Showing papers in "Journal of Biogeography in 2007"

Atlantic reef fish biogeography and evolution

Abstract: Aim To understand why and when areas of endemism (provinces) of the tropical Atlantic Ocean were formed, how they relate to each other, and what processes have contributed to faunal enrichment. Location Atlantic Ocean. Methods The distributions of 2605 species of reef fishes were compiled for 25 areas of the Atlantic and southern Africa. Maximum-parsimony and distance analyses were employed to investigate biogeographical relationships among those areas. A collection of 26 phylogenies of various Atlantic reef fish taxa was used to assess patterns of origin and diversification relative to evolutionary scenarios based on spatio-temporal sequences of species splitting produced by geological and palaeoceanographic events. We present data on faunal (species and genera) richness, endemism patterns, diversity buildup (i.e. speciation processes), and evaluate the operation of the main biogeographical barriers and/or filters. Results Phylogenetic (proportion of sister species) and distributional (number of shared species) patterns are generally concordant with recognized biogeographical provinces in the Atlantic. The highly uneven distribution of species in certain genera appears to be related to their origin, with highest species richness in areas with the greatest phylogenetic depth. Diversity buildup in Atlantic reef fishes involved (1) diversification within each province, (2) isolation as a result of biogeographical barriers, and (3) stochastic accretion by means of dispersal between provinces. The timing of divergence events is not concordant among taxonomic groups. The three soft (non-terrestrial) inter-regional barriers (mid-Atlantic, Amazon, and Benguela) clearly act as ‘filters’ by restricting dispersal but at the same time allowing occasional crossings that apparently lead to the establishment of new populations and species. Fluctuations in the effectiveness of the filters, combined with ecological differences among provinces, apparently provide a mechanism for much of the recent diversification of reef fishes in the Atlantic. Main conclusions Our data set indicates that both historical events (e.g. Tethys closure) and relatively recent dispersal (with or without further speciation) have had a strong influence on Atlantic tropical marine biodiversity and have contributed to the biogeographical patterns we observe today; however, examples of the latter process outnumber those of the former.

Living in the city: can anyone become an ‘urban exploiter'?

Abstract: Aim As urban landscapes expand, shifts in biodiversity are occurring. This is leading biogeographers and ecologists to consider human-dominated landscapes in their current work. One question that arises is: what characterizes those species that are widespread in the most highly urban environments compared with those restricted to less urbanized areas in the city? Here, we aim to identify the traits that enable species to become urban exploiters, i.e. to dominate highly urbanized surroundings. Identifying these traits may help us better predict and possibly mitigate the biotic homogenization occurring in these areas.

Analysis of factors implicated in the recent decline of Australia's mammal fauna

Abstract: Aim To assess whether eight factors thought to be involved in the extinction process can explain the pattern of recent decline in Australia's mammal fauna. Location Australia. Methods We compiled the first comprehensive lists of mammal species extant at the time of European settlement in each of Australia's 76 mainland regions, and assigned a current conservation status to each species in each region to derive an index of faunal attrition. We then sought to explain the observed region-to-region variation in attrition (the dependent variable) by building a series of models using variables representing the eight factors. Results A strong geographically based pattern of attrition emerged, with faunal losses being greatest in arid regions and least in areas of high rainfall. The Akaike information criterion showed support for one model that explained 93% of the region-to-region variation in attrition. Its six variables all made independent contributions towards explaining the observed variation. Two were environmental variables, namely mean annual rainfall (a surrogate for regional productivity) and environmental change (a measure of post-European disturbance). The other four were faunal variables, namely phylogenetic similarity, body-weight distribution, area (as a surrogate for extent of occurrence), and proportion of species that usually shelter on the ground (rather than in rock piles, burrows or trees). Main conclusions In combination with historical evidence, the analysis provides an explicit basis for setting priorities among regions and species. It also shows that the long-term recovery of populations of many species of Australian mammals will require introduced predator suppression as well as extensive habitat management that includes controlling feral herbivores. Specifically, habitat management should restore aspects of productivity relevant to the types of species at risk and ensure the continual availability of suitable refuges from physiological stressors.

Predicting species distributions from herbarium collections: does climate bias in collection sampling influence model outcomes?

Abstract: Aim Species distribution models and geographical information system (GIS) technologies are becoming increasingly important tools in conservation planning and decision-making. Often the rich data bases of museums and herbaria serve as the primary data for predicting species distributions. Yet key assumptions about the primary data often are untested, and violation of such assumptions may have consequences for model predictions. For example, users of primary data assume that sampling has been random with respect to geography and environmental gradients. Here we evaluate the assumption that plant voucher specimens adequately sample the climatic gradient and test whether violation of this assumption influences model predictions. Location Bolivia and Ecuador. Methods Using 323,711 georeferenced herbarium collections and nine climatic variables, we predicted the distribution of 76 plant species using maximum entropy models (MAXENT) with training points that sampled the climate environments randomly and training points that reflected the climate bias in the herbarium collections. To estimate the distribution of species, MAXENT finds the distribution of maximum entropy (i.e. closest to uniform) subject to the constraint that the expected value for each environmental variable under the estimated distribution matches its empirical average. The experimental design included species that differed in geographical range and elevation; all species were modelled with 20 and 100 training points. We examined the influence of the number of training points and climate bias in training points, elevation and range size on model performance using analysis of variance models. Results We found that significant parts of the climatic gradient were poorly represented in herbarium collections for both countries. For the most part, existing climatic bias in collections did not greatly affect distribution predictions when compared with an unbiased data set. Although the effects of climate bias on prediction accuracy were found to be greater where geographical ranges were characterized by high spatial variation in the degree of climate bias (i.e. ranges where the bias of the various climates sampled by collections deviated considerably from the mean bias), the greatest influence on model performance was the number of presence points used to train the model. Main conclusions These results demonstrate that predictions of species distributions can be quite good despite existing climatic biases in primary data found in natural history collections, if a sufficiently large number of training points is available. Because of consistent overprediction of models, these results also confirm the importance of validating models with independent data or expert opinion. Failure to include independent model validation, especially in cases where training points are limited, may potentially lead to grave errors in conservation decision-making and planning.

Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses

Abstract: Statistical phylogeographic studies contribute to our understanding of the factors that influence population divergence and speciation, and that ultimately generate biogeographical patterns. The use of coalescent modelling for analyses of genetic data provides a framework for statistically testing alternative hypotheses about the timing and pattern of divergence. However, the extent to which such approaches contribute to our understanding of biogeography depends on how well the alternative hypotheses chosen capture relevant aspects of species histories. New modelling techniques, which explicitly incorporate spatio-geographic data external to the gene trees themselves, provide a means for generating realistic phylogeographic hypotheses, even for taxa without a detailed fossil record. Here we illustrate how two such techniques – species distribution modelling and its historical extension, palaeodistribution modelling – in conjunction with coalescent simulations can be used to generate and test alternative hypotheses. In doing so, we highlight a few key studies that have creatively integrated both historical geographic and genetic data and argue for the wider incorporation of such explicit integrations in biogeographical studies.

Local and regional determinants of stream fish assemblage structure: inferences based on taxonomic vs. functional groups

Abstract: Aim To examine the roles of local and regional environmental variables and biotic interactions in determining the structure of local stream fish assemblages, and to compare results derived from analyses based on taxonomic and functional groups. Location Texas, USA. Methods Species abundance data were compiled for 157 stream fish assemblages in several river basins across Texas. Species were condensed into functional groups based on trophic and life-history characteristics. Local and regional environmental variables were either measured at each location or determined from scale maps and public-access data bases. The original taxonomic and functional group data sets were analysed using similarity indices, null models of co-occurrence, and direct and indirect ordination techniques. Results derived from taxonomic and functional group data sets are compared. Results Inferences regarding the relative roles of local and larger-scale factors in determining stream fish assemblage structure differ dramatically between analyses of taxonomic and functional groups. Taxonomic analyses suggest a prominent role of regional-scale environmental factors, and local assemblages sorted according to a biogeographic pattern. Functional group analyses suggest almost equal roles of factors representative of local and larger scales, and assemblages were distinguished by a habitat template irrespective of geographic region. Main conclusions The structure of local stream fish assemblages is determined ultimately by factors representing multiple scales, with the relative importance of each depending on the biological unit employed (species or functional groups). We suggest that analyses using functional groups can more directly infer ecological responses to environmental variation, and therefore may provide a more fruitful avenue for developing and testing ecological theory of community organization across biogeographic scales.

Contrasting responses of arable spiders to the landscape matrix at different spatial scales

Abstract: Aim Animal communities can be influenced by the composition of the surrounding landscape through immigration. Depending on habitat preferences, however, the effect of the landscape matrix can be positive or negative and can vary with scale. We tested this idea with arable spiders and tried to infer dispersal distances from relationships between local density and landscape composition at different spatial scales. Location Thirty-eight landscapes around the cities of Gottingen and Giessen, Germany. Methods Spiders were captured with pitfall traps in one field of winter wheat in each landscape. Landscape composition around the fields was characterized at 11 scales from 95 m to 3 km radius by land-use mapping and subsequent GIS analysis. Correlation tests were performed between landscape composition and local densities or species richness. Results In both study regions, local species richness was enhanced by non-crop habitats on a landscape scale. The overall densities of wolf spiders (Lycosidae), long-jawed spiders (Tetragnathidae), crab spiders (Thomisidae), and dwarf sheet spiders (Hahniidae) increased significantly in landscapes with high percentages of non-crop habitats. Out of the 40 species tested, 19 responded positively to the percentage of non-crop habitats in the surrounding landscape, and five responded negatively. Depending on the species, the spatial scales with the highest explanatory power ranged from 95 m to 3 km radius around the study fields, potentially reflecting dispersal distances. Main conclusions Arable spider species showed contrasting responses to the landscape context with respect both to the direction and to the spatial scale of the relationship. The variation in landscape requirements among species ensures high spider densities in a wide range of situations, which contributes to ecosystem resilience. However, species richness of arable spiders depends on heterogeneous landscapes with high percentages of non-crop habitats.

Predicting species distributions: a critical comparison of the most common statistical models using artificial species

Abstract: Aim To test statistical models used to predict species distributions under different shapes of occurrence-environment relationship. We addressed three questions: (1) Is there a statistical technique that has a consistently higher predictive ability than others for all kinds of relationships? (2) How does species prevalence influence the relative performance of models? (3) When an automated stepwise selection procedure is used, does it improve predictive modelling, and are the relevant variables being selected? Location We used environmental data from a real landscape, the state of California, and simulated species distributions within this landscape. Methods Eighteen artificial species were generated, which varied in their occurrence response to the environmental gradients considered (random, linear, Gaussian, threshold or mixed), in the interaction of those factors (no interaction vs. multiplicative), and on their prevalence (50% vs. 5%). The landscape was then randomly sampled with a large (n = 2000) or small (n = 150) sample size, and the predictive ability of each statistical approach was assessed by comparing the true and predicted distributions using five different indexes of performance (area under the receiver-operator characteristic curve, Kappa, correlation between true and predictive probability of occurrence, sensitivity and specificity). We compared generalized additive models (GAM) with and without flexible degrees of freedom, logistic regressions (general linear models, GLM) with and without variable selection, classification trees, and the genetic algorithm for rule-set production (GARP). Results Species with threshold and mixed responses, additive environmental effects, and high prevalence generated better predictions than did other species for all statistical models. In general, GAM outperforms all other strategies, although differences with GLM are usually not significant. The two variable-selection strategies presented here did not discriminate successfully between truly causal factors and correlated environmental variables. Main conclusions Based on our analyses, we recommend the use of GAM or GLM over classification trees or GARP, and the specification of any suspected interaction terms between predictors. An expert-based variable selection procedure was preferable to the automated procedures used here. Finally, for low-prevalence species, variability in model performance is both very high and sample-dependent. This suggests that distribution models for species with low prevalence can be improved through targeted sampling.

