Showing papers in "Journal of Biogeography in 2017"

A quantitative synthesis of the importance of variables used in MaxEnt species distribution models

Abstract: Aim To synthesize the species distribution modelling (SDM) literature to inform which variables have been used in MaxEnt models for different taxa and to quantify how frequently they have been important for species’ distributions. Location Global. Methods We conducted a quantitative synthesis analysing the contribution of over 400 distinct environmental variables to 2040 MaxEnt SDMs for nearly 1900 species representing over 300 families. Environmental variables were grouped into 24 related factors and results were analysed by examining the frequency with which variables were found to be most important, the mean contribution of each variable (at various taxonomic levels), and using TrueSkill™, a Bayesian skill rating system. Results Precipitation, temperature, bathymetry, distance to water and habitat patch characteristics were the most important variables overall. Precipitation and temperature were analysed most frequently and one of these variables was often the most important predictor in the model (nearly 80% of models, when tested). Notably, distance to water was the most important variable in the highest proportion of models in which it was tested (42% of 225 models). For terrestrial species, precipitation, temperature and distance to water had the highest overall contributions, whereas for aquatic species, bathymetry, precipitation and temperature were most important. Main conclusions Over all MaxEnt models published, the ability to discriminate occurrence from reference sites was high (average AUC = 0.92). Much of this discriminatory ability was due to temperature and precipitation variables. Further, variability (temperature) and extremes (minimum precipitation) were the most predictive. More generally, the most commonly tested variables were not always the most predictive, with, for instance, ‘distance to water’ infrequently tested, but found to be very important when it was. Thus, the results from this study summarize the MaxEnt SDM literature, and can aid in variable selection by identifying underutilized, but potentially important variables, which could be incorporated in future modelling efforts.

Bayesian estimation of the global biogeographical history of the Solanaceae

Abstract: Aim The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location Worldwide. Methods Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program ‘BioGeoBEARS’. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events. Results Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America. Main conclusions For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build-up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework.

A roadmap for island biology: 50 fundamental questions after 50 years of The Theory of Island Biogeography

Abstract: Aims The 50th anniversary of the publication of the seminal book, The Theory of Island Biogeography, by Robert H. MacArthur and Edward O. Wilson, is a timely moment to review and identify key research foci that could advance island biology. Here, we take a collaborative horizon-scanning approach to identify 50 fundamental questions for the continued development of the field. Location Worldwide. Methods We adapted a well-established methodology of horizon scanning to identify priority research questions in island biology, and initiated it during the Island Biology 2016 conference held in the Azores. A multidisciplinary working group prepared an initial pool of 187 questions. A series of online surveys was then used to refine a list of the 50 top priority questions. The final shortlist was restricted to questions with a broad conceptual scope, and which should be answerable through achievable research approaches. Results Questions were structured around four broad and partially overlapping island topics, including: (Macro)Ecology and Biogeography, (Macro)Evolution, Community Ecology, and Conservation and Management. These topics were then subdivided according to the following subject areas: global diversity patterns (five questions in total); island ontogeny and past climate change (4); island rules and syndromes (3); island biogeography theory (4); immigration–speciation–extinction dynamics (5); speciation and diversification (4); dispersal and colonization (3); community assembly (6); biotic interactions (2); global change (5); conservation and management policies (5); and invasive alien species (4). Main conclusions Collectively, this cross-disciplinary set of topics covering the 50 fundamental questions has the potential to stimulate and guide future research in island biology. By covering fields ranging from biogeography, community ecology and evolution to global change, this horizon scan may help to foster the formation of interdisciplinary research networks, enhancing joint efforts to better understand the past, present and future of island biotas.

The historical connections between the Amazon and the Atlantic Forest revisited

Abstract: Aim To assess ancient biotic connections between the Amazon Forest (AmF) and the Atlantic Forest (AtF) based on environmental niche modelling (ENM), palaeobiological, and molecular evidence; to test Por (1992)'s hypothesis of the south-eastern—north-western (SE—NW) route as the most important route in terms of frequency and duration; to evaluate past climatic conditions associated with the routes. Location South America. Methods We generated random points in climate space of AmF and AtF and identified two major climatic groups in the shared environmental space (colder and warmer) with a K-means cluster analysis. We modelled each climatic group using eleven algorithms of ENM and selected the best model, projecting the results back to 120 ka. We used published data on South American palaeopalynology, speleothem and travertine chronology for model validation. We also accessed vertebrate molecular studies and extracted the split timing of lineages distributed both in the AmF and the AtF to test Por (1992)'s hypothesis in more ancient times. Results Palynological and speleothem studies supported the results of our ENM models, indicating expansion of cold-adapted species along the SE—NW and NE routes in the LGM. The SE—NW route was also supported in the LIG, however, involving warm-adapted species. Our results support Por (1992)'s hypothesis and suggest that the SE—NW was established more than once in the past, involving different plant communities each time, adapted to different temperature conditions. Vertebrate molecular studies also support Por (1992)'s hypothesis and suggest that the SE—NW route was established since the Andean uplift. Main Conclusions The SE—NW route is the most ancient connection route between the AmF and the AtF and probably was established since the Andean uplift and the formation of the South American monsoon system. This route was established many times in the past, alternating by the distribution expansion of cold-adapted and warm-adapted plant communities.

