Showing papers in "Journal of Biogeography in 2012"

Correlation and process in species distribution models: bridging a dichotomy

Abstract: Within the field of species distribution modelling an apparent dichotomy exists between process-based and correlative approaches, where the processes are explicit in the former and implicit in the latter. However, these intuitive distinctions can become blurred when comparing species distribution modelling approaches in more detail. In this review article, we contrast the extremes of the correlative–process spectrum of species distribution models with respect to core assumptions, model building and selection strategies, validation, uncertainties, common errors and the questions they are most suited to answer. The extremes of such approaches differ clearly in many aspects, such as model building approaches, parameter estimation strategies and transferability. However, they also share strengths and weaknesses. We show that claims of one approach being intrinsically superior to the other are misguided and that they ignore the process–correlation continuum as well as the domains of questions that each approach is addressing. Nonetheless, the application of process-based approaches to species distribution modelling lags far behind more correlative (process-implicit) methods and more research is required to explore their potential benefits. Critical issues for the employment of species distribution modelling approaches are given, together with a guideline for appropriate usage. We close with challenges for future development of process-explicit species distribution models and how they may complement current approaches to study species distributions.

A realignment of marine biogeographic provinces with particular reference to fish distributions

Abstract: Marine provinces, founded on contrasting floras or faunas, have been recognized for more than 150 years but were not consistently defined by endemism until 1974. At that time, provinces were based on at least a 10% endemism and nested within biogeographic regions that covered large geographic areas with contrasting biotic characteristics. Over time, some minor adjustments were made but the overall arrangement remained essentially unaltered. In many provinces, data on endemism were still not available, or were available only for the most widely studied vertebrates (fishes), a problem that is ongoing. In this report we propose a realignment for three reasons. First, recent works have provided new information to modify or redefine the various divisions and to describe new ones, including the Mid-Atlantic Ridge, Southern Ocean, Tropical East Pacific and Northeast Pacific. Second, phylogeographic studies have demonstrated genetic subdivisions within and between species that generally corroborated provinces based on taxonomic partitions, with a notable exception at the Indian–Pacific oceanic boundary. Third, the original separation of the warm-temperate provinces from the adjoining tropical ones has distracted from their close phylogenetic relationships. Here we propose uniting warm-temperate and tropical regions into a single warm region within each ocean basin, while still recognizing provinces within the warm-temperate and tropical zones. These biogeographic subdivisions are based primarily on fish distribution but utilize other marine groups for comparison. They are intended to demonstrate the evolutionary relationships of the living marine biota, and to serve as a framework for the establishment of smaller ecological units in a conservation context.

Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents

Abstract: Aim Biotic interactions – within guilds or across trophic levels – have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of ‘species interaction distribution models’ (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices. Location Local to global. Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions. Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species’ effect and response traits. Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities.

The island species–area relationship: biology and statistics

Abstract: Aim We conducted the most extensive quantitative analysis yet undertaken of the form taken by the island species–area relationship (ISAR), among 20 models, to determine: (1) the best-fit model, (2) the best-fit model family, (3) the best-fit ISAR shape (and presence of an asymptote), (4) system properties that may explain ISAR form, and (5) parameter values and interpretation of the logarithmic implementation of the power model. Location World-wide. Methods We amassed 601 data sets from terrestrial islands and employed an information-theoretic framework to test for the best-fit ISAR model, family, and shape, and for the presence/absence of an asymptote. Two main criteria were applied: generality (the proportion of cases for which the model provided an adequate fit) and efficiency (the overall probability of a model, when adequate, being the best at explaining ISARs; evaluated using the mean overall AICc weight). Multivariate analyses were used to explore the potential of island system properties to explain trends in ISAR form, and to describe variation in the parameters of the logarithmic power model. Results Adequate fits were obtained for 465 data sets. The simpler models performed best, with the power model ranked first. Similar results were obtained at model family level. The ISAR form is most commonly convex upwards, without an asymptote. Island system traits had low descriptive power in relation to variation in ISAR form. However, the z and c parameters of the logarithmic power model show significant pattern in relation to island system type and taxon. Main conclusions Over most scales of space, ISARs are best represented by the power model and other simple models. More complex, sigmoid models may be applicable when the spatial range exceeds three orders of magnitude. With respect to the log power model, z-values are indicative of the process(es) establishing species richness and composition patterns, while c-values are indicative of the realized carrying capacity of the system per unit area. Variation in ISAR form is biologically meaningful, but the signal is noisy, as multiple processes constrain the ecological space available within island systems and the relative importance of these processes varies with the spatial scale of the system.

The partitioning of Africa: Statistically defined biogeographical regions in sub-Saharan Africa