Modelling the known and unknown plant biodiversity of the Amazon Basin

Abstract: Aims The overall aim of this study is to provide the data needed for Amazonian conservation and the sustainable management of the region. To this end I model the hypothetical distribution of plant species richness across the Amazon Basin, the distribution of the proportion of this species richness that can be accounted for by described species, and hence the distribution of the biodiversity which remains unknown. Location Amazonia, Neotropics. Methods Species richness across the Amazon Basin is estimated by comparing the occurrences of 1584 species of Magnoliophyta whose taxonomy and geographical distributions are relatively well known. These data are used to collate checklists for squares of 1° latitude by 1° longitude. Comparison of the checklists allows estimation of the relative expected diversity in the vicinity of each degree square. Summing the distributions of the hypothetical real ranges gives the proportion of the biodiversity that can be accounted for by described species. Subtraction of the second distribution from the first gives a distribution of the contribution to the overall biodiversity that the model predicts, potentially, results from as yet undescribed species. Results Collections documented in recent botanical monographs show an extremely biased distribution with the best knowledge being found in a very few relatively well-collected areas. At the degree square level, this model predicts that gamma biodiversity in the Amazon Basin is uniformly high across most of the basin. The model predicts that four large areas of the basin are particularly poorly known, and that they should contain large numbers of uncollected species. Main conclusions The model presented here highlights the difficulties of quantifying Amazonian plant diversity and its distribution. The low density of collections, and especially their extremely clumped distribution, undermines confidence in theories that seek to explain the apparent distribution of biodiversity. The model's prediction is substantially different from published predictions of the distribution of alpha diversity. Testing of this model in the areas identified as lacunae would require collecting programmes designed to collect fertile material of rare species. If the model's predictions are approximately accurate, the plant biodiversity of the Amazon Basin is considerably underestimated.

Evidence for Gondwanan vicariance in an ancient clade of gecko lizards

Abstract: Aim Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post-Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives. Location Africa, Asia, Europe, South America, Atlantic Ocean. Methods We used parsimony and partitioned Bayesian methods to analyse data from five nuclear genes to generate a phylogeny for the New World sphaerodactyl geckos and their close Old World relatives. We used dispersal-vicariance analysis to determine ancestral area relationships among clades, and divergence times were estimated from the phylogeny using nonparametric rate smoothing. Results We recovered a monophyletic group containing the New World sphaerodactyl genera, Coleodactylus, Gonatodes, Lepidoblepharis, Pseudogonatodes and Sphaerodactylus, and the Old World Gekkotan genera Aristelliger, Euleptes, Quedenfeldtia, Pristurus, Saurodactylus and Teratoscincus. The dispersal-vicariance analysis indicated that the ancestral area for this clade was North Africa and surrounding regions. The divergence between the New World spaherodactyl geckos and their closest Old World relative was estimated to have occurred c. 96 Myr BP. Main conclusions Here we provide the first molecular genetic phylogenetic hypothesis of the New World sphaerodactyl geckos and their closest Old World relatives. A combination of divergence date estimates and dispersal-vicariance analysis informed a biogeographical scenario indicating that the split between the sphaerodactyl geckos and their African relatives coincided with the Africa/South America split and the opening of the Atlantic Ocean. We resurrect the family name Sphaerodactylidae to represent the expanded sphaerodactyl clade.

Bioclimatology of beech (Fagus sylvatica L.) in the Eastern Alps: spatial and altitudinal climatic signals identified through a tree‐ring network

Abstract: Aim To identify the dominant spatial patterns of Fagus sylvatica radial growth in the Eastern Alps, and to understand their relationships to climate variation and bioclimatic gradients. Location Fourteen beech stands in the Eastern Alps, growing between 200 and 1500 m a.s.l. in Italy, Slovenia and Austria. Methods At each site, trees were sampled using increment borers or by taking discs from felled trees. Cores and discs were processed by measuring and crossdating ring width. Ring width series were standardized, averaged, and prewhitened to obtain site chronologies. Hierarchical Cluster Analysis (HCA) and Principal Components Analysis of prewhitened site chronologies were used to identify spatial and altitudinal growth patterns, related to the bioclimatic position of each stand. Bootstrap correlation and response functions were computed between monthly climatic variables and either principal component scores or composite chronologies from stands associated by HCA. The stability of dendroclimatic signals was analyzed by moving correlation functions (MCF). Correlation analysis (teleconnections) based on a data base of 37 Italian and Slovenian beech tree-ring chronologies revealed the spatial extent of principal component scores. Results Sampled trees were 200‐400 years old, representing the oldest beech trees that have been crossdated for the Alps to date. Maximum age was directly related to altitude and to the presence of historical forms of conservation. Treering parameters varied according to geographic patterns and the age of sampled trees. Stands were bioclimatically organized according to their location, and with reference to their elevation and distance from the Adriatic Sea. A direct response to winter temperature was found at all elevations. The altitudinal gradient ranged from low-elevation stands, characterized by a Mediterranean-type, late spring‐ summer drought signal, to mountain and high-elevation stands, characterized by a direct response to growing season temperature plus an inverse response to the previous year’s July temperature. The mountain and high-elevation signal was evident in Austria, the Central Alps and Slovenia, while the low-elevation signal was confined to mountains adjacent to the Adriatic Sea. MCF revealed trends in the response to climatic factors affecting tree-ring formation in mountain and high-mountain stands linked to climatic warming. Main conclusions Dendroclimatic networks can be used for bioclimatic studies of tree populations. A biogeographical separation emerged between the Alps and the Apennines at the upper elevations, while different degrees of mediterraneity distinguished sites at lower elevations. This information will be useful in assessing

