring Scheme (GIMS) for monitoring the remaining native island forests, using bryophytes, vascular plants, selected groups of arthropods and vertebrates as model taxa. As a basis for the GIMS, we also present new, optimized monitoring protocols for bryophytes and arthropods that were developed based on former standardized inventory protocols. Effective inventorying and monitoring of native island forests will require: (i) permanent plots covering diverse ecological gradients (e.g. elevation, age of terrain, anthropogenic disturbance); (ii) a multiple-taxa approach that is based on standardized and replicable protocols; (iii) a common set of indicator taxa and community properties that are indicative of native island forests’ welfare, building on, and harmonized with existing sampling and monitoring efforts; (iv) capacity building and training of local researchers, collaboration and continuous dialogue with local stakeholders; and (v) long-term commitment by funding agencies to maintain a global network of native island forest monitoring plots., We would like to thank all colleagues who supported this work for their inspiration in discussing the importance of island biodiversity monitoring within the project MACDIV (FCT-PTDC/BIABIC/0054/2014). Data were derived from previous projects NETBIOME-MOVECLIM (M2.1.2/F/04/2011/NET), NETBIOME-ISLANDBIODIV (NETBIOME/0003/2011). For the development of this paper the work of CR, MB, AG and IRA was partly supported respectively by grants FCT-SFRH/BPD/91357/2012, FCT-SFRH/BPD/86215/2012, FCT-SFRH/BPD/100017/2014 and FCT-SFRH/BPD/102804/2014. AMCS was supported by a Marie Curie Intra-European Fellowship (IEF 331623 ‘COMMSTRUCT’) and by a Juan de la Cierva Fellowship (IJCI-2014-19502) funded by the Spanish ‘Ministerio de Economía y Competitividad’. MF was funded by the Direcção Regional da Ciência, Tecnologia e Comunicações (DRCT) (M3.1.7/F/002/2011) and by the Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq (401045/2014-5), program Ciência sem Fronteiras funded by the University of Alcalá (Spain). SPR is supported by CNPq/Brazil. LBA’s worked on this manuscript within the project MOMENTOS (PTDC/BIA-BIC/5558/2014). GIMS will be implemented in La Réunion, with the DIVINES project (POE 2014-2020 FEDER) granted to DS and CAP at the University of La Réunion and to BL at the National Park of La Réunion.

© The Author(s) 2017., Species abundance distributions (SAD) are central to the description of diversity and have played a major role in the development of theories of biodiversity and biogeography. However, most work on species abundance distributions has focused on one single spatial scale. Here we used data on arthropods to test predictions obtained with computer simulations on whether dispersal ability influences the rate of change of SADs as a function of sample size. To characterize the change of the shape of the SADs we use the moments of the distributions: the skewness and the raw moments. In agreement with computer simulations, low dispersal ability species generate a hump for intermediate abundance classes earlier than the distributions of high dispersal ability species. Importantly, when plotted as function of sample size, the raw moments of the SADs of arthropods have a power law pattern similar to that observed for the SAD of tropical tree species, thus we conjecture that this might be a general pattern in ecology. The existence of this pattern allows us to extrapolate the moments and thus reconstruct the SAD for larger sample sizes using a procedure borrowed from the field of image analysis based on scaled discrete Tchebichef moments and polynomials., This work was funded by the FCT project MOMENTOS (PTDC/ BIA-BIC/5558/2014). AMCS was supported by a Marie Curie Intra-European Fellowship (IEF 331623 ‘COMMSTRUCT’) and by a Juan de la Cierva Fellowship (IJCI-2014-19502) funded by the Spanish ‘Ministerio de Economía y Competitividad’. IRA was supported by a FCT Fellowship (SFRH/BPD/102804/2014)

As societies realise the importance of maintaining biodiversity and, accordingly, acknowledge the need for monitoring, minimizing and compensating the impacts of socioeconomic activities, including transportation, more scientists will be called to address these societal challenges. Railway Ecology is emerging in this context as a relatively new field to identify and provide solutions to the specific environmental problems associated with the building and operation of railways, particularly their impacts on wildlife. This is an interdisciplinary field that uses and draws methods from other disciplines, ranging from ecology and genetics, to statistics and computer simulations. Here, we summarize the guidelines to address railway-related biodiversity conservation problems as they were identified in the several chapters of this book, and recommend lines for future research.

Numerous evolutionary studies have sought to explain the distribution of diversity across the limbs of the tree of life. At the same time, ecological studies have sought to explain differences in diversity and relative abundance within and among ecological communities. Traditionally, these patterns have been considered separately, but models that consider processes operating at the level of individuals, such as neutral biodiversity theory (NBT), can provide a link between them. Here, we compare evolutionary dynamics across a suite of NBT models. We show that NBT can yield phylogenetic tree topologies with imbalance closely resembling empirical observations. In general, metacommunities that exhibit greater disparity in abundance are characterized by more imbalanced phylogenetic trees. However, NBT fails to capture the tempo of diversification as represented by the distribution of branching events through time. We suggest that population-level processes might therefore help explain the asymmetry of phylogenetic trees, but that tree shape might mislead estimates of evolutionary rates unless the diversification process is modeled explicitly.