Abstract: Aim To test whether it is possible to establish a common biogeographical regionalization for plants and vertebrates in sub-Saharan Africa (the Afrotropical Region), using objective multivariate methods. Location Sub-Saharan Africa (Afrotropical Region). Methods We used 1° grid cell resolution databases for birds, mammals, amphibians and snakes (4142 vertebrate species) and c. 13% of the plants (5881 species) from the Afrotropical Region. These databases were analysed using cluster analysis techniques to define biogeographical regions. A β(sim) dissimilarity matrix was subjected to a hierarchical classification using the unweighted pair-group method with arithmetic averages (UPGMA). The five group-specific biogeographical regionalizations were compared against a regionalization developed from a combined database, and a regionalization that is maximally congruent with the five group-specific datasets was determined using a consensus classification. The regionalizations were interpreted against measures of spatial turnover in richness and composition for the five datasets as well as the combined dataset. Results We demonstrate the existence of seven well-defined and consistent biogeographical regions in sub-Saharan Africa. These regionalizations are statistically defined and robust between groups, with minor taxon-specific biogeographical variation. The proposed biogeographical regions are: Congolian, Zambezian, Southern African, Sudanian, Somalian, Ethiopian and Saharan. East Africa, the West African coast, and the transitions between the Congolian, Sudanian and Zambezian regions are unassigned. The Cape area in South Africa, Afromontane areas and the coastal region of East Africa do not emerge as distinct regions but are characterized by high neighbourhood heterogeneity, rapid turnover of species and high levels of narrow endemism. Main conclusions Species distribution data and modern cluster analysis techniques can be used to define biogeographical regions in Africa that reflect the patterns found in both vertebrates and plants. The consensus of the regionalizations between different taxonomic groups is high. These regions are broadly similar to those proposed using expert opinion approaches. Some previously proposed transitional zones are not recognized in this classification.

How to understand species' niches and range dynamics: a demographic research agenda for biogeography

Abstract: 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.

Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys

Abstract: Aim Capuchin monkey species are widely distributed across Central and South America. Morphological studies consistently divide the clade into robust and gracile forms, which show extensive sympatry in the Amazon Basin. We use genetic data to test whether Miocene or Plio-Pleistocene processes may explain capuchin species’ present distributions, and consider three possible scenarios to explain widespread sympatry. Location The Neotropics, including the Amazon and Atlantic Coastal Forest. Methods We sequenced the 12S ribosomal RNA and cytochrome b genes from capuchin monkey specimens. The majority were sampled from US museum collections and were wild-caught individuals of known provenance across their distribution. We applied a Bayesian discrete-states diffusion model, which reconstructed the most probable history of invasion across nine subregions. We used comparative methods to test for phylogeographic association and dispersal rate variation. Results Capuchins contained two well supported monophyletic clades, the morphologically distinct ‘gracile’ and ‘robust’ groups. The time-tree analysis estimated a late Miocene divergence between Cebus and Sapajus and a subsequent Plio-Pleistocene diversification within each of the two clades. Bayesian analysis of phylogeographic diffusion history indicated that the current wide-ranging sympatry of Cebus and Sapajus across much of the Amazon Basin was the result of a single explosive late Pleistocene invasion of Sapajus from the Atlantic Forest into the Amazon, where Sapajus is now sympatric with gracile capuchins across much of their range. Main conclusions The biogeographic history of capuchins suggests late Miocene geographic isolation of the gracile and robust forms. Each form diversified independently, but during the Pleistocene, the robust Sapajus expanded its range from the Atlantic Forest to the Amazon, where it has now encroached substantially upon what was previously the exclusive range of gracile Cebus. The genus Cebus, as currently recognized, should be split into two genera to reflect the Miocene divergence and two subsequent independent Pliocene radiations: Cebus from the Amazon and Sapajus from the Atlantic Forest.

Modelling the effect of size on the aerial dispersal of microorganisms

Abstract: Aim We investigate the long-standing question of whether the small size of microbes allows most microbial species to colonize all suitable sites around the globe or whether their ranges are limited by opportunities for dispersal. In this study we use a modelling approach to investigate the effect of size on the probability of between-continent dispersal using virtual microorganisms in a global model of the Earths atmosphere.

Climatic stability in the Brazilian Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot

Abstract: Aim To investigate the historical distribution of the Cerrado across Quaternary climatic fluctuations and to generate historical stability maps to test: (1) whether the ‘historical climate’ stability hypothesis explains squamate reptile richness in the Cerrado; and (2) the hypothesis of Pleistocene connections between savannas located north and south of Amazonia. Location The Cerrado, a savanna biome and a global biodiversity hotspot distributed mainly in central Brazil. Methods We generated occurrence datasets from 1000 presence points randomly selected from the entire distribution of the Cerrado, as determined by two spatial definitions. We modelled the potential Cerrado distribution by implementing a maximum-entropy machine-learning algorithm across four time projections: current, mid-Holocene (6 ka), Last Glacial Maximum (LGM, 21 ka) and Last Interglacial(LIG,120 ka).Wegeneratedhistoricalstabilitymaps(refugialareas)by overlappingpresence/absenceprojectionsofallscenarios,andcheckedconsistencies withqualitativecomparisonswithavailablefossilpollenrecords.Webuiltaspatially explicit simultaneous autoregressive model to explore the relationship between current climate, climatic stability, and squamate species richness. Results Models predicted the LGM and LIG as the periods of narrowest and widest Cerrado distributions, respectively, and were largely corroborated by palynological evidence. We found evidence for two savanna corridors (eastern coastal during the LIG, and Andean during the LGM) and predicted a large