Dry spots and wet spots in the Andean hotspot

Abstract: Aim To explain the relationship between topography, prevailing winds and precipitation in order to identify regions with contrasting precipitation regimes and then compare floristic similarity among regions in the context of climate change. Location Eastern slope of the tropical Andes, South America. Methods We used information sources in the public domain to identify the relationship between geology, topography, prevailing wind patterns and precipitation. Areas with contrasting precipitation regimes were identified and compared for their floristic similarity. Results We identify spatially separate super-humid, humid and relatively dry regions on the eastern slope of the Andes and show how they are formed by the interaction of prevailing winds, diurnally varying atmospheric circulations and the local topography of the Andes. One key aspect related to the formation of these climatically distinct regions is the South American low-level jet (SALLJ), a relatively steady wind gyre that flows pole-ward along the eastern slopes of the Andes and is part of the gyre associated with the Atlantic trade winds that cross the Amazon Basin. The strongest winds of the SALLJ occur near the ‘elbow of the Andes’ at 18° S. Super-humid regions with mean annual precipitation greater than 3500 mm, are associated with a ‘favourable’ combination of topography, wind-flow orientation and local air circulation that favours ascent at certain hours of the day. Much drier regions, with mean annual precipitation less than 1500 mm, are associated with ‘unfavourable’ topographic orientation with respect to the mean winds and areas of reduced cloudiness produced by local breezes that moderate the cloudiness. We show the distribution of satellite-estimated frequency of cloudiness and offer hypotheses to explain the occurrence of these patterns and to explain regions of anomalously low precipitation in Bolivia and northern Peru. Floristic analysis shows that overall similarity among all circumscribed regions of this study is low; however, similarity among super-humid and humid regions is greater when compared with similarity among dry regions. Spatially separate areas with humid and super-humid precipitation regimes show similarity gradients that are correlated with latitude (proximity) and precipitation. Main conclusions The distribution of precipitation on the eastern slope of the Andes is not simply correlated with latitude, as is often assumed, but is the result of the interplay between wind and topography. Understanding the phenomena responsible for producing the observed precipitation patterns is important for mapping and modelling biodiversity, as well as for interpreting both past and future climate scenarios and the impact of climate change on biodiversity. Super-humid and dry regions have topographic characteristics that contribute to local climatic stability and may represent ancestral refugia for biodiversity; these regions are a conservation priority due to their unique climatic characteristics and the biodiversity associated with those characteristics.

Biogeographical relationships among tropical forests in north‐eastern Brazil

Abstract: Aim To use parsimony analysis of endemicity and cladistic analysis of distributions and endemism to evaluate two hypotheses addressing biogeographical relationships among Amazonia, the Caatinga forest enclaves, Pernambuco Centre and the southern Atlantic Forest. Location North-eastern Brazil, South America. Methods To find the most parsimonious areagram we analysed a matrix composed of the presence (1) or absence (0) of 745 taxa (i.e. 293 genera and 452 species of woody plants) within 16 localities belonging to the four large regions addressed in this study. Results One most parsimonious areagram was found and it shows a basal separation between the southern Atlantic Forest and all other regions. This break is followed by a separation between all Caatinga forest enclaves (except Baturite ´) from a cluster composed of Baturite ´, the Pernambuco Centre and Amazonia. In

Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation

Abstract: Aim The aim of this study is to analyse the distribution pattern of the botanical collecting effort in Amazonia so that it can be accounted for when interpreting phytogeographical patterns such as inferred species ranges We also develop a mechanistic and transparent method for taking into account the bias in collecting effort when estimating likelihoods of species occurrences Location Amazonia, Neotropics Methods We utilized electronic data sets of georeferenced herbarium collections (1,063,530 in total) We plotted collecting localities (68,246 in total) on maps overlaid with 1° and 05° square grids, and analysed collecting effort using a geographical information system (GIS) We also drew a map of Thiessen polygons, using collecting localities as polygon centres, to visualize collecting density in a scale-independent way We then created a ‘collecting activity landscape’ in which well-collected areas appear as peaks and poorly studied areas as valleys We demonstrate how this surface can be utilized when estimating species distributions Results The data available to us confirm that botanical collecting activity is still severely biased in Amazonia The uncollected area represents 43% of the total area of Amazonia, while another 28% is poorly collected and only 2% can be considered relatively well collected The Thiessen polygon network represents an improvement in the presentation of collecting intensity compared with square grids Main conclusions The maps of botanical collecting effort in the Neotropics should be used for visually correcting phytogeographical interpretations With the help of GIS applications the observed spatial bias in collecting effort can be utilized in estimating the likelihood of occurrence of species in a repeatable manner These estimates, in turn, can be used for various purposes in basic and applied science as well as in decision-making The biased collecting effort should, in the long run, be corrected by further field work in unexplored areas, which can be identified with the maps presented here

Molecular dating of the ‘Gondwanan’ plant family Proteaceae is only partially congruent with the timing of the break‐up of Gondwana

Abstract: Aim The flowering plant family Proteaceae is putatively of Gondwanan age, with modern and fossil lineages found on all southern continents. Here we test whether the present distribution of Proteaceae can be explained by vicariance caused by the break-up of Gondwana. Location Africa, especially southern Africa, Australia, New Zealand, South America, New Caledonia, New Guinea, Southeast Asia, Sulawesi, Tasmania. Methods We obtained chloroplast DNA sequence data from the rbcL gene, the rbcL-atpB spacer, and the atpB gene from leaf samples of forty-five genera collected from the field and from living collections. We analysed these data using Bayesian phylogenetic and molecular dating methods, with five carefully selected fossil calibration points to obtain age estimates for the nodes within the family. Results Four of eight trans-continental disjunctions of sister groups within our sample of the Proteaceae post-date the break-up of Gondwana. These involve independent lineages, two with an Africa-Australia disjunction, one with an Africa–South America disjunction, and one with a New Zealand–Australasia disjunction. The date of the radiation of the bird-pollinated Embothriinae corresponds approximately to the hypothesized date of origin of nectar-feeding birds in Australia. Main conclusions The findings suggest that disjunct distributions in Proteaceae result from both Gondwanan vicariance and transoceanic dispersal. Our results imply that ancestors of some taxa dispersed across oceans rather than rafting with Gondwanan fragments as previously thought. This finding agrees with other studies of Gondwanan plants in dating the divergence of Australian, New Zealand and New Caledonian taxa in the Eocene, consistent with the existence of a shared, ancestral Eocene flora but contrary to a vicariance scenario based on accepted geological knowledge.

