Showing papers in "Ecography in 2010"

ENMTools: a toolbox for comparative studies of environmental niche models

Abstract: We present software that facilitates quantitative comparisons of environmental niche models (ENMs). Our software quantifies similarity of ENMs generated using the program Maxent and uses randomization tests to compare observed similarity to that expected under different null hypotheses. ENMTools is available online free of charge from .

SAM: a comprehensive application for Spatial Analysis in Macroecology

Abstract: SAM (Spatial Analysis in Macroecology) is a freeware application that offers a comprehensive array of spatial statistical methods, focused primarily on surface pattern spatial analysis. SAM is a compact, but powerful stand-alone software, with a user-friendly, menu-driven graphical interface. The methods available in SAM are the most commonly used in macroecology and geographical ecology, and range from simple tools for exploratory graphical analysis (e.g. mapping and graphing) and descriptive statistics of spatial patterns (e.g. autocorrelation metrics), to advanced spatial regression models (e.g. autoregression and eigenvector filtering). Download of the software, along with the user manual, can be downloaded online at the SAM website: (permanent URL at ).

A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity

Abstract: The term beta diversity has been used to refer to a wide variety of phenomena. Although all of these encompass some kind of compositional heterogeneity between places, many are not related to each other in any predictable way. The present two-part review aims to put the different phenomena that have been called beta diversity into a common conceptual framework, and to explain what each of them measures. In this first part, the focus is on defining a beta component of diversity. This involves deciding what diversity is and how the observed total or gamma diversity (g) is partitioned into alpha (a) and beta (b) components. Several different definitions of ‘‘beta diversity’’ that result from these decisions have been used in the ecological literature. True beta diversity is obtained when the total effective number of species in a dataset (true gamma diversity g) is multiplicatively partitioned into the effective number of species per compositionally distinct

The uncertain nature of absences and their importance in species distribution modelling

Abstract: Species distribution models (SDM) are commonly used to obtain hypotheses on either the realized or the potential distribution of species. The reliability and meaning of these hypotheses depends on the kind of absences included in the training data, the variables used as predictors and the methods employed to parameterize the models. Information about the absence of species from certain localities is usually lacking, so pseudo-absences are often incorporated to the training data. We explore the effect of using different kinds of pseudo-absences on SDM results. To do this, we use presence information on Aphodius bonvouloiri, a dung beetle species of well-known distribution. We incorporate different types of pseudo-absences to create different sets of training data that account for absences of methodological (i.e. false absences), contingent and environmental origin. We used these datasets to calibrate SDMs with GAMs as modelling technique and climatic variables as predictors, and compare these results with geographical representations of the potential and realized distribution of the species created independently. Our results confirm the importance of the kind of absences in determining the aspect of species distribution identified through SDM. Estimations of the potential distribution require absences located farther apart in the geographic and/or environmental space than estimations of the realized distribution. Methodological absences produce overall bad models, and absences that are too far from the presence points in either the environmental or the geographic space may not be informative, yielding important overestimations. GLMs and Artificial Neural Networks yielded similar results. Synthetic discrimination measures such as the Area Under the Receiver Characteristic Curve (AUC) must be interpreted with caution, as they can produce misleading comparative results. Instead, the joint examination of ommission and comission errors provides a better understanding of the reliability of SDM results.

A common currency for the different ways in which patches and links can contribute to habitat availability and connectivity in the landscape

Abstract: Graph structures and habitat availability metrics are two recent and complementary approaches for analysing landscape connectivity. They have gained rapid popularity and provided significant conceptual improvements for decision making in conservation planning. We present a further methodological development of the habitat availability concept and metrics by partitioning them into three separate fractions that quantify the different ways in which individual landscape elements can contribute to overall habitat connectivity and availability in the landscape, including stepping stone effects. These fractions are derived from the same concept, are measured in the same units and can be directly compared and combined within a unifying framework. This avoids the problematic and, so far, usual combination of metrics coming from different backgrounds and the arbitrary weighting of connectivity considerations in a broader context of conservation alternatives. We analyse how the relative importance of each fraction varies with species traits. In addition, we show how the critical patches differ for each of the fractions by analysing various forest habitats in the province of Lleida (NE Spain). We discuss the conceptual and conservation implications of this approach, which can be adapted to different degrees of ecological and spatial detail within the graph while still maintaining a coherent framework for the identification of critical elements in the landscape network.