Global habitat suitability of cold-water octocorals

Abstract: Aim Three-quarters of Octocorallia species are found in deep waters. These cold-water octocoral colonies can form a major constituent of structurally complex habitats. The global distribution and the habitat requirements of deep-sea octocorals are poorly understood given the expense and difficulties of sampling at depth. Habitat suitability models are useful tools to extrapolate distributions and provide an understanding of ecological requirements. Here, we present global habitat suitability models and distribution maps for seven suborders of Octocorallia: Alcyoniina, Calcaxonia, Holaxonia, Scleraxonia, Sessiliflorae, Stolonifera and Subselliflorae. Location Global. Methods We use maximum entropy modelling to predict octocoral distribution using a database of 12,508 geolocated octocoral specimens and 32 environmental grids resampled to 30 arc-second (approximately 1km 2) resolution. Additionally, a meta-analysis determined habitat preferences and niche overlap between the different suborders of octocorals. Results Suborder Sessiliflorae had the widest potential habitat range, but all records for all suborders implied a habitat preference for continental shelves and margins, particularly the North and West Atlantic and Western Pacific Rim. Temperature, salinity, broad scale slope, productivity, oxygen and calcite saturation state were identified as important factors for determining habitat suitability. Less than 3% of octocoral records were found in waters undersaturated for calcite, but this result is affected by a shallow-water sampling bias. Main conclusions The logistical difficulties, expense and vast areas associated with deep-sea sampling leads to a gap in the knowledge of faunal distributions that is difficult to fill without predictive modelling. Global distribution estimates are presented, highlighting many suitable areas which have yet to be studied. We suggest that approximately 17% of oceans are suitable for at least one suborder but 3.5% may be suitable for all seven. This is the first global habitat suitability modelling study on the distribution of octocorals and forms a useful resource for researchers, managers and conservationists. © 2012 Blackwell Publishing Ltd.

Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests

Abstract: Aim The tropical Andes are a world biodiversity hotspot With diverse biomes and dramatic, geologically recent mountain uplift, they offer a system to study the relative contributions of geological and biome history to species richness There are preliminary indications that historical species assembly in the Andes has been influenced by physiographical heterogeneity and that distinct biomes have evolved in relative isolation despite physical proximity Here we test this ‘Andean biotic separation hypothesis’ by focusing on the low-elevation, seasonally dry tropical forest (SDTF) biome to determine whether patterns of plant diversification within the SDTF differ from those in mid- and high-elevation biomes Location Tropical Andes, South America Methods Densely sampled time-calibrated phylogenies for five legume genera (Amicia, Coursetia, Cyathostegia, Mimosa and Poissonia) containing species endemic to the Andean SDTF biome were used to investigate divergence times and levels of geographical structure Geographical structure was measured using isolation-by-distance methods Meta-analysis of time-calibrated phylogenies of Andean plant groups was used to compare the pattern and tempo of endemic species diversification between the major Andean biomes Results Long-term persistence of SDTF in the Andes is suggested by old stem ages (5–27 Ma) of endemic genera/clades within genera, and deep divergences coupled with strong geographical structure among and within species Comparison of species diversification patterns among different biomes shows that the relatively old, geographically confined pattern of species diversification in SDTF contrasts with the high-elevation grasslands that show rapid and recent radiations driven by ecological opportunities Main conclusions The SDTF biome has a long history in the Andes We suggest that the diverse SDTF flora has been assembled gradually over the past c 19 Ma from lineages exhibiting strong phylogenetic niche conservatism These patterns suggest that Andean SDTFs have formed stable and strongly isolated ‘islands’ despite the upheavals of Andean uplift Indeed, the Andean SDTFs may represent some of the most isolated and evolutionarily persistent continental plant communities, similar in many respects to floras of remote oceanic islands

An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA

Abstract: Aim Current evidence from temperate studies suggests that ectomycorrhizal (ECM) fungi require overland routes for migration because of their obligate symbiotic associations with woody plants. Despite their key roles in arctic ecosystems, the phylogenetic diversity and phylogeography of arctic ECM fungi remains little known. Here we assess the phylogenetic diversity of ECM communities in an isolated, formerly glaciated, high arctic archipelago, and provide explanations for their phylogeographic origins. Location Svalbard. Methods We generated and analysed internal transcribed spacer (ITS) nuclear ribosomal DNA sequences from both curated sporocarp collections (from Svalbard) and soil polymerase chain reaction (PCR) clone libraries (from Svalbard and the North American Arctic), compared these with publicly available sequences in GenBank, and estimated the phylogenetic diversity of ECM fungi in Svalbard. In addition, we conducted coalescent analyses to estimate migration rates in selected species. Results Despite Svalbard’s geographic isolation and arctic climate, its ECM fungi are surprisingly diverse, with at least 72 non-singleton operational taxonomic units (soil) and 109 phylogroups (soil + sporocarp). The most species-rich genera are Thelephora/Tomentella, Cortinarius and Inocybe, followed by Hebeloma, Russula, Lactarius, Entoloma, Sebacina, Clavulina, Laccaria, Leccinum and Alnicola. Despite the scarcity of available reference data from other arctic regions, the majority of the phylogroups (73.4%) were also found outside Svalbard. At the same time, all putative Svalbard ‘endemics’ were newly sequenced taxa from diverse genera with massive undocumented diversity. Overall, our results support long-distance dispersal more strongly than vicariance and glacial survival. However, because of the high variation in nucleotide substitution rates among fungi, allopatric persistence since the Pliocene, although unlikely, cannot be statistically rejected. Results from the coalescent analyses suggest recent gene flow among different arctic areas. Main conclusions Our results indicate numerous recent colonization events and suggest that long-distance, transoceanic dispersal is widespread in arctic ECM fungi, which differs markedly from the currently prevailing view on the dispersal capabilities of ECM fungi. Our molecular evidence indicates that long-distance dispersal has probably played a major role in the phylogeographic history of some ECM fungi in the Northern Hemisphere. Our results may have implications for studies on the biodiversity, ecology and conservation of arctic fungi in general.