A comparison of altitudinal species richness patterns of bryophytes with other plant groups in Nepal, Central Himalaya

Abstract: Aim To explore species richness patterns in liverworts and mosses along a central Himalayan altitudinal gradient in Nepal (100-5500 m a.s.l.) and to compare these patterns with patterns observed for ferns and flowering plants. We also evaluate the potential importance of Rapoport's elevational rule in explaining the observed richness patterns for liverworts and mosses.Location Nepal, Central Himalaya.Methods We used published data on the altitudinal ranges of over 840 Nepalese mosses and liverworts to interpolate presence between maximum and minimum recorded elevations, thereby giving estimates of species richness for 100-m altitudinal bands. These were compared with previously published patterns for ferns and flowering plants, derived in the same way. Rapoport's elevational rule was assessed by correlation analyses and the statistical significance of the observed correlations was evaluated by Monte Carlo simulations.Results There are strong correlations between richness of the four groups of plants. A humped, unimodal relationship between species richness and altitude was observed for both liverworts and mosses, with maximum richness at 2800 m and 2500 m, respectively. These peaks contrast with the richness peak of ferns at 1900 m and of vascular plants, which have a plateau in species richness between 1500 and 2500 m. Endemic liverworts have their maximum richness at 3300 m, whereas non-endemic liverworts show their maximum richness at 2700 m. The proportion of endemic species is highest at about 4250 m. There is no support from Nepalese mosses for Rapoport's elevational rule. Despite a high correlation between altitude and elevational range for Nepalese liverworts, results from null simulation models suggest that no clear conclusions can be made about whether liverworts support Rapoport's elevational rule.Main conclusions Different demands for climatic variables such as available energy and water may be the main reason for the differences between the observed patterns for the four plant groups. The mid-domain effect may explain part of the observed pattern in moss and liverwort richness but it probably only works as a modifier of the main underlying relationship between climate and species richness.

Vicariance patterns in the Mediterranean Sea: East-west cleavage and low dispersal in the endemic seagrass Posidonia oceanica

Abstract: Aim The seagrass, Posidonia oceanica is a clonal angiosperm endemic to the Mediterranean Sea. Previous studies have suggested that clonal growth is far greater than sexual recruitment and thus leads to low clonal diversity within meadows. However, recently developed microsatellite markers indicate that there are many different genotypes, and therefore many distinct clones present. The low resolution of markers used in the past limited our ability to estimate clonality and assess the individual level. New high-resolution dinucleotide microsatellites now allow genetically distinct individuals to be identified, enabling more reliable estimation of population genetic parameters across the Mediterranean Basin. We investigated the biogeography and dispersal of P. oceanica at various spatial scales in order to assess the influence of different evolutionary factors shaping the distribution of genetic diversity in this species.

Is a new paradigm emerging for oceanic island biogeography

Abstract: Following several decades during which two dissimilar and incompatible models (equilibrium and vicariance) dominated island biogeography, recent publications have documented patterns that point the way towards a new paradigm that includes elements of both models, as well as some novel aspects. Many of these seminal contributions have been made possible by the recent development of robust, temporally calibrated phylogenies used in concert with increasingly precise and reliable geological reconstructions of oceanic regions. Although a new general model of oceanic island biogeography has not yet been proposed, in this brief overview I present six hypotheses that summarize aspects of the emerging paradigm. These hypotheses deal with: the frequency of dispersal over oceanic water barriers by terrestrial organisms; the existence of substantial variation in the amount of dispersal (and gene flow) within a given set of related species within a given archipelago; the frequency, extent and impact on species richness of diversification within archipelagos; the frequent correlation of island age and the age of the species that live on the island; the long-term persistence of species on oceanic islands; and the occasional recolonization of continents by species from clades that diversified on islands. Identifying, testing, and seeking means of synthesizing these and other emerging hypotheses may allow a new conceptual paradigm to emerge.

Introducing a new (freeware) tool for palynology

Abstract: We present a multiple-access key and searchable data base to Neotropical pollen that is available as freeware. The data base is based on FileMaker 5 and contains c. 6000 images of >1000 taxa. All pollen images are of acetolysed grains collected from vouchered herbarium specimens. The selection of taxa to be included in the data base is predicated upon their probable occurrence in lake sedimentary records, which in turn was based on their flower structure, sexual mechanisms and ecology. The multiple-access key is a forgiving format as it can be used with incomplete data or where the researcher cannot decide between the choices offered. The data base is downloadable and is compatible with both Mac and PC platforms.

A geometric morphometric approach to the study of ecogeographical and clinal variation in vervet monkeys

Abstract: Aim To examine and visualize clines in size and shape of Cercopithecus aethiops Linneus, 1758 (Primate, Cercopithecidae) skulls, and to investigate environmental factors which might best explain the observed variation. Location Sub-Saharan Africa. Methods Eighty-six three-dimensional anatomical landmarks were used to describe 306 skulls of adult C. aethiops sampled over its entire distribution. Geometric morphometric methods for the quantitative analysis of form variation were applied. Size and shape variables were computed and regressed onto geographical coordinates and environmental variables (elevation, temperature, rainfall, moisture and Shannon rainfall diversity index) using both linear and curvilinear models. Components (geographical, environmental, spatially structured environmental and residual) of ecogeographical variation in skull form were partitioned using partial regression. A novel approach for summarizing and visualizing nonlinear patterns of clinal variation using surface rendering of three-dimensional shapes is presented. Results Clinal variation in size and shape was highly significant, and was best described by curvilinear models. There were strong similarities between females and males. The cline in size was especially pronounced, explaining up to about 40% of observed variation, and was mainly longitudinal rather than latitudinal. A major trend of clinal shape variation also occurred from west to east, and corresponded to an expansion of the face relative to the neurocranium in the west. In the east, skulls also tended to be deeper and with narrower zygomatic arches. Geography and the spatially structured environmental component were the major contributors to the explained variance in size in both sexes, but the proportion of variance explained by the latter was smaller in females. In contrast, geography and environment explained similar amounts of variation in shape and their contribution was about twice that of the spatially structured environmental component. About 60–80% of variation in skull form was not explained by any variable in the analysis. The main factors influencing skull size differed in females and males, with rainfall being very influential in males. Both female and male skull shapes were strongly affected by average annual rainfall. Main conclusions A strong spatial and environmental basis to variations in African vervet monkey skull form was evident. However, the observed pattern did not conform to predictions based on Bergmann's rule. Rainfall consistently emerged as an important predictor, which may contribute to intraspecific variation in the size and shape of vervet monkey skulls through its effect on habitat productivity.