A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena

Abstract: The present two-part review aims to put the different phenomena that have been called "beta diversity" over the years into a common conceptual framework and to explain what each of them measures. The first part (Tuomisto 2010) discussed basic definitions of "beta diversity". Each arises from a different way of combining a definition of "diversity" with a definition of its alpha component and with a mathematical relationship between the alpha and gamma components. This second part assumes that an appropriate basic definition of a beta component (which may or may not be true beta diversity) has been chosen, and the focus here will be on how to quantify it for a given dataset. About twenty different approaches have been used for this purpose. It turns out that only two of these approaches accurately quantify the selected beta component: one does so for the entire dataset, and the other for two sampling units at a time. The other approaches actually quantify other phenomena, such as mean species turnover between sampling units, compositional gradient length (with or without reference to an external gradient), distinctness of a focal sampling unit, rate of species accumulation with increasing sampling effort, rate of compositional turnover along an external gradient, or the rate of decay in compositional similarity with increasing geographical distance. Although most of these phenomena can be expressed as a function of a beta component of diversity, they do not equal a beta component of diversity. Many of these derived variables are not even numerically correlated with the beta component on which they are based, which needs to be taken into account when interpreting the results. The effects of sampling decisions when results are extrapolated beyond the available data will also be discussed.

Going against the flow: potential mechanisms for unexpected downslope range shifts in a warming climate

Abstract: J. Lenoir (lenoir.john@gmail.com), The Ecoinformatics & Biodiversity Group, Dept of Biological Sciences, Aarhus Univ., Ny Munkegade 114,DK-8000 Aarhus C, Denmark and AgroParisTech, UMR1092 AgroParisTech-INRA, Laboratoire d’Etude des Ressources Foreˆt-Bois (LERFoB),14 rue Girardet, FR-54000 Nancy, France. J.-C. Ge´gout, AgroParisTech, UMR1092 AgroParisTech-INRA, Laboratoire d’Etude desRessources Foreˆt-Bois (LERFoB), 14 rue Girardet, FR-54000 Nancy, France, and Center for Advanced Studies in Ecology and Biodiversity(CASEB), Depto de Ecologia, Pontificia Univ., Cato´lica de Chile, Alameda 340 C.P. 6513677, Santiago, Chile. A. Guisan, Fac. of Biologyand Medicine, Dept of Ecology & Evolution, Univ. of Lausanne, Baˆtiment Biophore, CH-1015 Lausanne, Switzerland. P. Vittoz, Fac. ofBiology and Medicine, Dept of Ecology & Evolution, Univ. of Lausanne, Baˆtiment Biophore, CH-1015 Lausanne, Switzerland and Fac. ofGeosciences and Environment, Univ. of Lausanne, Baˆtiment Biophore, CH-1015 Lausanne, Switzerland. T. Wohlgemuth and N. E.Zimmermann, Swiss Federal Research Inst. for Forest Snow and Landscape Research WSL, Zu¨rcherstrasse 111, CH-8903 Birmensdorf,Switzerland. S. Dullinger, Vienna Inst. for Nature Conservation and Analyses, Giessergasse 6/7, AT-1090 Vienna, Austria, and Fac. Centrefor Biodiversity, Dept of Conservation Biology, Vegetation and Landscape Ecology, Univ. of Vienna, Rennweg 14, AT-1030 Vienna, Austria. H. Pauli, Inst. of Mountain Research: Man and the Environment (IGF) of the Austrian Academy of Sciences, c/o Fac. Centre for Biodiversity,Dept of Conservation Biology, Vegetation and Landscape Ecology, Univ. of Vienna, Rennweg 14, AT-1030 Vienna, Austria. W. Willner,Vienna Inst. for Nature Conservation and Analyses, Giessergasse 6/7, AT-1090 Vienna, Austria. J.-C. Svenning, The Ecoinformatics &Biodiversity Group, Dept of Biological Sciences, Aarhus Univ., Ny Munkegade 114, DK-8000 Aarhus C, Denmark.

Variation partitioning as a tool to distinguish between niche and neutral processes

Abstract: We assess the potential of different forms of variation partitioning to distinguish between environmental control and dispersal limitation in communities structured by combinations of niche and neutral processes. Simulation data reveal interactions between dispersal limitation, environmental control, and the spatial structure of environmental factors in the detected levels of variance fractions. The degree of dispersal limitation contributes to both the pure environmental and pure spatial variance partitions. This undermines the common practice of interpreting these partitions as direct expressions of niche and neutral processes, respectively. Furthermore, the proportion of variation attributed to environmental variation depends not only on the strength of environmental control, but also on the specific spatial configuration of the environmental variable. This has important implications for the interpretation of empirical studies. In particular, use of these analytical techniques to compare processes governing community structure among different study systems is unwarranted, as the results will reflect not only differences in the strength of the processes of interest, but also the influence of the unique spatial arrangement of the environmental variables in each system.