Connecting dynamic vegetation models to data – an inverse perspective

Abstract: Dynamic vegetation models provide process-based explanations of the dynamics and the distribution of plant ecosystems. They offer significant advantages over static, correlative modelling approaches, particularly for ecosystems that are outside their equilibrium due to global change or climate change. A persistent problem, however, is their parameterization. Parameters and processes of dynamic vegetation models (DVMs) are traditionally determined independently of the model, while model outputs are compared to empirical data for validation and informal model comparison only. But field data for such independent estimates of parameters and processes are often difficult to obtain, and the desire to include better descriptions of processes such as biotic interactions, dispersal, phenotypic plasticity and evolution in future vegetation models aggravates limitations related to the current parameterization paradigm. In this paper, we discuss the use of Bayesian methods to bridge this gap. We explain how Bayesian methods allow direct estimates of parameters and processes, encoded in prior distributions, to be combined with inverse estimates, encoded in likelihood functions. The combination of direct and inverse estimation of parameters and processes allows a much wider range of vegetation data to be used simultaneously, including vegetation inventories, species traits, species distributions, remote sensing, eddy flux measurements and palaeorecords. The possible reduction of uncertainty regarding structure, parameters and predictions of DVMs may not only foster scientific progress, but will also increase the relevance of these models for policy advice.

Global patterns of amphibian phylogenetic diversity

Abstract: Aim Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location Global; equal-area grid cells of approximately 10,000 km2. Methods We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index and the total taxonomic distinctness (TTD) index, because we found that the variance of the other two indices we examined (average taxonomic distinctness and mean root distance) strongly depended on species richness. We then identified regions with unusually high or low phylogenetic diversity given the underlying level of species richness by using the residuals from the global relationship of species richness and phylogenetic diversity. Results Phylogenetic diversity as measured by either Faith’s PD or TTD was strongly correlated with species richness globally, while the other two indices showed very different patterns. When either Faith’s PD or TTD was tested against species richness, residuals were strongly spatially structured. Areas with unusually low phylogenetic diversity for their associated species richness were mostly on islands, indicating large radiations of few lineages that have successfully colonized these archipelagos. Areas with unusually high phylogenetic diversity were located around biogeographic contact zones in Central America and southern China, and seem to have experienced high immigration or in situ diversification rates, combined with local persistence of old lineages. Main conclusions We show spatial structure in the residuals of the relationship between species richness and phylogenetic diversity, which together with the positive relationship itself indicates strong signatures of evolutionary history on contemporary global patterns of amphibian species richness. Areas with unusually low and high phylogenetic diversity for their associated richness demonstrate the importance of biogeographic barriers to dispersal, colonization and diversification processes.

Delimiting the geographical background in species distribution modelling

Abstract: P.A. and A.J.-V. were supported by the Juan de la Cierva research program awarded by the Ministerio de Ciencia e Innovacion – Fondo Social Europeo, and partly by the project CGL2009-11316/BOS – Fondos FEDER. P.A. is in Portugal thanks to a Jose Castillejo fellowship (2010–11) granted by the Ministerio de Ciencia e Innovacion.

Forest composition in Mediterranean mountains is projected to shift along the entire elevational gradient under climate change

Abstract: Aim Species distribution models have been used frequently to assess the effects of climate change on mountain biodiversity. However, the value and accuracy of these assessments have been hampered by the use of low-resolution data for species distributions and climatic conditions. Herein we assess potential changes in the distribution and community composition of tree species in two mountainous regions of Spain under specific scenarios of climate change using data with a high spatial resolution. We also describe potential changes in species distributions and tree communities along the entire elevational gradient. Location Two mountain ranges in southern Europe: the Central Mountain Range (central west of the Iberian Peninsula), and the Iberian Mountain Range (central east). Methods We modelled current and future distributions of 15 tree species (Eurosiberian, sub-Mediterranean and Mediterranean species) as functions of climate, lithology and availability of soil water using generalized linear models (logistic regression) and machine learning models (gradient boosting). Using multivariate ordination of a matrix of presence/absence of tree species obtained under two Intergovernmental Panel on Climate Change (IPCC) scenarios (A2 and B2) for two different periods in the future (2041–70 and 2071–2100), we assessed the predicted changes in the composition of tree communities. Results The models predicted an upward migration of communities of Mediterranean trees to higher elevations and an associated decline in communities of temperate or cold-adapted trees during the 21st century. It was predicted that 80–99% of the area that shows a climate suitable for cold– wet-optimum Eurosiberian coniferous and broad-leaved species will be lost. The largest overall changes were predicted for Mediterranean species found currently at low elevations, such as Pinus halepensis, Pinus pinaster, Quercus ilex ssp. ballota and Juniperus oxycedrus, with sharp increases in their range of 350%. Main conclusions It is likely that areas with climatic conditions suitable for cold-adapted species will decrease significantly under climate warming. Large changes in species ranges and forest communities might occur, not only at high elevations within Mediterranean mountains but also along the entire elevational gradient throughout this region, particularly at low and mid-elevations. Mediterranean mountains might lose their key role as refugia for cold-adapted species and thus an important part of their genetic heritage.

Eight (and a half) deadly sins of spatial analysis

Abstract: Biogeography is spatial by nature. Over the past 20 years, the literature related to the analysis of spatially structured data has exploded, much of it focused on a perceived problem of spatial autocorrelation and ways to deal with it. However, there are a number of other issues that permeate the biogeographical and macroecological literature that have become entangled in the spatial autocorrelation web. In this piece I discuss some of the assumptions that are often made in the analysis of spatially structured data that can lead to misunderstandings about the nature of spatial data, the methods used to analyse them, and how results can be interpreted.