West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event‐based tree fitting

Abstract: Aim Recent studies suggest that if constrained by prevailing wind or ocean currents dispersal may produce predictable, repeated distribution patterns. Dispersal mediated by the West Wind Drift (WWD) and Antarctic Circumpolar Current (AAC) has often been invoked to explain the floristic similarities of Australia, South America and New Zealand. If these systems have been important dispersal vectors then eastward dispersal ‐ from Australia to New Zealand and the western Pacific to South America ‐ is expected to predominate. We investigate whether phylogenies for Southern Hemisphere plant groups provide evidence of historical dispersal asymmetry and more specifically whether inferred asymmetries are consistent with the direction of the WWD/AAC. Location Southern Hemisphere. Methods We assembled a data set of 23 published phylogenies for plant groups that occur in New Zealand, Australia and/or South America. We used parsimonybased tree fitting to infer the number and direction of dispersals within each group. Observed dispersal asymmetries were tested for significance against a distribution of expected values. Results Our analyses suggest that dispersal has played a major role in establishing present distributions and that there are significant patterns of asymmetry in Southern Hemisphere dispersal. Consistent with the eastward direction of the WWD/ACC, dispersal from Australia to New Zealand was inferred significantly more often than in the reverse direction. No significant patterns of dispersal asymmetry were found between the western Pacific landmasses and South America. However, eastward dispersal was more frequently inferred between Australia and South America, while for New Zealand‐South American events westward dispersal was more common. Main conclusions Our results suggest that eastward circumpolar currents have constrained the dispersal of plants between Australia and New Zealand. However, the WWD/ACC appear to have had less of an influence on dispersal between the western Pacific landmasses and South America. This observation may suggest that differences in dispersal mechanism are important ‐ direct wind or water dispersal vs. stepping-stone dispersal along the Antarctic coast. While our analyses provide useful preliminary insights into dispersal asymmetry in the Southern Hemisphere we will need larger data sets and additional methodological advances in order to test fully these dispersal patterns and infer processes from phylogenetic data.

Reliability of pollen ratios for environmental reconstructions on the Tibetan Plateau

Abstract: Aim Pollen ratios are widely used to gain palaeovegetation and palaeoclimatic information from fossil pollen spectra, although their applicability has seldom been tested with modern pollen data. I used a data set of 113 lake-surface sediments from the eastern Tibetan Plateau to test the reliability of several pollen ratios. Location The lake-surface pollen spectra cover a wide range of vegetation types (temperate desert, temperate steppe, alpine desert, alpine steppe, high-alpine meadow, sub-alpine shrub, coniferous and mixed forest) and climatic conditions (mean July temperature, TJuly: 4.0–17.4°C; mean annual precipitation, Pann: 104–670 mm). Methods Lake-surface sediments were analysed palynologically, and several pollen ratios were calculated. These ratios were interpreted with respect to vegetation and climatic conditions. Results The arboreal pollen sum (AP) was highest in samples from forested areas and was significantly correlated with Pann (r2 = 0.44). In non-forested areas, samples from large lakes and from lakes surrounded by sparse vegetation had increased AP values, suggesting that AP is a useful vegetation density indicator. Artemisia/Chenopodiaceae (A/C) ratios were lowest in desert areas and were positively correlated with Pann (r2 = 0.25). The aridity pollen index was inappropriate for inferring (palaeo-)climatic information from samples on the eastern Tibetan Plateau as it had no significant correlation with the environmental factors. Artemisia/Cyperaceae (A/Cy) ratios had a significant correlation with TJuly (r2 = 0.23), but only a weak correlation with Pann, which indicates that the A/Cy ratio is applicable as a temperature indicator. Furthermore, it is a valuable tool for the differentiation of high-alpine meadow from steppe vegetation. Main conclusions AP sum, A/C ratio and A/Cy ratio are useful tools for qualitative and semi-quantitative palaeoenvironmental reconstruction on the Tibetan Plateau; however, the results obtained should not be interpreted quantitatively.

Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids

Abstract: Aim To test the hypothesis that continental drift drives diversification of organisms through vicariance, we selected a group of primitive arachnids which originated before the break-up of Pangaea and currently inhabits all major landmasses with the exception of Antarctica, but lacks the ability to disperse across oceanic barriers. Location Major continental temperate to tropical landmasses (North America, South America, Eurasia, Africa, Australia) and continental islands (Bioko, Borneo, Japan, Java, New Caledonia, New Guinea, New Zealand, Sri Lanka, Sulawesi, Sumatra). Methods Five kb of sequence data from five gene regions for more than 100 cyphophthalmid exemplars were analysed phylogenetically using different methods, including direct optimization under parsimony and maximum likelihood under a broad set of analytical parameters. We also used geological calibration points to estimate gross phylogenetic time divergences. Results Our analyses show that all families except the Laurasian Sironidae are monophyletic and adhere to clear biogeographical patterns. Pettalidae is restricted to temperate Gondwana, Neogoveidae to tropical Gondwana, Stylocellidae to Southeast Asia, and Troglosironidae to New Caledonia. Relationships between the families inhabiting these landmasses indicate that New Caledonia is related to tropical Gondwana instead of to the Australian portion of temperate Gondwana. The results also concur with a Gondwanan origin of Florida, as supported by modern geological data. Main conclusions By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats, but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted. Our results strongly support the presence of a circum-Antarctic clade of formerly temperate Gondwanan species, a clade restricted to tropical Gondwana and a Southeast Asian clade that originated from a series of early Gondwanan terranes that rifted off northwards from the Devonian to the Triassic and accreted to tropical Laurasia. The relationships among the Laurasian species remain more

Reconciling approaches to biogeographical regionalization: a systematic and generic framework examined with a case study of the Australian continent