When and how should biotic interactions be considered in models of species niches and distributions

Abstract: Biotic interactions can influence the ranges and abundances of species, but no clear guidelines exist for integrating them into correlative models of niches and distributions. Niche/distributional models characterize environmental/habitat suitability or species presence using predictor variables unaffected by (= unlinked to) the population of the focal species. Such variables (termed ‘scenopoetic’) typically have been considered to include only abiotic factors. In contrast, population–demographic approaches model the abundance of the focal species by including linked predictor variables, which frequently are biotic interactors. Nevertheless, a focal species might hold no, or negligible, population-level effects on its biotic interactors. Hence, contrary to current theory, such interactors would represent unlinked variables valid and potentially very useful for niche/distributional models. Consideration of population-level effects indicates that facilitators and affecting amensals (species that negatively affect another species but are not affected by it) constitute unlinked variables, but commensals and affected amensals do not. For competitors, mutualists, predators/prey, consumers/resources, and parasites/hosts, additional information is necessary. Specifically, available ecological/natural history information for the particular species involved (e.g. regarding specificity) and theory regarding ecological networks can allow identification of interactors that are likely to be unlinked or nearly so. Including an unlinked biotic interactor as a predictor variable in a niche/distributional model should improve predictions when the effects of the biotic interactor vary across the study region, or in another place or time period. Other relevant interactors must be taken into account by post-processing a niche/distributional model, or via population–demographic models that require abundance data over time. This framework should improve current correlative models and highlights areas requiring progress.

Patterns and dynamics of European vegetation change over the last 15,000 years

Abstract: Aim: Palaeoecological reconstructions document past vegetation change, with estimates of fast shifts in species distributions. The resulting rates of plant spread are often not matched by model simulations of climate-driven vegetation dynamics. Genetic surveys of extant plant populations document directions of the post-glacial spread of trees, challenging traditional interpretations. Our aim is to examine an updated continental pollen data set from Europe in the light of the new ideas about vegetation dynamics emerging from genetic research and vegetation modelling studies. LocationEurope. Methods: We use pollen data from the European Pollen Database (EPD) to construct interpolated maps of pollen percentages documenting changes in the distribution and abundance of major plant genera and the grass family in Europe over the last 15,000years. Results: Our analyses confirm high rates of post-glacial spread with at least 1000myear(-1) for Corylus, Ulmus and Alnus and average rates of 400myear(-1) for Tilia, Quercus, Fagus and Carpinus. The late Holocene expansions of Picea and Fagus populations in many European regions cannot be explained by migrational lag. Both taxa shift their population centres towards the Atlantic coast suggesting that climate may have played a role in the timing of their expansions. The slowest rates of spread were reconstructed for Abies. Main conclusions: The calculated rates of post-glacial plant spread are higher in Europe than those from North America, which may be due to more rapid shifts in climate mediated by the Gulf Stream and westerly winds. Late Holocene anthropogenic land use practices in Europe had major effects on individual taxa, which in combination with climate change contributed to shifts in areas of abundance and dominance. The high rates of spread calculated from the European pollen data are consistent with rapid tracking of early Holocene climate change by common tree species, documenting that plants can spread fast tracing their climate space, regardless of their dispersal strategy.

Global variation in the beta diversity of lake macrophytes is driven by environmental heterogeneity rather than latitude

Abstract: Additional co-authors: Gana Gecheva, Patrick Grillas, Jennifer Hauxwell, Seppo Hellsten, Jan Hjort, Mark V. Hoyer, Agnieszka Kolada, Minna Kuoppala, Torben Lauridsen, En‒Hua Li, Balazs A. Lukacs, Marit Mjelde, Alison Mikulyuk, Roger P. Mormul, Jun Nishihiro, Beat Oertli, Laila Rhazi, Mouhssine Rhazi, Laura Sass, Christine Schranz, Martin Sondergaard, Takashi Yamanouchi, Qing Yu, Haijun Wang, Xiao‒Ke Zhang, Jani Heino

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Abstract: Aim Coral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth. Location Shallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG). Methods Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera. Results Corals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C- to D-dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)-based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera. Main conclusions Our study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host–symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing ‘Future Ocean’ conditions.