Of mice and mammoths: evaluations of causal explanations for body size evolution in insular mammals

Abstract: Aim We investigated the hypothesis that the insular body size of mammals results from selective forces whose influence varies with characteristics of the focal islands and the focal species, and with interactions among species (ecological displacement and release). Location Islands world-wide. Methods We assembled data on the geographic characteristics (area, isolation, maximum elevation, latitude) and climate (annual averages and seasonality of temperature and precipitation) of islands, and on the ecological and morphological characteristics of focal species (number of mammalian competitors and predators, diet, body size of mainland reference populations) that were most relevant to our hypothesis (385 insular populations from 98 species of extant, non-volant mammals across 248 islands). We used regression tree analyses to examine the hypothesized contextual importance of these factors in explaining variation in the insular body size of mammals. Results The results of regression tree analyses were consistent with predictions based on hypotheses of ecological release (more pronounced changes in body size on islands lacking mammalian competitors or predators), immigrant selection (more pronounced gigantism in small species inhabiting more isolated islands), thermoregulation and endurance during periods of climatic or environmental stress (more pronounced gigantism of small mammals on islands of higher latitudes or on those with colder and more seasonal climates), and resource subsidies (larger body size for mammals that utilize aquatic prey). The results, however, were not consistent with a prediction based on resource limitation and island area; that is, the insular body size of large mammals was not positively correlated with island area. Main conclusions These results support the hypothesis that the body size evolution of insular mammals is influenced by a combination of selective forces whose relative importance and nature of influence are contextual. While there may exist a theoretical optimal body size for mammals in general, the optimum for a particular insular population varies in a predictable manner with characteristics of the islands and the species, and with interactions among species. This study did, however, produce some unanticipated results that merit further study ‐ patterns associated with Bergmann’s rule are amplified on islands, and the body size of small mammals appears to peak at intermediate and not maximum values of latitude and island isolation.

Niche breadth, rarity and ecological characteristics within a regional flora spanning large environmental gradients

Abstract: Aim Species specialization, which plays a fundamental role in niche differentiation and species coexistence, is a key biological trait in relation to the responses of populations to changing environments. Species with a limited niche breadth are considered to experience a higher risk of extinction than generalist species. This work aims to measure the degree of specialization in the regional flora of the French Alps and test whether species specialization is related to species rarity and ecological characteristics. Location This study was conducted in the French Alps region, which encompasses a large elevational gradient over a relatively limited area (26,000 km 2 ). Methods Specialization was estimated for approximately 1200 plant species found in the region. Given the inherent difficulty of pinpointing the critical environmental niche axes for each individual species, we used a co-occurrencebased index to estimate species niche breadths (specialization index). This comprehensive measurement included crucial undetermined limiting niche factors, acting on both local and regional scales, and related to both biotic and abiotic interactions. The specialization index for each species was then related to a selection of plant typologies such as Grime strategies and Raunkiaer life-forms, and to two measurements of plant rarity, namely regional area of occupancy and local abundance. Results Specialist species were mainly found in specific and harsh environments such as wetlands, cold alpine habitats and dry heathlands. These species were usually geographically restricted but relatively dominant in their local communities. Although none of the selected traits were sufficient predictors of specialization, pure competitors were over-represented amongst generalist species, whereas stress-tolerant species tended to be more specialized. Main conclusions Our results suggest that co-occurrence-based indices of niche breadth are a satisfactory method for inferring plant specialization using large species samples across very heterogeneous environments. Our results are an empirical validation of the tolerance‐dominance trade-off and also provide interesting insights into the long-standing question of which biological properties characterize species with narrow niche breadth that are potentially threatened by global changes in the environment.

Gut travellers: Internal dispersal of aquatic organisms by waterfowl

Abstract: Aim Patterns of high biodiversity among less mobile organisms throughout isolated locations suggest that passive dispersal importantly contributes to biodiversity We examined the contribution of waterbirds to the dispersal of plant seeds and macroinvertebrates between aquatic wetlands Birds are renowned vectors for seeds of terrestrial plants, but less is known about their role in more dispersal-dependent aquatic systems We therefore performed a meta-analysis on bird-mediated endozoochorous dispersal of aquatic species Location Our review included studies that collected data world-wide Methods We analysed data from 81 peer-reviewed publications on endozoochorous dispersal of aquatic plant seeds and macroinvertebrates by waterbirds Results In total, 36% of 1581 waterbird droppings collected in the field contained one or more intact propagules, with macroinvertebrates found almost as frequently as plant seeds Positive droppings contained on average 33 intact propagules, of which one-third were viable In 728 trials from 17 published feeding experiments 24% of the ingested propagules were retrieved intact, with c 65% both viable and intact As many as 17 species of Anatidae and Rallidae were involved in the dispersal of at least 39 species of macroinvertebrates and seeds from 97 species of plants across a wide taxonomic range Smaller propagules seemed less affected by digestion than larger ones We provide a first quantitative model that can be used to estimate waterbird-mediated dispersal of propagules between wetlands This model indicates that an average waterbird has the potential to disperse five viable propagules after flying more than 100 km, and one additional propagule after flying 300 km Main conclusions We demonstrate that waterbirds have the potential to transport a wide variety of aquatic plants and animals over several hundreds of kilometres High survival of propagules might be explained by propagule adaptations or by the digestive adaptations of birds, whereby energy absorption is thought to be maximized rather than assimilation efficiency Our meta-analysis suggests that waterbirds might contribute significantly to wetland biodiversity around the world, despite several limitations to our current knowledge We outline avenues for future research to address these knowledge gaps