Abstract: Aim To develop a systematic and generic framework for biogeographical regionalizations that can assist in reconciling different approaches and advance their application as a research tool. Location The Australian continent is used as a case study. Methods A review of approaches to biogeographical regionalization revealed two basic methodologies: the integrated survey method and the parametric approach. To help reconcile these different approaches, we propose a simple, four-step, flexible and generic framework. (1) Identification of the thematic foci from the three main themes (composition and evolutionary legacy; ecosystem drivers; ecosystem responses). (2) Proposal of a theory defining the purpose. (3) Application of a numeric agglomerative classification procedure that requires the user to make explicit assumptions about attributes, the number of classification groups, the spatial unit of analysis, and the metric for measuring the similarity of these units based on their attribute values. (4) Acquisition of spatial estimates of the required input attribute data. For this case study, an agglomerative classification strategy was applied using the functions within patn 3.03, a software package facilitating large-scale, multivariate pattern analysis. The input data to the classifications were continental coverages of 11 environmental variables and three indices of gross primary productivity stored at a grid cell resolution of c. 250 m. The spatial units of analysis were surface hydrological units (SHU), which were derived from a continental digital elevation model based on the contributing areas to stream segments or the area draining into a local sink where there is no organized drainage. The Minkowski series (Euclidean distance) was selected as the association measure to allow weightings to be applied to the variables. Results Two new biogeographical regionalizations of the Australian continent were generated. The first was an environmental domain classification, based on 11 climatic, terrain and soil attributes. This regionalization can be used to address hypotheses about the relationship between environmental distance and evolutionary processes. The classification produced 151 environmental groups. The second was a classification of primary productivity regimes based on estimates of the gross primary productivity of the vegetation cover calculated from moderate resolution imaging spectroradiometer (MODIS) normalized difference vegetation index (NDVI) data and estimates of radiation. This classification produced 50 groups, and can be used to examine hypotheses concerning productivity regimes and animal life-history strategies. The productivity classification does not capture all the properties related to biological carrying capacity, process rates and differences in the characteristic biodiversity of ecosystems. Some of these ecologically significant properties are captured by the environmental domain classification. Main conclusions Our framework can be applied to all terrestrial regions, and the necessary data for the analyses presented here are now available at global scales. As the spatial predictions generated by the classifications can be tested by comparison with independent data, the approach facilitates exploratory analysis and further hypothesis generation. Integration of the three themes in our framework will contribute to a more comprehensive approach to biogeography.

Glacial refugia for summer-green trees in Europe and south-west Asia as proposed by ECHAM3 time-slice atmospheric model simulations

Abstract: Aim To generate maps of potential refugia for summer-green trees during the Last Glacial Maximum (LGM). Locations Southern Europe and south-western Asia. Methods Time-slice simulations of the atmospheric climate with the ECHAM3 model are used for the LGM. Limiting factors beyond which cool and warm groups of deciduous trees cannot grow (such as temperature in growing degree days, minimum monthly temperature and precipitation in summer) are chosen. A limited validation by fossil pollen and charcoal records from LGM sites was done. Results Two sets of maps extending from Europe to the Caspian region for cool and warm summer-green trees are presented. Three criteria are combined using contour lines to indicate confidence levels. Small areas within the three southern peninsulas of Europe (Spain, Italy and Greece) are highlighted as possible refugia for summer-green trees. Further, areas that have remained poorly known are now proposed as refugia, including the Sakarya–Kerempe region in northern Turkey, the east coast of the Black Sea and the area south of the Caspian Sea. Main conclusions The maps produced in this study could be used to facilitate better long-term management for the protection of European and south-western Asian biodiversity.

Brazilian Páramos IV. Phytogeography of the campos de altitude

Abstract: Aim This contribution treats the phytogeography of the contemporary campos de altitude flora, with a focus on patterns at the level of genus. Comparative analysis using data from 17 other sites in Latin America is used to describe phytogeographical patterns at the continental scale. Results are combined with those of previous publications to shed light on the biogeographical origins of contemporary floristic patterns in the high mountains of south-east Brazil. Location The campos de altitude are a series of cool-humid, mountaintop grass- and shrublands found above elevations of 1800–2000 m in south-east Brazil, within the biome of the Atlantic Forest. Methods Vascular floras are compiled for the three best-known campos de altitude sites, and for 17 other highland and lowland locations in Latin America. Floras are binned into phytogeographical groups based on centres of diversity/origin. Floristic and geographical distances are calculated for all location-pairs; Mantel tests are used to test for relationships between patterns in geographical distance, and floristic and climatic similarity. Multivariate statistics are carried out on the similarity matrices for all genera, and for each phytogeographical group. Predominant life-forms, pollination and dispersal syndromes are determined for each genus in the campos de altitude flora, and proportional comparisons are made between phytogeographical groups. Supporting evidence from previously published literature is used to interpret analytical results. Results Two-thirds of the genera in the campos de altitude are of tropical ancestry; the remainder are of temperate-zone or cosmopolitan ancestry. Most campos de altitude genera are phanerophytes and hemicryptophytes, insect pollinated, and wind or gravity dispersed, but there are significant differences in the distribution of these traits among phytogeographical groups. The campos de altitude show stronger floristic similarities with other Brazilian mountain sites and distant Andean sites than with nearby low- and middle-elevation sites; these similarities are best explained by climatic similarities. Floristic similarities among sites for temperate genera are better explained by ‘sinuous’ distance (e.g. measured along the spines of mountain ranges) than by direct distance; similarities in tropical genera are more related to direct distance. Different phytogeographical groups appear to be responding to different climatic signals. Main conclusions Many taxa currently living at the summits of the south-east Brazilian Highlands trace their ancestry to temperate latitudes. Patterns of endemism and diversity in the south-east Brazilian mountains point to climatically driven allopatry as a principal mechanism for speciation. The tropical component of the campos de altitude flora is primarily derived from drier, highland environments of the Brazilian interior; the temperate component rises in importance with elevation, but never reaches the levels seen in the tropical Andes. Most temperate taxa in the campos de altitude appear to have arrived via migration through favourable habitat rather than by recent, long-distance dispersal. At least 11% of the plant species in the campos de altitude study sites are directly shared with the Andes. Palynofloras show that the campos de altitude have significantly contracted over the past 10,000 years, as regional temperatures have warmed and become more humid.