Do metacommunities vary through time? Intermittent rivers as model systems

Abstract: Aim Metacommunity assembly mechanisms have been traditionally considered stable through time. However, in highly dynamic systems with varying local environmental conditions and patch connectivity, communities are likely to experience temporal shifts in their assembly mechanisms. Here, we used a set of perennial (PR) and intermittent (IR) rivers to assess if assembly mechanisms vary seasonally in response to flow intermittence. Location Mediterranean climate region (100,000 km2), Spain. Methods We used a modelling approach to assess the relative effect of environmental sorting and dispersal-based processes on aquatic invertebrate metacommunities within and across river types at four distinct hydrological periods. We used local environmental variables to assess environmental sorting, and considered geographical, network and topographical distances as different dispersal surrogates. Linear mixed effect models accounting for the non-independence of pairwise distances were used to assess the relationships between community dissimilarity and distance matrices. Results Assembly mechanisms were more temporally stable in PR than in IR. In PR, community dissimilarities were equally related to environmental and geographical distances suggesting codominance of species sorting and dispersal-based assembly mechanisms. In IR, environmental distance best explained community dissimilarities during the dry period when flow cessation imposes strong environmental sorting, whereas metacommunity organization was much more stochastic during the rewetting period when high flows may randomly reorganize communities. Dispersal processes dominated assembly mechanisms between PR and IR during the rewetting period suggesting an increase in recolonization processes linking both river types following the dry period. Geographical and topographical distances best explained community variability, suggesting that overland dispersal dominates in river networks fragmented by drying events. Main conclusions Aquatic invertebrate metacommunity assembly mechanisms vary seasonally in response to changes in hydrological conditions. The temporal dimension should be better incorporated into metacommunity studies in highly dynamic systems such as intermittent rivers.

In and out of the Qinghai-Tibet Plateau: divergence time estimation and historical biogeography of the large arctic-alpine genus Saxifraga L.

Abstract: Aim Geologically dynamic areas often harbour remarkable levels of biodiversity. Among other factors, mountain building is assumed to be a precondition for species radiation, and yet, the potential role of immigration as a source of biodiversity prior to radiation is often neglected. Here, we studied the biogeographical history of the large genus Saxifraga to unravel the role played by the Qinghai-Tibet Plateau (QTP) for the diversification of this genus and to understand factors that have led to the establishment of high biodiversity in and around this region. Location QTP and surrounding mountain ranges and worldwide distribution range of Saxifraga. Methods Using a total of 420 taxa (321 ingroup taxa) comprising more than 60% of extant Saxifraga species, we studied the evolutionary history of Saxifraga by performing phylogenetic analyses (maximum likelihood and Bayesian inference on nuclear ITS and plastid trnL–trnF, matK sequences), divergence time estimation (using uncorrelated log-normal clock models and four fossil constraints in beast) and ancestral range estimation (using BioGeoBEARS). Results Saxifraga originated in North America around 74 (64–83) Ma, dispersed to South America and northern Asia during its early diversification and colonized Europe and the QTP region by the Late Eocene. The QTP region was colonized several times independently, followed in some lineages by rapid radiations, temporally coinciding with recent uplifts of the Hengduan Mountains at the southeastern fringe of the QTP. Subsequently, several lineages dispersed out of Tibet. Main conclusions Immigration, recent rapid radiation and lineage persistence were all important processes for the establishment of a rich species stock of Saxifraga in the QTP region. Because floristic exchanges between the neighbouring areas and the QTP region were bi-directional, the spatio-temporal evolution of Saxifraga contrasts with the ‘out of QTP’ pattern, which has often been assumed for northern temperate plants.

Avian migration and the distribution of malaria parasites in New World passerine birds

Abstract: Aim: Migrating birds transport their parasites, often over long distances, but little is known about the transfer of these parasites to resident hosts in either the wintering or breeding ranges of the migratory host populations. We investigated the haemosporidian parasite faunas of migratory and resident birds to determine connections among distant parasite faunas, plausibly brought about by migratory host populations. Location: Samples were obtained, primarily during or shortly after the local breeding season, throughout the Americas, from the United States through the Caribbean Basin and into northern South America. Methods: Infections were identified by PCR and sequencing of parasite DNA in avian blood samples. The analyses were based on c. 4700 infections representing 79 parasite lineages of Plasmodium and Haemoproteus spp. Geographical connections of lineages between regions in the Americas were compared to those in the Euro-African migration system, where migration distances are longer for many host species and the migrant and resident avifaunas in the wintering areas are phylogenetically more divergent. Results: Haemosporidian lineages exhibited considerable variation in distribution in the Americas, and patterns of distribution differ markedly between the Americas and the Euro-African migration system. In particular, few lineages were recovered from resident species in both temperate and tropical latitudes, particularly in the Euro-African system, in which a large proportion of lineages were restricted to migrants. Parasite lineages in the Euro-African system exhibited considerable phylogenetic conservatism in their distributions, that is, a tendency of related lineages to exhibit similar geographical distributions. In contrast, clades of parasites in the Americas displayed more geographical diversity, with four of 12 clades exhibiting all four of the distribution types representing the combinations of resident and migrant host species in both temperate and tropical latitudes. Main conclusions: Long-distance migrants connect communities of avian haemosporidian parasites in breeding and wintering areas with disparate avifaunas and different vector communities. The degree of parasite lineage sharing between migrants and residents in breeding and wintering areas appears to reflect, to a large degree, the taxonomic similarity of migrants to the resident species in both areas. (Less)

The origin of species richness patterns along environmental gradients: uniting explanations based on time, diversification rate and carrying capacity