Niche and area of distribution modeling: a population ecology perspective

Abstract: Statistical modeling of areas of distribution of species by correlative analysis of the environmental features of known presences has become widespread. However, to a large degree, the logic and the functioning of many of these applications remain obscure, not only due to the fact that some of the modeling methods are intrinsically complex (neural networks, genetic algorithms, generalized additive models, for example), but mainly because the role of other ecological processes affecting the species distributions sometimes is not explicitly stated. Resorting to fundamental principles of population ecology, a scheme of analysis based on separation of three factors affecting species distributions (environment, biotic interactions and movements) is used to clarify some results of niche modeling exercises. The area of distribution of a virtual species which was generated by both environmental and biotic factors serves to illustrate the possibility that, at coarse resolutions, the distribution can be approximately recovered using only information about the environmental factors and ignoring the biotic interactions. Finally, information on the distribution of a butterfly species, Baronia brevicornis, is used to illustrate the importance of interpreting the results of niche models by including hypothesis about one class of movements. The results clarify the roles of the three factors in interpreting the results of using correlative approaches to modeling species distributions or their niches.

New trends in species distribution modelling

Abstract: N. E. Zimmermann (niklaus.zimmermann@wsl.ch) and P. B. Pearman, Land Use Dynamics, Swiss Federal Research Inst. WSL, Zurcherstrasse 111, CH-8903 Birmensdorf, Switzerland. T. C. Edwards, U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unit and Dept of Wildland Resources, Utah State Univ., Logan, UT 84322-5290, USA. C. H. Graham, Dept of Ecology and Evolution, Stony Brook Univ., NY 11794, USA. J.-C. Svenning, Ecoinformatics and Biodiversity Group, Dept of Biological Sciences, Aarhus Univ., Ny Munkegade 114, DK-8000 Aarhus C., Denmark.

A comparative approach to understanding factors limiting abundance patterns and distributions in a fig tree–fig wasp mutualism

Abstract: This work is supported by a National Research Foundation postdoctoral fellowship to MW and Grant number FA2007050800023 to JMG.

Biodiverse, a tool for the spatial analysis of biological and related diversity

Abstract: Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix (e.g. genetic dissimilarity) relationships. The explosion in georeferenced biological specimen and survey data means there is an increasing need for such tools. Biodiverse supports four processes: 1) linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2) spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3) spatially constrained agglomerative cluster analyses; and 4) randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface and scripts. Biodiverse can be downloaded from .

Biotic and abiotic variables show little redundancy in explaining tree species distributions

Abstract: Abiotic factors such as climate and soil determine the species fundamental niche, which is further constrained by biotic interactions such as interspecific competition. To parameterize this realized niche, species distribution models (SDMs) most often relate species occurrence data to abiotic variables, but few SDM studies include biotic predictors to help explain species distributions. Therefore, most predictions of species distributions under future climates assume implicitly that biotic interactions remain constant or exert only minor influence on large-scale spatial distributions, which is also largely expected for species with high competitive ability. We examined the extent to which variance explained by SDMs can be attributed to abiotic or biotic predictors and how this depends on species traits. We fit generalized linear models for 11 common tree species in Switzerland using three different sets of predictor variables: biotic, abiotic, and the combination of both sets. We used variance partitioning to estimate the proportion of the variance explained by biotic and abiotic predictors, jointly and independently. Inclusion of biotic predictors improved the SDMs substantially. The joint contribution of biotic and abiotic predictors to explained deviance was relatively small (� 9%) compared to the contribution of each predictor set individually (� 20% each), indicating that the additional information on the realized niche brought by adding other species as predictors was largely independent of the abiotic (topo-climatic) predictors. The influence of biotic predictors was relatively high for species preferably growing under low disturbance and low abiotic stress, species with long seed dispersal distances, species with high shade tolerance as juveniles and adults, and species that occur frequently and are dominant across the landscape. The influence of biotic variables on SDM performance indicates that community composition and other local biotic factors or abiotic processes not included in the abiotic predictors strongly influence prediction of species distributions. Improved prediction of species’ potential distributions in future climates and communities may assist strategies for sustainable forest management.

Extinction debt on oceanic islands

Abstract: Habitat destruction is the leading cause of species extinctions. However, there is typically a time-lag between the reduction in habitat area and the eventual disappearance of the remnant populations. These “surviving but ultimately doomed” species represent an extinction debt. Calculating the magnitude of such future extinction events has been hampered by potentially inaccurate assumptions about the slope of species–area relationships, which are habitat- and taxon-specific. We overcome this challenge by applying a method that uses the historical sequence of deforestation in the Azorean Islands, to calculate realistic and ecologically-adjusted species–area relationships. The results reveal dramatic and hitherto unrecognized levels of extinction debt, as a result of the extensive destruction of the native forest:>95%, in<600 yr. Our estimations suggest that more than half of the extant forest arthropod species, which have evolved in and are dependent on the native forest, might eventually be driven to extinction. Data on species abundances from Graciosa Island, where only a very small patch of secondary native vegetation still exists, as well as the number of species that have not been found in the last 45 yr, despite the extensive sampling effort, offer support to the predictions made. We argue that immediate action to restore and expand native forest habitat is required to avert the loss of numerous endemic species in the near future.