The relationships between net primary productivity, human population density and species conservation

Abstract: Aim In this study, I determine the relationships between net primary productivity (NPP), human population density, species richness and land use. I also examine the implications of human settlement patterns for species conservation. Location Australia. Methods I document the associations between NPP, human population density and the species richness of birds, butterflies and mammals using correlations and spatial regressions. I also assess changes in land-use with NPP and population density, focussing particularly on protected areas. An initial exploration into the implications of the NPP-population density relationship for regional conservation strategies is provided. Results Human population density increases with NPP suggesting that available energy may be a key driving force of human settlement patterns. The species richness of each taxonomic group and geographically restricted species also increases with NPP leading to substantial overlap between species diversity and populated regions. The percentage of land designated as minimal use decreases considerably with increasing human population density and NPP, while intensive agriculture is confined entirely to areas of high NPP. There are strong negative relationships between the size of Australia’s National Parks and human population density and NPP. Small parks are often surrounded by relatively dense settlements, but have high average NPP, while large parks are mostly isolated and characterized by low productivity. There are no areas in the highest quartile of NPP that also occur in the most sparsely populated regions, presenting challenges for conservation strategies wanting to protect productive areas under the least threat of human development. Main conclusions Human population density and species richness respond similarly to variation in NPP, leading to spatial congruence between human settlements and productive, species rich regions. Planning strategies are required that minimize the potential threat posed by human development to diverse ecosystems and maximize the underlying productivity of protected areas. Reducing the level of threat may require stabilizing the size of the human population, while capturing larger areas of relatively high productivity in the conservation reserve system would lead to greater protection of local diversity.

Fire, fuels and restoration of ponderosa pine–Douglas fir forests in the Rocky Mountains, USA

Abstract: Aim Forest restoration in ponderosa pine and mixed ponderosa pine‐Douglas fir forests in the US Rocky Mountains has been highly influenced by a historical model of frequent, low-severity surface fires developed for the ponderosa pine forests of the Southwestern USA. A restoration model, based on this low-severity fire model, focuses on thinning and prescribed burning to restore historical forest structure. However, in the US Rocky Mountains, research on fire history and forest structure, and early historical reports, suggest the low-severity model may only apply in limited geographical areas. The aim of this article is to elaborate a new variable-severity fire model and evaluate the applicability of this model, along with the low-severity model, for the ponderosa pine‐Douglas fir forests of the Rocky Mountains. Location Rocky Mountains, USA. Methods The geographical applicability of the two fire models is evaluated using historical records, fire histories and forest age-structure analyses. Results Historical sources and tree-ring reconstructions document that, near or before ad 1900, the low-severity model may apply in dry, low-elevation settings, but that fires naturally varied in severity in most of these forests. Low-severity fires were common, but high-severity fires also burned thousands of hectares. Tree regeneration increased after these high-severity fires, and often attained densities much greater than those reconstructed for Southwestern ponderosa pine forests. Main conclusions Exclusion of fire has not clearly and uniformly increased fuels or shifted the fire type from low- to high-severity fires. However, logging and livestock grazing have increased tree densities and risk of high-severity fires in some areas. Restoration is likely to be most effective which seeks to (1) restore variability of fire, (2) reverse changes brought about by livestock grazing and logging, and (3) modify these land uses so that degradation is not repeated.

Seamounts: identity crisis or split personality?

Abstract: At present, researchers propose that over 14,000 seamounts exist and, like their terrestrial analogues, function like islands. In addition, seamounts are described as oases, biodiversity hotspots, and lush coral/sponge gardens. Here I discuss the extent to which these tenets regarding seamounts may be inappropriate, suffer from a lack of support, and be over-generalizations of a broad range of environmental types encountered on seamounts. Ultimately, for seamount science to progress, we need to challenge our conventional wisdom on these habitats and the extent to which all seamounts function in a similar manner.

Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea)

Abstract: Aim The olive tree is considered one of the best indicators of the Mediterranean climate. The species’ distribution is associated with geographical and bioclimatic factors, as well as being influenced by a long period of cultivation. Despite concerted efforts of different research groups, the origin of the Mediterranean olive tree still remains elusive. In the present study, relationships between taxa and populations covering the entire range of Olea europaea were investigated using both maternal (plastid genome) and biparental (nuclear genome) markers to disclose evolutionary patterns in the olive complex. Phylogenetic and phylogeographical results of the two-genome analyses were interpreted in a biogeographical context. Location Mediterranean, temperate and subtropical floristic regions of the Old World. Methods Phylogeographical reconstructions of plastid DNA polymorphism were performed using microsatellites, restriction sites and indels on a wide sample of 185 representative trees across the Old World, including 28 herbarium specimens from remote areas. Additionally, the potential utility of one ITS-1 pseudogene for phylogenetic analyses was explored using Bayesian and maximum parsimony approaches on a subsample of 38 olive trees. Results Forty plastid haplotypes were recognized and split into two lineages and seven sublineages. The analysis of ITS-1 sequences also allowed the identification of seven well differentiated groups. Distribution of plastid and ribosomal DNA lineages was congruent, but particular cases of phylogenetic incongruence were disclosed (particularly in the Sahara and Madeira). Lastly, two divergent ITS-1 copies were isolated from the same sample of four individuals of different subspecies. Main conclusions Phylogenetic congruence of both ITS-1 and plastid lineages suggested an evolutionary scenario of predominant isolation during the PlioPleistocene in Macaronesia, the Mediterranean, southern Africa, eastern Africa and Asia. The Saharan desert appeared to have played an important role of vicariant barrier between southern and northern African populations in early times. Incongruence of some plastid and nuclear results, as well as intermingled ITS-1 copies of different lineages in single individuals, was interpreted as a result of recurrent reticulation events in the olive complex. We identified an ancient hybrid zone from the Sahara to north-eastern African mountains, where divergent plastid and nuclear lineages still co-exist. Results of this paper, and previous studies, suggest that the cultivated olive originated from a pre-Quaternary Mediterranean ancestor, with no evidence for a recent hybrid origin. In contrast, a continuous process of olive domestication through local hybridization events of cultivated trees with natural populations may have brought about a remarkably high genomic diversity among cultivated trees across the Mediterranean.