Abstract: Aims Patterns of species richness, such as the remarkable biodiversity of tropical regions, have been documented and studied for centuries. However, their underlying evolutionary and ecological causes are still incompletely understood. A commonly stated paradigm in the literature is that high richness in some habitats is directly caused by one of three competing explanations: (1) greater time-for-speciation (earlier colonization), (2) more rapid diversification rates (faster speciation relative to extinction) or (3) higher carrying capacity. However, these three explanations have been relatively little studied using theoretical approaches (especially in terms of comparing all three). Furthermore, empirical studies give conflicting results about their relative importance. Here, we use simulations to study the processes that drive richness patterns along environmental gradients. Location Globally applicable. Methods We use individual-based and trait-based modelling of eco-evolutionary dynamics to simulate the evolutionary radiation of a clade across five habitats with differing ecological conditions, and track patterns of species richness within and between habitats over time. We specifically address the roles of time and diversification rates in explaining richness patterns and the potential impact of carrying capacity. Main results and conclusions Contrary to the widespread paradigm, we find that variation in carrying capacity can underlie differences in diversification rates and time-for-speciation among habitats. Therefore, carrying capacity is not a competing, alternative explanation for richness patterns. We also find that the time-for-speciation effect dominates richness patterns over short time-scales, whereas diversification rates dominate over longer time-scales. These latter observations can help reconcile the seemingly conflicting results of many empirical studies, which find that some patterns are explained by time and others by differences in diversification rates.

Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China

Abstract: Aim Hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history. Mountain uplifts are known to catalyse species radiation but their impact on evolutionarily stable taxa such as many trees remains little understood. The oak Quercus aquifolioides is endemic to yet widely distributed across the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we investigate how the region's Neogene and Quaternary history has driven the species' past population dynamics and the resulting extant patterns of intraspecific diversity. Location Hengduanshan Biodiversity Hotspot in SW China. Methods We sampled 58 populations throughout the species range and genotyped a total of 959 individuals at four chloroplast DNA fragments and 11 nuclear microsatellite loci. Phylogenetic reconstructions, molecular dating techniques and ancestral area reconstructions were used in combination with population genetic statistics to infer the biogeographical history of Q. aquifolioides. The phylogeographical study was complemented by a survey of fossil records and a niche modelling exercise. Results Combined molecular and fossil evidence indicates that Q. aquifolioides descended during the late Miocene from the central Qinghai-Tibet Plateau into Tibet and the western Sichuan Plateau, and from there, into the area of highest endemism in the Hengduan Mountains sensu lato. Great apparent population stability and a haplotype ‘radiation’ in this area contrasted with marked extinction–recolonization dynamics and reduced population diversity in Tibet. We found evidence for extremely limited seed gene flow but extensive pollen gene flow (global FST: cpDNA = 0.98, nSSR = 0.07) with signals of asymmetric pollen dispersal from the Hengduan Mountains into Tibet. Main conclusion Our results provide insights of unprecedented detail into the ancient biogeographical history of the Hengduanshan Biodiversity Hotspot, suggesting that past environmental changes in the region may have catalysed radiative diversifications within species much in the same way as among species.

Global patterns of interaction specialization in bird–flower networks

Abstract: Aim Among the world's three major nectar-feeding bird taxa, hummingbirds are the most phenotypically specialized for nectarivory, followed by sunbirds, while the honeyeaters are the least phenotypically specialized taxa. We tested whether this phenotypic specialization gradient is also found in the interaction patterns with their floral resources. Location Americas, Africa, Asia and Oceania/Australia. Methods We compiled interaction networks between birds and floral resources for 79 hummingbird, nine sunbird and 33 honeyeater communities. Interaction specialization was quantified through connectance (C), complementary specialization (H2′), binary (QB) and weighted modularity (Q), with both observed and null-model corrected values. We compared interaction specialization among the three types of bird–flower communities, both independently and while controlling for potential confounding variables, such as plant species richness, asymmetry, latitude, insularity, topography, sampling methods and intensity. Results Hummingbird–flower networks were more specialized than honeyeater–flower networks. Specifically, hummingbird–flower networks had a lower proportion of realized interactions (lower C), decreased niche overlap (greater H2′) and greater modularity (greater QB). However, we found no significant differences between hummingbird– and sunbird–flower networks, nor between sunbird– and honeyeater–flower networks. Main conclusions As expected, hummingbirds and their floral resources have greater interaction specialization than honeyeaters, possibly because of greater phenotypic specialization and greater floral resource richness in the New World. Interaction specialization in sunbird–flower communities was similar to both hummingbird–flower and honeyeater–flower communities. This may either be due to the relatively small number of sunbird–flower networks available, or because sunbird–flower communities share features of both hummingbird–flower communities (specialized floral shapes) and honeyeater–flower communities (fewer floral resources). These results suggest a link between interaction specialization and both phenotypic specialization and floral resource richness within bird–flower communities at a global scale.