Within-taxon niche structure: niche conservatism, divergence and predicted effects of climate change

Abstract: Several studies have observed that taxa below the level of species can vary in the degree to which they differ from one another in the environmental space they occupy. These patterns of within-species niche variation raise the question of whether these differences should be considered when developing models for predicting the potential effects of climate change on species distributions. We address this question with two divergent datasets, one on sister species and subspecies from the European herpetofauna, the other on subspecies of breeding birds in North America. Atlas and observation data come from the Atlas of Amphibians and Reptiles in Europe and the North American Breeding Bird Survey, respectively.

Understanding (insect) species distributions across spatial scales

Abstract: J. Hortal (j.hortal@imperial.ac.uk), NERC Centre for Population Biology, Div. of Biology, Imperial College London, Silwood Park Campus,Ascot, Berkshire SL5 7PY, UK. N. Roura-Pascual, A`rea de Biodiversitat, Centre Tecnolo`gic Forestal de Catalunya, Ctra. de St. Llorenc¸ deMorunys Km 2, ES-25280 Solsona, Catalonia, Spain. N. J. Sanders, Dept of Ecology and Evolutionary Biology, Univ. of Tennessee, Knoxville,TN 37996, USA. C. Rahbek, Center for Macroecology, Evolution, and Climate, Dept of Biology, Univ. of Copenhagen, Universitetsparken15, DK-2100 Copenhagen O, Denmark.

The Great American Biotic Interchange revisited

Abstract: The “Great American Biotic Interchange” (GABI) is regarded as a defining event in the biogeography of the Americas. It is hypothesized to have occurred when the Isthmus of Panama closed ca three million years ago (Ma), ending the isolation of South America and permitting the mixing of its biota with that of North America. This view of the GABI is based largely upon the animal fossil record, but recent molecular biogeographic studies of plants that show repeated instances of long-distance dispersal over major oceanic barriers suggest that perhaps the land bridge provided by the isthmus may have been less necessary for plant migration. Here we show that plants have significantly earlier divergence time estimates than animals for historical migration events across the Isthmus of Panama region. This difference in timing indicates that plants had a greater propensity for dispersal over the isthmus before its closure compared with animals. The GABI was therefore asynchronous for plants and animals, which has fundamental implications for the historical assembly of tropical biomes in the most species-rich forests on the planet.

Species distribution models reveal apparent competitive and facilitative effects of a dominant species on the distribution of tundra plants

Abstract: Abiotic factors are considered strong drivers of species distribution and assemblages. Yet these spatial patterns are also influenced by biotic interactions. Accounting for competitors or facilitators may improve both the fit and the predictive power of species distribution models (SDMs). We investigated the influence of a dominant species, Empetrum nigrum ssp. hermaphroditum, on the distribution of 34 subordinate species in the tundra of northern Norway. We related SDM parameters of those subordinate species to their functional traits and their co-occurrence patterns with E. hermaphroditum across three spatial scales. By combining both approaches, we sought to understand whether these species may be limited by competitive interactions and/or benefit from habitat conditions created by the dominant species. The model fit and predictive power increased for most species when the frequency of occurrence of E. hermaphroditum was included in the SDMs as a predictor. The largest increase was found for species that 1) co-occur most of the time with E. hermaphroditum, both at large (i.e. 750 m) and small spatial scale (i.e. 2 m) or co-occur with E. hermaphroditum at large scale but not at small scale and 2) have particularly low or high leaf dry matter content (LDMC). Species that do not co-occur with E. hermaphroditum at the smallest scale are generally palatable herbaceous species with low LDMC, thus showing a weak ability to tolerate resource depletion that is directly or indirectly induced by E. hermaphroditum. Species with high LDMC, showing a better aptitude to face resource depletion and grazing, are often found in the proximity of E. hermaphroditum. Our results are consistent with previous findings that both competition and facilitation structure plant distribution and assemblages in the Arctic tundra. The functional and co-occurrence approaches used were complementary and provided a deeper understanding of the observed patterns by refinement of the pool of potential direct and indirect ecological effects of E. hermaphroditum on the distribution of subordinate species. Our correlative study would benefit being complemented by experimental approaches.