Breach of the northern Rocky Mountain geoclimatic barrier: initiation of range expansion by the mountain pine beetle

Abstract: Aim Our aim is to examine the historical breach of the geoclimatic barrier of the Rocky Mountains by the mountain pine beetle (Dendroctonus ponderosae Hopkins). This recent range expansion from west of the North American continental divide into the eastern boreal forest threatens to provide a conduit to naive pine hosts in eastern North America. We examine the initial expansion events and determine potential mechanism(s) of spread by comparing spread patterns in consecutive years to various dispersal hypotheses such as: (1) meso-scale atmospheric dispersal of insects from source populations south-west of the Rocky Mountains in British Columbia (i.e. their historical range), (2) anthropogenic transport of infested plant material, and (3) spread of insect populations across adjacent stands via corridors of suitable habitat. Location British Columbia, Canada. Methods We explore potential mechanism(s) of invasion of the mountain pine beetle using spatial point process models for the initial 3 years of landscape-level data collection, 2004–2006. Specifically, we examine observed patterns of infestation relative to covariates reflecting various dispersal hypotheses. We select the most parsimonious models for each of the initial 3 years of invasion using information criteria statistics. Results The initial range expansion and invasion of the beetle was characterized by aerial deposition along a strong north-west to south-east gradient, with additional aerial deposition and localized dispersal from persisting populations in following years. Main conclusions Following deposition of a wave front of mountain pine beetles parallel to the Rocky Mountains via meso-scale atmospheric dispersal, the areas of highest intensity of infestations advanced up to 25 km north-east towards jack pine (Pinus banksiana) habitat in a single year. There appeared to be no association between putative anthropogenic movement of infested materials and initial range expansion of the mountain pine beetle across the continental divide.

Latitudinal variation in blue tit and great tit nest characteristics indicates environmental adjustment

Abstract: Aim The laying of eggs and the building of a nest structure to accommodate them are two of the defining characteristics of members of the class Aves. Nest structures vary considerably across avian taxa and for many species the design of the completed nest can have important consequences for both parents and their offspring. While nest characteristics are expected to vary adaptively in response to environmental conditions, large-scale spatial variation in nest characteristics has been largely overlooked. Here, we examined the effects of latitudinal variation in spring temperatures on nest characteristics, including insulatory properties, and reproductive success of blue tits, Cyanistes caeruleus, and great tits, Parus major. Location Great Britain. Methods Nests and reproductive data were collected from seven study sites, spread over five degrees of latitude. Then, the nest insulatory properties were determined before the nests were separated into either nest base material or cup lining material. Results As spring temperatures increased with decreasing latitude, the mass of the nest base material did not vary in either species, whilst the mass of the cup lining material and nest insulatory properties decreased in both species. This suggests that in response to increasing temperatures the breeding female reduces the mass of the cup lining material thereby maintaining an appropriate microclimate for incubating and brooding. The mean laying dates of both species advanced with decreasing latitude and increasing spring temperatures, although reproductive success did not vary. Main conclusions This is the first study to demonstrate that birds are systematically adjusting their nest structure in response to variation in ambient temperatures across large spatial scales. Therefore, nest composition reliably indicates environmental conditions and we suggest that studies of nest structure may be sentinels for the early signs of rapid climate change.

West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago

Abstract: Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever-changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location Asia, Southeast Asia, Malesia. Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL–F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF–rpl32 spacer, rpl32–trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated-rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal–extinction–cladogenesis model, and with a Bayesian approach to dispersal–vicariance analysis. Results The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene. Begonia section Petermannia (> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of Malesian Begonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea-level fluctuations during the Pleistocene.

Horizontal and elevational phylogeographic patterns of Himalayan and Southeast Asian forest passerines (Aves: Passeriformes)

Abstract: Aim Zoogeographic patterns in the Himalayas and their neighbouring Southeast Asian mountain ranges include elevational parapatry and ecological segregation, particularly among passerine bird species. We estimate timings of lineage splits among close relatives from the north Palaearctic, the Sino-Himalayan mountain forests and from adjacent Southeast Asia. We also compare phylogeographic affinities and timing of radiation among members of avian communities from different elevational belts. Location East Asia. Methods We reconstructed molecular phylogenies based on a mitochondrial marker (cytochrome b) and multilocus data sets for seven passerine groups: Aegithalidae, Certhiidae (Certhia), Fringillidae (Pyrrhula), Paridae (Periparus), Phylloscopidae, Regulidae and Timaliidae (Garrulax sensu lato). Molecular dating was carried out using a Bayesian approach applying a relaxed clock in beast. Time estimates were inferred from three independent calibrations based on either a fixed mean substitution rate or fixed node ages. The biogeographic history of each group was reconstructed using a parsimony-based approach. Results Passerine radiation in Southeast Asia can be divided into roughly three major phases of separation events. We infer that an initial Miocene radiation within the Southeast Asian region included invasions of (sub)tropical faunal elements from the Indo-Burmese region to the Himalayan foothills and further successive invasions to Central Asia and Taiwan towards the early Pliocene. During two further Pliocene/Pleistocene phases, the subalpine mountain belt of the Sino-Himalayas was initially invaded by boreal species with clear phylogenetic affinities to the north Palaearctic taiga belt. Most terminal splits between boreal Himalayan/Chinese sister taxa were dated to the Pleistocene. Main conclusions Extant patterns of elevational parapatry and faunal transition in the Sino-Himalayas originated from successive invasions from different climatic regions. The initiation of Southeast Asian passerine diversification and colonization of the Himalayan foothills in the mid-Miocene coincides with the postulated onset of Asian monsoon climate and the resulting floral and faunal turnovers. Patterns of elevational parapatry were established by southward invasions of boreal avifaunal elements to the subalpine Sino-Himalayan forest belt that were strongly connected to climate cooling towards the end of the Pliocene. Current patterns of allopatry and parapatry in boreal species (groups) were shaped through Pleistocene forest fragmentation in East Asia.