Global patterns in the divergence between phylogenetic diversity and species richness in terrestrial birds

Abstract: Aim The conservation value of sites is often based on species richness (SR). However, metrics of phylogenetic diversity (PD) reflect a community's evolutionary potential and reveal the potential for additional conservation value above that based purely on SR. Although PD is typically correlated with SR, localized differences in this relationship have been found in different taxa. Here, we explore geographical variation in global avian PD. We identify where PD is higher or lower than expected (from SR) and explore correlates of those differences, to find communities with high irreplaceability, in terms of the uniqueness of evolutionary histories. Location Global terrestrial. Methods Using comprehensive avian phylogenies and global distributional data for all extant birds, we calculated SR and Faith's PD, a widely applied measure of community PD, across the terrestrial world. We modelled the relationship between avian PD for terrestrial birds and its potential environmental correlates. Analyses were conducted at a global scale and also for individual biogeographical realms. Potential explanatory variables of PD included SR, long-term climate stability, climatic diversity (using altitudinal range as a proxy), habitat diversity and proximity to neighbouring realms. Results We identified areas of high and low relative PD (rPD; PD relative to that expected given SR). Areas of high rPD were associated with deserts and islands, while areas of low rPD were associated with historical glaciation. Our results suggest that rPD is correlated with different environmental variables in different parts of the world. Main conclusions There is geographical variation in avian rPD, much of which can be explained by putative drivers. However, the importance of these drivers shows pronounced regional variation. Moreover, the variation in avian rPD differs substantially from patterns found for mammals and amphibians. We suggest that PD adds additional insights about the irreplaceability of communities to conventional metrics of biodiversity based on SR, and could be usefully included in assessments of site valuation and prioritization.

Metacommunity structuring in Himalayan streams over large elevational gradients: the role of dispersal routes and niche characteristics

Abstract: Aim To examine metacommunity structuring in stream communities over large elevational gradients by disentangling physical and environmental structuring and the importance of different dispersal routes and niche characteristics. Location Headwater streams in three catchments in the Hindu-Kush Himalaya of central and eastern Nepal. Methods We explored metacommunity structuring of stream invertebrates (including deconstructed assemblages by niche position and breadth) using a combination of approaches, including the elements of metacommunity structure and distance–decay relationships. We compared the importance of dispersal routes, elevation and local environmental conditions through five distance matrices: Euclidean, topographic, river network, elevational and environmental. Results Communities were structured along the elevational gradient with clear turnover apparent in two catchments, with Clementsian (compartmentalized) and Gleasonian (individualistic) distributions. Local environment played a minor role, and the selected distance matrices (i.e. elevation, three physical distances and environment) varied between catchments and niche groups. Contrary to expectation, specialists were more spatially than environmentally controlled, potentially reflecting dispersal limitation. Main conclusions In these physically dominated systems, local environment was overridden by dispersal limitation, particularly when considering specialists. Where barriers were not limiting dispersal, niche sorting along the elevational gradients represented the key structuring force. Overall, our findings reveal the importance of elevation and the spatial arrangement of sites in structuring metacommunities. We emphasize the value of considering physical structuring and spatial extent in modulating species sorting in metacommunities.

On the origins of marine-derived freshwater fishes in South America

Abstract: AIM: The South American fish fauna is renowned for its extraordinary diversity. The majority of this diversity is restricted to few major clades that have ancient associations to freshwater habitats. However, at a higher taxonomic level, the South American ichthyofauna is enriched by an extraordinary number of marine derived lineages – lineages that are endemic to freshwaters, but derived from marine ancestors. Here, we test palaeogeographical hypotheses that attempt to explain the origins and exceptional diversity of marine derived fishes in rivers of South America. LOCATION: South America. METHODS: We analysed time‐calibrated molecular phylogenies, ancestral reconstructions and biogeographical patterns for multiple independent marine‐derived lineages. RESULTS: Five of the ten marine‐derived lineages in our analysis have biogeographical patterns and stem ages consistent with invasion from the Atlantic Ocean during the Oligocene or Eocene. Drums and pufferfishes reveal patterns and ages that were consistent with the Miocene marine incursion hypothesis. The Amazonian halfbeak is the only lineage younger than the Miocene and invaded Amazonian freshwaters less than a million years ago. MAIN CONCLUSION: Our results suggest Miocene marine incursions and the Pebas Mega‐Wetland may not explain the high diversity of marine derived lineages in South America. Instead, the Pebas Mega‐Wetland may have created a fertile opportunity for diversification of some, but not all marine‐derived lineages.

Mobile hotspots and refugia of avian diversity in the mountains of south‐west China under past and contemporary global climate change