Determinants of palm species distributions across Africa: the relative roles of climate, non-climatic environmental factors, and spatial constraints

Abstract: Most of the Earth's biodiversity resides in the tropics. However, a comprehensive understanding of which factors control range limits of tropical species is still lacking. Climate is often thought to be the predominant range-determining mechanism at large spatial scales. Alternatively, species’ ranges may be controlled by soil or other environmental factors, or by non-environmental factors such as biotic interactions, dispersal barriers, intrinsic population dynamics, or time-limited expansion from place of origin or past refugia. How species ranges are controlled is of key importance for predicting their responses to future global change. Here, we use a novel implementation of species distribution modelling (SDM) to assess the degree to which African continental-scale species distributions in a keystone tropical group, the palms (Arecaceae), are controlled by climate, non-climatic environmental factors, or non-environmental spatial constraints. A comprehensive data set on African palm species occurrences was assembled and analysed using the SDM algorithm Maxent in combination with climatic and non-climatic environmental predictors (habitat, human impact), as well as spatial eigenvector mapping (spatial filters). The best performing models always included spatial filters, suggesting that palm species distributions are always to some extent limited by non-environmental constraints. Models which included climate provided significantly better predictions than models that included only non-climatic environmental predictors, the latter having no discernible effect beyond the climatic control. Hence, at the continental scale, climate constitutes the only strong environmental control of palm species distributions in Africa. With regard to the most important climatic predictors of African palm distributions, water-related factors were most important for 25 of the 29 species analysed. The strong response of palm distributions to climate in combination with the importance of non-environmental spatial constraints suggests that African palms will be sensitive to future climate changes, but that their ability to track suitable climatic conditions will be spatially constrained.

The profound influence of the Late-Pliocene Panamanian uplift on the exchange, diversification, and distribution of New World Birds

Abstract: Separated throughout most of the Cenozoic era, North and South America were joined during the mid-Pliocene when the uplift of Panama formed a land bridge between these two continents. The fossil record indicates that this connection allowed an unprecedented degree of inter-continental exchange to occur between unique, previously isolated biotic assemblages, a phenomenon now recognized as the “Great American Biotic Interchange”. However, a relatively poor avian fossil record has prevented our understanding the role of the land bridge in shaping New World avian communities. To address the question of avian participation in the GABI, we compiled 64 avian phylogenetic studies and applied a relaxed molecular clock to estimate the timing of trans-isthmus diversification events. Here, we show that a significant pulse of avian interchange occurred in concert with the isthmus uplift. The avian exchange was temporally consistent with the well understood mammalian interchange, despite the presumed greater vagility of birds. Birds inhabiting a variety of habitats and elevational zones responded to the newly available corridor. Within the tropics, exchange was equal in both directions although between extratropical and tropical regions it was not. Avian lineages with Nearctic origins have repeatedly invaded the tropics and radiated throughout South America; whereas, lineages with South American tropical origins remain largely restricted to the confines of the Neotropical region. This previously unrecognized pattern of asymmetric niche conservatism may represent an important and underappreciated contributor to the latitude diversity gradient.

How much do we overestimate future local extinction rates when restricting the range of occurrence data in climate suitability models

Abstract: M. Barbet-Massin (barbet@mnhn.fr) and F. Jiguet, Muse´um National d’Histoire Naturelle, UMR 7204 MNHN-CNRS-UPMC, Centre deRecherches sur la Biologie des Populations d’Oiseaux, 55 Rue Buffon, FR-75005 Paris, France. W. Thuiller, Laboratoire d’Ecologie Alpine,UMR-CNRS 5553, Univ. Joseph Fourier, BP 53, FR-38041 Grenoble Cedex 9, France.Climate suitability models are used to make projections of species’ potential future distribution under climate change.When studying the species richness with such modeling methods, the extent of the study range is of particularimportance, especially when the full range of occurrence is not considered for some species, often because of geographicalor political limits. Here we examine biases induced by the use of range-restricted occurrence data on predicted changes inspecies richness and predicted extinction rates, at study area margins. We compared projections of future suitable climatespace for 179 bird species breeding in Iberia and North Africa (27 of them breeding only in North Africa thoughpotential colonizers in Europe), using occurrence data from the full Western Palaearctic (WP) species range and from theoften-considered European-restricted range. Current and future suitable climatic spaces were modeled using an ensembleforecast technique applied to five general circulation models and three climate scenarios, with eight climatic variables andeight modeling techniques. The use of range-restricted compared to the full WP occurrence data of a species led to anunderestimate of its suitable climatic space. The projected changes in species richness across the focus area (Iberia) variedconsiderably according to the occurrence data we used, with higher local extinction rates with European-restricted data(on average 38 vs 12% for WP data). Modeling results for species currently breeding only in North Africa revealedpotential colonization of the Iberian Peninsula (from a climatic point of view), which highlights the necessity to considerspecies outside the focus area if interested in forecasted changes in species richness. Therefore, the modeling of currentand future species richness can lead to misleading conclusions when data from a restricted range of occurrence is used.Consequently, climate suitability models should use occurrence data from the complete distribution range of species, orat least within biogeographical areas.