Roads can have drastic impacts on wildlife populations. Although there is wide recognition of the negative impacts caused by roads and a wealth of practical studies, there is a lack of theoretical work that can be used to predict the impact of road networks or to implement mitigation measures. Here, using Skellam’s diffusion model, we develop analytic and numerical approaches to analyze the impact of road networks on the survival of populations. Our models show that the viability of a population is determined not only by road density but also by the size and shape of patches. Accordingly, we studied the minimum size of a patch to sustain a population with given diffusion and growth parameters. We provide simple formulas to estimate the minimum patch size, and illustrate the importance of shape with square and rectangular patches. Our models also allow the estimation of time to extinction after road construction for a population in a patch smaller than that of the minimum size. Finally, using numerical computations we illustrate how the spatial arrangement of fences strongly affects both the equilibrium density and the spatial distribution of populations, and that not all fence layouts are equally effective. We anticipate that our methods provide a tool to assess the impact of geometrical features of road networks on wildlife and that they can be used to design mitigation measures to prevent the decline and extinction of populations in an anthropogenically disturbed landscape.

This article reviews existing models linking land-use change to biodiversity dynamics, both when native habitats are lost or when the landscape structure of countryside areas is modified. It covers both phenomenological models such as the species–area relationship and process-based models such as source-sink population models.

Copyright © 2012 The Authors. Ecography © 2012 Nordic Society Oikos. Species abundance distributions are an essential tool in describing the biodiversity of ecological communities. We now know that their shape changes as a function of the size of area sampled. Here we analyze the scaling properties of species abundance distributions by using the moments of the logarithmically transformed number of individuals. We find that the moments as a function of area size are well fitted by power laws and we use this pattern to estimate the species abundance distribution for areas larger than those sampled. To reconstruct the species abundance distribution from its moments, we use discrete Tchebichef polynomials. We exemplify the method with data on tree and shrub species from a 50 ha plot of tropical rain forest on Barro Colorado Island, Panama. We test the method within the 50 ha plot, and then we extrapolate the species abundance distribution for areas up to 5 km2. Our results project that for areas above 50 ha the species abundance distributions have a bimodal shape with a local maximum occurring for the singleton classes and that this maximum increases with sampled area size.

Although fractals have been applied in ecology for some time, multifractals have, in contrast, received little attention. In this article, we apply multifractals to the species-area relationship and species abundance distributions. We highlight two results: first, species abundance distributions collected at different spatial scales may collapse into a single curve after appropriate renormalization, and second, the power-law form of the species-area relationship and the Shannon, Simpson, and Berger-Parker diversity indices belong to a family of equations relating the species number, species abundance, and area through the moments of the species abundance-probability density function. Explicit formulas for these diversity indices, as a function of area, are derived. Methods to obtain the multifractal spectra from a data set are discussed, and an example is shown with data on tree and shrub species collected in a 50-ha plot on Barro Colorado Island, Panama. Finally, we discuss the implications of the multifractal formalism to the relationship between species range and abundance and the relation between the shape of the species abundance distribution and area.

New roads, agricultural projects, logging, and mining are claiming an ever greater area of once-pristine Amazonian forest. The Mil- lennium Ecosystems Assessment (MA) forecasts the extinction of a large fraction of Amazonian tree species based on projected loss of forest cover over the next several decades. How accurate are these estimates of extinction rates? We use neutral theory to estimate the number, relative abundance, and range size of tree species in the Amazon metacommunity and estimate likely tree-species ex- tinctions under published optimistic and nonoptimistic Amazon scenarios. We estimate that the Brazilian portion of the Amazon Basin has (or had) 11,210 tree species that reach sizes >10 cm DBH (stem diameter at breast height). Of these, 3,248 species have population sizes >1 million individuals, and, ignoring possible climate-change effects, almost all of these common species persist under both optimistic and nonoptimistic scenarios. At the rare end of the abundance spectrum, however, neutral theory predicts the existence of 5,308 species with

Introduction To better understand biodiversity scaling, it may be useful to characterize the biodiversity scaling relationships that arise from the neutral perspective. This exercise will help in formulating quantitative null hypotheses for observed biodiversity scaling relationships. Here we use the term biodiversity to refer not only to species richness, but also to relative species abundance, and biodiversity scaling to refer to how patterns of biodiversity change on increasing sampling (spatial) scales. The study of biodiversity includes questions about the spatial dispersion and geographic range of species, relative species abundance, endemism, and beta diversity, the turnover of species across landscapes. A full discussion of all-taxa biodiversity scaling in the context of neutral theory is beyond the scope of the present theory because the theory currently applies only to communities of trophically similar species (a tree community, for example). It is also individual based rather than biomass based. Despite these limitations neutral theory is nevertheless a mechanistic, dynamical theory of community assembly based on fundamental demographic processes (birth, death, dispersal, speciation) – even though its postulated assembly rules are extremely simple. Under current neutral theory, speciation, ecological drift (demographic stochasticity in birth and deaths), and dispersal govern the presence or absence and the abundance of species in communities over local to global scales. Extinction is also critically important, but under neutrality, the extinction rate can be predicted once the other three processes are known. Neutral theory asserts that, to a first approximation, trophically similar species are identical (symmetric) in these vital rates on a per-capita basis. According to the theory, species develop differences in abundance due to demographic stochasticity and accidents of dispersal. Once species become differentiated in abundance, their expected fates diverge. Common species are expected to have longer life spans and to be more persistent members of local communities than rare species.