Abstract: Aim To identify hotspots of endemic and non-endemic avian diversity in the mountains of south-west China and delineate biodiversity corridors that connect the faunas of northern and southern Asia. To understand how biodiversity and endemism in this region has been maintained through palaeoclimate change. Location The mountains of south-west China, spanning an elevational gradient > 7000 m. Methods We used the distributional data of 752 breeding birds to investigate current patterns of diversity across elevational and geographical space. We simulated species richness under palaeoclimate models of global temperature change, assessing changes in species richness. Results Contemporary species richness of non-endemic birds peaked at 800–1800 m elevation, while endemic richness peaked at 2000–3000 m. Richness of non-endemic birds was highest in the southern Hengduan Mountains and Yungui Plateau, while endemic richness peaked further north, extending into the mountains along the western edge of the Sichuan Basin. Under global warming models, species richness remained high throughout the Hengduan Mountains region. Under global cooling models, the Sichuan Basin showed increased richness. Conclusions Endemism peaked in the mountains along the western edge of the Sichuan Basin, highlighting the importance of this region in promoting and maintaining diversity. This region has likely functioned as a biodiversity corridor, bridging the Palaearctic and Oriental biotas to the north and south. Climate simulations suggest that the mountains of south-west China can accommodate upslope range shifts in response to warming, but low elevation specialists may have experienced increased extinction probabilities during cold periods in the recent past, which may in part explain the current mid-elevation diversity peak. During glacial periods the Sichuan Basin likely served as a warm refugium for montane birds. Steep environmental heterogeneity has been a key to maintaining high diversity and endemism in the region during palaeoclimate change. These same features will likely shape the effects of future climate change on biodiversity in the region.

Pollen‐inferred millennial changes in landscape patterns at a major biogeographical interface within Europe

Abstract: Aim The regional co-occurrence of contrasting bioclimatic elements (warm-temperate, continental, boreal, arctic-alpine) may be shaped by the distribution of their glacial or post-glacial refugia We tested this hypothesis using pollen proxies in a region where such refugia are expected, but not unequivocally demonstrated Location East-Central Europe (Western Carpathians and adjacent regions) Methods We compiled pollen spectra from 112 sites distributed across various landscapes for six time-periods from the Late Glacial to the present Compositional patterns were assessed by principal coordinates analyses (PCoA) with a sensitivity analysis based on a bootstrap technique Site PCoA scores were interpolated geographically and correlated with palaeoclimatic models Results Consistently over the last 15,000 years, the first ordination axis sorted samples according to the proportion of deciduous temperate trees, while the second axis consistently followed an altitudinal gradient that coincided with temperature The principal gradient was more important than the altitudinal gradient except for the Late Glacial and Bronze & Iron Ages, when both gradients were of similar importance The fine-grained pattern in the present mountain landscape was formed as late as during early modern colonization Main conclusions Since the Late Glacial, the landscape has been differentiated into temperate, continental and cold regions This finding supports the hypothesis that refugia are a key factor for understanding current biogeography in Central Europe The Late Glacial occurrence of temperate trees is unlikely to be explained only by gradual migrations from southern Europe Humid but relatively warm mountains hence might have acted as glacial refugia of temperate forest species, while lowlands and leeward basins might have acted as post-glacial refugia of steppe grasslands The strong contrast between forested (temperate) and more open continental landscapes during the Early Holocene seems to correspond with recent diversity patterns Our results highlight the relevance of integrating past landscape trajectories into modern biogeographical models

Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of African forests since late Miocene

Abstract: Aim Grammomys are mostly arboreal rodents occurring in forests, woodlands and thickets throughout sub-Saharan Africa. We investigated whether the divergence events within the genus follow the existing evolutionary scenario for the development of African forests since the late Miocene. Location Sub-Saharan African forests and woodlands. Methods We inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus. We mapped the genetic diversity, estimated the divergence times by a relaxed clock model and compared evolution of the genus with forest history. Results Phylogenetic analysis confirms the monophyly of Grammomys and reveals five main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in Guineo-Congolese forests; (2) the selousi group with a distribution mainly in coastal forests of southern and eastern Africa; (3) the dolichurus group restricted to the easternmost part of South Africa; (4) the macmillani group in the northern part of eastern and Central Africa with one isolated species in Guinean forests; and (5) the surdaster group, widely distributed in eastern Africa south of the equator. Every group contains well supported sublineages suggesting the existence of undescribed species. The earliest split within the genus (groups 1 vs. 2–5) occurred in the late Miocene and coincides with the formation of the Rift Valley which resulted in the east–west division of the initially pan-African forest. The subsequent separation between groups (2 vs. 3–5) also dates to the end of the Miocene and suggests the split between Grammomys from coastal to upland forests in eastern Africa followed by a single dispersal event into western Africa during the Pleistocene. Conclusions The evolutionary history of the genus Grammomys closely reflects the accepted scenario of major historical changes in the distribution of tropical African forests since the late Miocene.

Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate

Abstract: Aim To uncover geographical and temporal patterns of diversification in the puffbird genus Malacoptila, focusing on the influence of landscape and palaeoclimate evolution as drivers of diversification. Location Neotropical, with an emphasis on the Amazon basin. Methods We sequenced eight mtDNA and nuclear gene regions of 176 individuals belonging to seven of the eight recognized Malacoptila species. Concatenated and time calibrated coalescent multi-locus phylogenies, along with a Bayesian species delimitation analysis, were performed for the genus. Phylogeographical and historical demography patterns were reconstructed for the Amazonian species. Ancestral ranges estimation was performed in BioGeoBEARS. Results Our analysis recovered 23 reciprocally monophyletic lineages within Malacoptila. All currently recognized species were recovered as monophyletic. With the exception of M. semicincta, all species presented some level of intraspecific phylogeographical structure, varying up to 10 reciprocally monophyletic phylogroups (M. rufa). The distributions of these lineages are generally coincident with known Neotropical areas of endemism (AE). Main Conclusion Our results corroborate the influence of Andean uplift and the Plio-Pleistocene establishment of the current drainage system in Amazonia as likely drivers of diversification. The spatially structured genetic diversity that exists within Malacoptila is underestimated by current taxonomy and provides another example of widespread cryptic avian endemism in the Neotropics.