Do larger frugivores move seeds further? Body size, seed dispersal distance, and a case study of a large, sedentary pigeon

Abstract: Aim World-wide declines in large-bodied frugivores may change seed deposition patterns dramatically if body mass influences seed dispersal-related traits, such as dispersal distance We quantified movement patterns and seed dispersal distances by Hemiphaga novaeseelandiae (kereru), the fifth-largest surviving pigeon world-wide We then reviewed how body mass affects seed dispersal distance among fruit-eating birds globally Location Taranaki and Canterbury, New Zealand Methods We radio-tracked 24 kereru, following each bird continuously for up to 85 h, for a total of 43 tracking-days during the peak fruiting season (February–April) We estimated seed dispersal distances for three fleshy-fruited species using a mechanistic model based on kereru movements and seed retention times We analysed global data for volant avian frugivores to determine the effect of body mass on time spent in fruiting trees, seed retention time, and dispersal distance Results Kereru were highly sedentary, with an average of 32 ± 39 (mean ± SD) minutes and maximum of 315 minutes between flights Kereru flew a mean of 77 ± 159 m and maximum of 1457 m in a single flight They dispersed 66–87% of ingested seeds away from the parent plant Mean seed dispersal distances for Beilschmiedia tawa, Vitex lucens and Pseudopanax arboreus were 95, 98 and 61 m, respectively, with all species dispersed up to 1469 m For all three species, 79–88% of seeds were dispersed 1 km from the parent plant Globally, both the mean time spent in fruiting trees and seed retention time increased with increasing frugivore body mass However, retention time increased faster, and therefore the dispersal distance and percentage of seeds moved away from the parent increased with body mass Main conclusions Despite sedentary behaviour, kereru disperse many seeds away from the parent plant due to their even longer gut passage time, a function of their large size Large-bodied frugivores are disproportionately important as dispersers not only because they can swallow larger fruits, but also because they are more likely to deposit seeds away from the parent plant and at greater distances

Accounting for multi‐scale spatial autocorrelation improves performance of invasive species distribution modelling (iSDM)

Abstract: Aim Analyses of species distributions are complicated by various origins of spatial autocorrelation (SAC) in biogeographical data. SAC may be particularly important for invasive species distribution models (iSDMs) because biological invasions are strongly influenced by dispersal and colonization processes that typically create highly structured distribution patterns. We examined the efficacy of using a multi-scale framework to account for different origins of SAC, and compared non-spatial models with models that accounted for SAC at multiple levels. Location We modelled the spatial distribution of an invasive forest pathogen, Phytophthora ramorum, in western USA. Methods We applied one conventional statistical method (generalized linear model, GLM) and one nonparametric technique (maximum entropy, Maxent) to a large dataset on P. ramorum occurrence (n = 3787) to develop four types of model that included environmental variables and that either ignored spatial context or incorporated it at a broad scale using trend surface analysis, a local scale using autocovariates, or multiple scales using spatial eigenvector mapping. We evaluated model accuracies and amounts of explained spatial structure, and examined the changes in predictive power of the environmental and spatial variables. Results Accounting for different scales of SAC significantly enhanced the predictive capability of iSDMs. Dramatic improvements were observed when fine-scale SAC was included, suggesting that local range-confining processes are important in P. ramorum spread. The importance of environmental variables was relatively consistent across all models, but the explanatory power decreased in spatial models for factors with strong spatial structure. While accounting for SAC reduced the amount of residual autocorrelation for GLM but not for Maxent, it still improved the performance of both approaches, supporting our hypothesis that dispersal and colonization processes are important factors to consider in distribution models of biological invasions. Main conclusions Spatial autocorrelation has become a paradigm in biogeography and ecological modelling. In addition to avoiding the violation of statistical assumptions, accounting for spatial patterns at multiple scales can enhance our understanding of dynamic processes that explain ecological mechanisms of invasion and improve the predictive performance of static iSDMs.