A meta‐analysis of isolation by distance: relic or reference standard for landscape genetics?

Abstract: Isolation by distance (IBD) has been a common measure of genetic structure among populations and is based on Euclidean distances among populations. Whereas IBD does not incorporate geographic complexity (e.g. dispersal barriers, corridors) that may better predict genetic structure, a new approach (landscape genetics) joins landscape ecology with population genetics to better model genetic structure. Should IBD be set aside or should it persist as the most simple model in landscape genetics? We evaluated the status of IBD by collecting and analyzing results of 240 IBD data sets among diverse taxa and study systems. IBD typically represented a low proportion of variance in genetic structure (mean r2=0.22) in part because many studies included relatively few populations (mean=11). The number of populations studied (N) was asymptotically related to IBD significance; a study with 9 populations has only 50% probability of significance, while one with >23 populations will have 90% probability of significance. Surprisingly, ectothermic animals were significantly (p=0.0018) more likely to have significant IBD than endotherms, which suggests a metabolic basis underlying gene flow rates. We also observed marginally significant effects on IBD significance for a) taxa in general and b) dispersal modes within actively-dispersing endotherms. Other factors analyzed (genetic markers, genetic distances, habitats, active or passive dispersal, plant growth form) did not significantly affect IBD, likely related to typical N. For multiple reasons we conclude that IBD should continue as the simplest reference standard against which all other, more complex models should be compared in landscape genetics research.

Beyond bioclimatic envelopes: dynamic species' range and abundance modelling in the context of climatic change

Abstract: B. Huntley (brian.huntley@durham.ac.uk), D. G. Hole and S. G. Willis, Ecosystem Science Centre, School of Biological and Biomedical Sciences, Durham Univ., South Road, Durham DH1 3LE, UK. P. Barnard, Birds & Environmental Change Partnership, Climate Change and BioAdaptation Div., South African National Biodiversity Inst., Kirstenbosch Research Centre, P/Bag X7, Claremont 7735, Cape Town, South Africa, and Percy FitzPatrick Inst. of African Ornithology, DST/NRF Centre of Excellence, Univ. of Cape Town, Rondebosch 7701, Cape Town, South Africa. R. Altwegg, Birds & Environmental Change Partnership, Climate Change and BioAdaptation Div., South African National Biodiversity Inst., Kirstenbosch Research Centre, P/Bag X7, Claremont 7735, Cape Town, South Africa, and Animal Demography Unit, Dept of Zoology, Univ. of Cape Town, Rondebosch 7701, Cape Town, South Africa. L. Chambers, Centre for Australian Weather & Climate Research Bureau of Meteorology, GPO Box 1289, Melbourne, Victoria 3001, Australia. B. W. T. Coetzee, Birds & Environmental Change Partnership, Climate Change and BioAdaptation Div., South African National Biodiversity Inst., Kirstenbosch Research Centre, P/Bag X7, Claremont 7735, Cape Town, South Africa, and Centre for Invasion Biology, Dept of Botany and Zoology, Stellenbosch Univ., Private Bag X1, Matieland 7602, South Africa. L. Gibson, Dept of Environment & Conservation, PO Box 51, Wanneroo WA 6946, Australia. P. A. R. Hockey, Percy FitzPatrick Inst. of African Ornithology, DST/NRF Centre of Excellence, Univ. of Cape Town, Rondebosch 7701, Cape Town, South Africa. G. F. Midgley, Birds & Environmental Change Partnership, Climate Change and BioAdaptation Div., South African National Biodiversity Inst., Kirstenbosch Research Centre, P/Bag X7, Claremont 7735, Cape Town, South Africa. L. G. Underhill, Animal Demography Unit, Dept of Zoology, Univ. of Cape Town, Rondebosch 7701, Cape Town, South Africa.

Contrasting environmental and regional effects on global pteridophyte and seed plant diversity.