Network biogeography of a complex island system: the Aegean Archipelago revisited

Abstract: Aim The Aegean Archipelago has been the focal research area for identifying and testing several ecological and evolutionary patterns, yet its biogeographical subdivision has been somewhat overlooked, with the processes driving the assembly of the Aegean island plant communities still remaining largely unclear. To bridge this gap, we identify the biogeographical modules (highly linked subgroups of islands and plant taxa) within the Aegean Archipelago. Location The Aegean Archipelago, Greece. Methods We used a network approach to detect island biogeographical roles and modules, based on a large and detailed database including 1498 Aegean endemic and subendemic plant taxa distributed on 59 Aegean Islands and five adjacent mainland areas. Results The Aegean was divided into six biogeographical modules; the network was significantly modular. None of the modules displayed all four possible biogeographical roles (connectors, module hubs, network hubs, peripherals). Six new biogeographical regions in the Aegean were identified. Main conclusions The borders of the six biogeographical regions in the Aegean correspond well to the region's palaeogeographical evolution from the middle Miocene to the end of the Pleistocene. The Central Aegean acts as an ecogeographical filter for the distribution of several plant lineages across the Aegean Sea, while there seems to be a N–S-oriented biogeographical barrier in the Aegean corresponding to the palaeogeographical situation during the middle Ionian. These biogeographical barriers have been fundamental for both plants and animals.

Structural bias in aggregated species‐level variables driven by repeated species co‐occurrences: a pervasive problem in community and assemblage data

Abstract: Aim Species attributes are often used to explain diversity patterns across assemblages/communities. However, repeated species co-occurrences can generate spatial pattern and strong statistical relationships between aggregated attributes and richness in the absence of biological information. Our aim is to increase awareness of this problem. Location North America. Methods We generated empirical species richness patterns using two data structures: (1) birds gridded from range maps and (2) tree communities from the US Forest Service's Forest Inventory and Analysis. We analysed richness using linear regression, regression trees, generalized additive models, geographically weighted regression and simultaneous autoregression, with ‘random intrinsic variables’ as predictors generated by assigning random numbers to species and calculating averages in assemblages. We then generated simulations in which species with cohesive or patchy distributions are placed with respect to the North American temperature gradient with or without a broad-scale richness gradient. Random intrinsic variables are again used as predictors of richness. Finally, we analysed one simulated scenario with random intrinsic variables as both response and predictor variables. Results The models of bird and tree richness often explained moderate to large proportions of the variance. Regression trees, geographically weighted regression and simultaneous autoregression were very sensitive to the problem; generalized additive models were moderately affected, as was multiple regression to a lesser extent. In the virtual data, the variance explained increased with increasing species co-occurrences, but neither range cohesion, a richness gradient nor spatial autocorrelation in predictors had major impacts on the variance explained. The problem persisted when the response variable was also a random intrinsic variable. Main conclusions Repeated species co-occurrences can generate strong spurious relationships between richness and aggregated species attributes. It is important to realize that models utilizing assemblage variables aggregated from species-level values, as well as maps illustrating their spatial patterns, cannot be taken at face value.

Islands as biological substrates: classification of the biological assemblage components and the physical island types

Abstract: Aim Biological suites on marine islands attract the attention of many researchers because their natural seclusion enables a variety of key processes to be studied in considerable detail. The present-day classification of marine-island biotic systems is based largely on 19th Century ideas, specifically those of Darwin and Wallace. However, along a number of fronts, knowledge has advanced dramatically, particularly regarding the dynamic ‘solid’ Earth (plate tectonics, ocean-floor thermal-cooling subsidence, mantle-plume hotspots, etc.), as well as the behaviour of the planet's liquid and gaseous envelopes, today and in the geological past. This manuscript serves as an introduction to a series of articles aimed at providing the biological/biogeographical community with an overview of the current understanding of the physical settings of the marine islands, that is, the substrates upon which the biotas accumulate and develop. Location Global. Results I propose separate classification systems for the biotic assemblage components and the physical island types to replace the current mixed scheme of recent continental, ancient continental and oceanic. The lifeforms can be assigned to one of four classes reflecting how an organism's founder ancestors colonized an island: recent land bridge, recent ice-sheet, overwater dispersed and deep-time vicariant (an island may host two or more of these types). The nomenclature for the islands reflects their geo-physical setting and has the advantage of indicating the ontogenetic path the landmass is on. In turn, this may feed back into the way the hosted biology is viewed. Four major categories are recognized: continental, island arc, composite terrane and mantle-plume hotspot, plus a handful of left-overs. These groups can be further split into between three and nine types. Main conclusion Separating the classifications of the island biotic assemblage components and the physical island varieties (of which there are many sorts) makes it possible to assign all islands and their biotas unambiguously. It thus provides an appreciably more nuanced scheme than Wallace's threefold system.