‘Out‐of‐Africa’ dispersal of tropical floras during the Miocene climatic optimum: evidence from Uvaria (Annonaceae)

Abstract: Aim African–Asian disjunctions are common in palaeotropical taxa, and are typically explained by reference to three competing hypotheses: (1) ‘rafting’ on the Indian tectonic plate, enabling Africa-to-Asia dispersal; (2) migration via Eocene boreotropical forests; and (3) transoceanic long-distance dispersal. These hypotheses are tested using Uvaria (Annonaceae), which is distributed in tropical regions of Africa, Asia and Australasia. Recent phylogenetic reconstructions of the genus show a clear correlation with geographical provenance, indicating a probable origin in Africa and subsequent dispersal to Asia and then Australasia. Ancestral areas and migration routes are inferred and compared with estimates of divergence times in order to distinguish between the prevailing dispersal hypotheses. Location Palaeotropics. Methods Divergence times in Uvaria are estimated by analysing the sequences of four DNA regions (matK, psbA–trnH spacer, rbcL and trnL–F) from 59 Uvaria species and 77 outgroup species, using a Bayesian uncorrelated lognormal (UCLD) relaxed molecular clock. The ancestral area of Uvaria and subsequent dispersal routes are inferred using statistical dispersal–vicariance analysis (s-diva). Results Uvaria is estimated to have originated in continental Africa 31.6 Ma [95% highest posterior density (HPD): 38.4–25.1 Ma] between the Middle Eocene and Late Oligocene. Two main migration events during the Miocene are identified: dispersal into Madagascar around 17.0 Ma (95% HPD: 22.3–12.3 Ma); and dispersal into Asia between 21.4 Ma (95% HPD: 26.7–16.7 Ma) and 16.1 Ma (95% HPD: 20.1–12.1 Ma). Main conclusions Uvaria fruits are widely reported to be consumed by primates, and are therefore unlikely candidates for successful long-distance transoceanic dispersal. The other biogeographical hypotheses, involving rafting on the Indian tectonic plate, and dispersal via the European boreotropical forests associated with the Eocene thermal maximum, can be discounted due to incongruence with the divergence time estimates. An alternative scenario is suggested, involving dispersal across Arabia and central Asia via the tropical forests that developed during the late Middle Miocene thermal maximum (17–15 Ma), associated with the ‘out-of-Africa’ dispersal of primates. The probable route and mechanism of overland dispersal between Africa and Asia for tropical plant groups during the Miocene climatic optimum are clarified based on the Uvaria data.

Patterns of beta diversity in Europe: the role of climate, land cover and distance across scales

Abstract: Aim We test the prediction that beta diversity (species turnover) and the decay of community similarity with distance depend on spatial resolution (grain). We also study whether patterns of beta diversity are related to variability in climate, land cover or geographic distance and how the independent effects of these variables depend on the spatial grain of the data. Location Europe, Great Britain, Finland and Catalonia. Methods We used data on European birds, plants, butterflies, amphibians and reptiles, and data on British plants, Catalonian birds and Finnish butterflies. We fitted two or three nested grids of varying resolutions to each of these datasets. For each grid we calculated differences in climate, differences in land-cover composition (CORINE) and beta diversity (bsim, bJaccard) between all pairs of grid cells. In a separate analysis we looked specifically at pairs of adjacent grid cells (the first distance class). We then used variation partitioning to identify the magnitude of independent statistical associations (i.e. independent effects in the statistical sense) of climate, land cover and geographic distance with spatial patterns of beta

Temperature dependence of the reproduction niche and its relevance for plant species distributions

Abstract: The distribution and abundance of plant species are intimately related to their reproductive success, which in turn is affected by a large number of environmental variables. Yet, reproductive success is rarely taken into account in species distribution models (SDMs). In this paper we examine the extent to which consideration of the reproduction niche and its relationship with temperature could improve SDMs. We review the literature on plant reproductive responses to temperature and the influence of these relationships on species range delimitation. We define the reproduction niche and discuss how temperature influences several stages of the reproductive process. Furthermore, we review examples that illustrate how the reproduction niche influences species distributions and discuss how aspects of the reproduction niche could be considered in SDMs. We show that the reproduction niche fundamentally influences species distributions and that in principle it is easy to include aspects of the reproduction niche in SDMs, although sufficient data are only available for a restricted number of species. Bayesian methods and inverse parameterization may be the most efficient way to use existing data.

Snails can survive passage through a bird’s digestive system

Abstract: Aim Predation is generally viewed as a factor that limits the distribution of animal prey species. However, in certain instances, such as seed dispersal, predation may enhance the dispersal capability of prey species. In a prior study, we found that land snails are preyed upon by the Japanese white-eye (Zosterops japonicus) and the brown-eared bulbul (Hypsipetes amaurotis) in the Ogasawara Islands. In this paper we provide experimental and field evidence indicating that land snails could potentially be dispersed through bird predation. Location Hahajima Island of the Ogasawara Islands in the western Pacific. Methods Experimentation was first performed to test whether the land snail Tornatellides boeningi could remain alive after being swallowed and passed through the bird digestive system. Next, in order to investigate the potential role of internal bird transport and dispersal of this snail, we investigated the relationship between the distribution of population genetic diversity in the snail and the regional geographical abundance of predatory birds. The population genetic structure of T. boeningi and isolation by distance were inferred with Arlequin. The association between nucleotide diversity in T. boeningi populations and population density of predators was examined using a generalized linear mixed model. We conducted a likelihood ratio test for the full model and for another model that removed the fixed effect. Results Of the 119 snails fed to Japanese white-eyes and 55 snails fed to brown-eared bulbuls, 14.3% and 16.4% of the snails, respectively, passed through the gut alive. Additionally, one snail gave birth to juveniles after emerging from a bird’s gut. Significant heterogeneity among the populations of T. boeningi on Hahajima was indicated using AMOVA; however, there was no evidence of isolation by distance. A positive correlation was found between levels of mitochondrial DNA variation among and within T. boeningi populations and the density of Japanese white-eyes in the wild. Main conclusions Bird predation appears to be a method of dispersal for T. boeningi, and our results suggest that bird-mediated dispersal plays a role in land snail population structure.