Abstract: Pteridophytes (ferns and fern-allies) represent the second-largest group of vascular plants, but their global biogeography remains poorly studied. Given their functional biology, pteridophytes are expected to show a more pronounced relation to water availability and a higher dispersal ability compared to seed plants. We test these assertions and document the global pattern of pteridophyte richness across 195 mainland and 106 island regions. Using non-spatial and spatial simple and multiple regression models, we analyze geographic trends in pteridophyte and seed plant richness as well as pteridophyte proportions in relation to environmental and regional variables. We find that pteridophyte and seed plant richness are geographically strongly correlated (all floras: r=0.68, mainland: r=0.82, island floras: r=0.77), but that the proportions of pteridophytes in vascular plant floras vary considerably (0–70%). Islands (mean=15.3%) have significantly higher proportions of pteridophytes than mainland regions (mean=3.6%). While the relative proportions of pteridophytes on islands show a positive relationship with geographic isolation, proportions in mainland floras increase most strongly along gradients of water availability. Pteridophyte richness peaks in humid tropical mountainous regions and is lowest in deserts, arctic regions, and on remote oceanic islands. Regions with Mediterranean climate, outstanding extra-tropical centres of seed plant richness, are comparatively poor in pteridophytes. Overall, water-energy variables and topographical complexity are core predictors of both mainland pteridophyte and seed plant richness. Significant residual richness across biogeographic regions points to an important role of idiosyncratic regional effects. Although the same variables emerge as core predictors of pteridophyte and seed plant richness, water availability is clearly a much stronger constraint of pteridophyte richness. We discuss the different limitations of gametophytes and sporophytes that might have limited the ability of pteridophytes to extensively diversify under harsh environmental conditions. Our results point to an important role of taxon-specific functional traits in defining global richness gradients.

Assessing ecosystem threats from global and regional change: hierarchical modeling of risk to sagebrush ecosystems from climate change, land use and invasive species in Nevada, USA

Abstract: Global change poses significant challenges for ecosystem conservation. At regional scales, climate change may lead to extensive shifts in species distributions and widespread extirpations or extinctions. At landscape scales, land use and invasive species disrupt ecosystem function and reduce species richness. However, a lack of spatially explicit models of risk to ecosystems makes it difficult for science to inform conservation planning and land management. Here, I model risk to sagebrush (Artemisia spp.) ecosystems in the state of Nevada, USA from climate change, land use/land cover change, and species invasion. Risk from climate change is based on an ensemble of 10 atmosphere-ocean general circulation model (AOGCM) projections applied to two bioclimatic envelope models (Mahalanobis distance and Maxent). Risk from land use is based on the distribution of roads, agriculture, and powerlines, and on the spatial relationships between land use and probability of cheatgrass Bromus tectorum invasion in Nevada. Risk from land cover change is based on probability and extent of pinyon-juniper (Pinus monophylla; Juniperus spp.) woodland expansion. Climate change is most likely to negatively impact sagebrush ecosystems at the edges of its current range, particularly in southern Nevada, southern Utah, and eastern Washington. Risk from land use and woodland expansion is pervasive throughout Nevada, while cheatgrass invasion is most problematic in the northern part of the state. Cumulatively, these changes pose major challenges for conservation of sagebrush and sagebrush obligate species. This type of comprehensive assessment of ecosystem risk provides managers with spatially explicit tools important for conservation planning.

Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America

Abstract: Understanding how historical processes have either similarly, or differentially, shaped the evolution of lineages or biotic assemblages is important for a broad spectrum of fields. Gaining such understanding can be particularly challenging, however, especially for regions that have a complex geologic and biological history. In this study we apply a broad comparative approach to distill such regional biogeographic perspectives, by characterizing sets of divergence times for major biogeographic boundaries estimated from multiple codistributed lineages of snakes. We use a large combined (mitochondrial gene sequence) phylogeographic/phylogenetic dataset containing several clades of snakes that range across Middle America the tropical region between Mexico and northwestern South America. This region is known for its complex tectonic history, and poorly understood historical biogeography. Based on our results, we highlight how phylogeographic transition zones between Middle and South America and the Nicaragua Depression appear to have undergone multiple episodes of diversification in different lineages. This is in contrast to other examples we find where apparently a single vicariant period is shared across multiple lineages. We specifically evaluate the distributions of divergence time estimates across multiple lineages and estimate the number of temporal periods of lineage diversification per biogeographic break. Overall, our results highlight a great deal of shared temporal divergence, and provide important hypotheses for yet unstudied lineages. These multi-lineage comparisons across multiple spatial and temporal scales provide excellent predictive power for identifying the roles of geology, climate, ecology and natural history in shaping regional biodiversity.

Ecological history and latent conservation potential: Large and giant tortoises as a model for taxon substitutions

Abstract: Starting in the late 1970s, ecologists began unraveling the role of recently extinct large vertebrates in evolutionary ecology and ecosystem dynamics. Three decades later, practitioners are now considering the role of ecological history in conservation practice, and some have called for restoring missing ecological functions and evolutionary potential using taxon substitutes - extant, functionally similar taxa - to replace extinct species. This pro-active approach to biodiversity conservation has proved controversial. Yet, rewilding with taxon substitutes, or ecological analogues, is now being integrated into conservation and restoration programmes around the world. Empirical evidence is emerging that illustrates how taxon substitutions can restore missing ecological functions and evolutionary potential. However, a major roadblock to a broader evaluation and application of taxon substitution is the lack of practical guidelines within which they should be conducted. While the International Union for Conservation of Nature's reintroduction guidelines are an obvious choice, they are unsuitable in their current form. We recommend necessary amendments to these guidelines to explicitly address taxon substitutions. A second impediment to empirical evaluations of rewilding with taxon substitutions is the sheer scale of some proposed projects; the majority involves large mammals over large areas. We present and discuss evidence that large and giant tortoises (family Testudinidae) are a useful model to rapidly provide empirical assessments of the use of taxon substitutes on a comparatively smaller scale. Worldwide, at least 36 species of large and giant tortoises went extinct since the late Pleistocene, leaving 32 extant species. We examine the latent conservation potential, benefits, and risks of using tortoise taxon substitutes as a strategy for restoring dysfunctional ecosystems. We highlight how, especially on islands, conservation practitioners are starting to employ extant large tortoises in ecosystems to replace extinct tortoises that once played keystone roles. © 2010 The Authors. Journal compilation © 2010 Ecography.

Fundamental biogeographic patterns across the Mexican Transition Zone: an evolutionary approach

Abstract: Transition zones, located at the boundaries between biogeographic regions, represent events of biotic hybridization, promoted by historical and ecological changes. They deserve special attention, because they represent areas of intense biotic interaction. In its more general sense, the Mexican Transition Zone is a complex and varied area where Neotropical and Nearctic biotas overlap, from southwestern USA to Mexico and part of Central America, extending south to the Nicaraguan lowlands. In recent years, panbiogeographic analyses have led to restriction of the Mexican Transition Zone to the montane areas of Mexico and to recognize five smaller biotic components within it. A cladistic biogeographic analysis challenged the hypothesis that this transition zone is biogeographically divided along a north-south axis at the Transmexican Volcanic Belt, as the two major clades found divided Mexico in an east-west axis. This implies that early Tertiary geological events leading to the convergence of Neotropical and Nearctic elements may be younger (Miocene) than those that led to the east-west pattern (Paleocene). The Mexican Transition Zone consists of five biogeographic provinces: Sierra Madre Occidental, Sierra Madre Oriental, Transmexican Volcanic Belt, Sierra Madre del Sur, and Chiapas. Within this transition zone, at least four cenocrons have been identified: Paleoamerican, Nearctic, Montane Mesoamerican, and Tropical Mesoamerican. Future studies should continue refining the identification of cenocrons and the reconstruction of a geobiotic scenario, as well as integrating ecological biogeographic studies, to allow a more complete understanding of the patterns and processes that have caused the biotic complexity of this transition zone.

Sampling in ecology and evolution – bridging the gap between theory and practice

Abstract: C. H. Albert (cecile.albert@m4x.org) and W. Thuiller, Laboratoire d’Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Bp 53,FR-38041 Grenoble Cedex 9, France. N. G. Yoccoz, Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics,Univ. of Tromso, NO-9037 Tromso, Norway. T. C. Edwards, Jr, U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unitand Wildland Resources, Utah State Univ., Logan, UT 84322-5290, USA. C. H. Graham, Dept of Ecology and Evolution, Stony BrookUniv., Stony Brook, NY 11794, USA. N. E. Zimmermann, Land Use Dynamics, Swiss Federal Research Inst. WSL, CH-8903 Birmensdorf,Switzerland.Sampling is a key issue for answering most ecological and evolutionary questions. The importance of developing arigorous sampling design tailored to specific questions has already been discussed in the ecological and sampling literatureand has provided useful tools and recommendations to sample and analyse ecological data. However, sampling issues areoften difficult to overcome in ecological studies due to apparent inconsistencies between theory and practice, oftenleading to the implementation of simplified sampling designs that suffer from unknown biases. Moreover, we believe thatclassical sampling principles which are based on estimation of means and variances are insufficient to fully address manyecological questions that rely on estimating relationships between a response and a set of predictor variables over time andspace. Our objective is thus to highlight the importance of selecting an appropriate sampling space and an appropriatesampling design. We also emphasize the importance of using prior knowledge of the study system to estimate models orcomplex parameters and thus better understand ecological patterns and processes generating these patterns. Using a semi-virtual simulation study as an illustration we reveal how the selection of the space (e.g. geographic, climatic), in whichthe sampling is designed, influences the patterns that can be ultimately detected. We also demonstrate the inefficiency ofcommon sampling designs to reveal response curves between ecological variables and climatic gradients. Further, we showthat response-surface methodology, which has rarely been used in ecology, is much more efficient than more traditionalmethods. Finally, we discuss the use of prior knowledge, simulation studies and model-based designs in definingappropriate sampling designs. We conclude by a call for development of methods to unbiasedly estimate nonlinearecologically relevant parameters, in order to make inferences while fulfilling requirements of both sampling theory andfield work logistics.