Implications and alternatives of assigning climate data to geographical centroids

Abstract: Aim When precise coordinate data for training species distribution models (SDMs) are lacking, climatic variables are often assigned to centroids of geopolitically defined regions, frequently counties This is problematic because approximations using centroids may not be representative of the regional climate or the locality from where species actually occur, thus leading to spurious conclusions We evaluated county centroid climate versus simple alternatives for assigning climate to species observations in the absence of precise occurrence data Location United States of America Methods We assessed the disparity between the actual climate of all points within a county and metrics estimating county climate using the climate of geographical centroid, mean county climate and median county climate To further evaluate the performance of these metrics, we generated SDMs of four common species using these estimates and compared the results with observed species distributions (red trillium, Pacific trillium, tall thistle and annual fleabane) Finally, we projected future ranges for annual fleabane to examine the difference in predicted range change between models Results Mean and median climate metrics were significantly better fits for approximating the climate of specimen records than climate of the geographical centroid Moreover, county mean climate SDMs were the most similar to SDMs using actual coordinate data In contrast, models applying climate to county centroid significantly overpredicted species range This had implications for future projections of annual fleabane SDMs: the county centroid model predicted a decrease in suitable habitats for this species while other models predicted an increase Main conclusions County centroid climate, although commonly applied, is not suitable for SDMs as a means to approximate species climate when locality data are less precise When only county level data are available, and more computationally intensive methods of accounting for spatial uncertainty cannot be readily implemented, we suggest considering mean county climate as an alternative

The ecological niche and distribution of Neanderthals during the Last Interglacial

Abstract: Aim In this paper, we investigate the role of climate and topography in shaping the distribution of Neanderthals (Homo neanderthalensis) at different spatial scales. To this end, we compiled the most comprehensive data set on the distribution of this species during the Last Interglacial optimum (MIS 5e) available to date. This was used to calibrate a palaeo-species distribution model, and analyse variable importance at continental and local scales. Location Europe and Irano-Turanian region (20° N to 70° N, 10° W to 70° E). Methods We used archaeological records and palaeoclimatic and topographic predictors to calibrate a model based on an ensemble of generalized linear models fitted with different combinations of predictors and weighted background data. Area under the curve scores computed by leave-one-out were used to assess variable importance at the continental scale, while local regression combined with recursive partition trees was used to assess variable importance at the local scale. Results Annual rainfall and winter temperatures were the most important predictors at the continental scale, while topography and summer rainfall defined habitat suitability at the local scale. The highest habitat suitability scores were observed along the Mediterranean coastlines. Mountain ranges and continental plains showed low habitat suitability values. Main conclusions The model results confirmed that abiotic drivers played an important role in shaping Neanderthals distribution during the Last Interglacial. The high suitability of the Mediterranean coastlines and the low suitability values of most sites at the northern and eastern distribution limits (Germany, Hungary, Ukraine) challenge the notion of Neanderthals as a species with preference for colder environments.

Diversification in arid mountains: biogeography and cryptic diversity of Pristurus rupestris rupestris in Arabia

Abstract: Aim To understand the patterns of genetic, geographical and morphological diversification in the Arabian gecko subspecies Pristurus rupestris rupestris, and to discuss the various processes that generate and shape diversity in arid mountain ranges. Location Hajar Mountains, south-eastern Arabian Peninsula. Methods We sampled 466 individuals across the entire range of P. r. rupestris in the Hajar Mountains and sequenced one mitochondrial gene for all the samples, and one extra mitochondrial and four nuclear genes for a subset of 75 specimens. A total of 155 individuals were characterized morphologically. Multilocus coalescent-based methods were used for species delimitation, for phylogenetic inference of species trees and to investigate the diversification dynamics. Multivariate statistics were used to analyse morphological data. Results Our molecular methods revealed 14 candidate species hidden within the subspecies P. r. rupestris. Diversification started c. 15 Ma, but most of the lineages have evolved in the last 7 Ma of the mountains’ orogeny, producing a mosaic of allopatric taxa. Secondary interchange has occurred between high and low elevation lineages, and along the mountain chain between unrelated lineages formerly separated by mountain blocks. Morphological variation between the 14 candidate species is slight, but a high elevation robust morphotype is identified. Main conclusions Our results support the notion that mountain ranges constitute important centres of diversification in arid regions, and also act as ‘species pumps’ into surrounding areas. We also demonstrate that arid mountains may constitute important reservoirs of cryptic diversity, even in common and widespread species. This, and previous evidence, suggest that the Hajar Mountains are a biological hotspot and an important reservoir of diversity. We therefore suggest that these mountains should be a priority focal point for conservation in Arabia.

Following the Antarctic Circumpolar Current: patterns and processes in the biogeography of the limpet Nacella (Mollusca: Patellogastropoda) across the Southern Ocean

Abstract: Aim We use an integrative biogeographical approach to further understand the evolution of an important Southern Ocean marine benthic element, the limpet genus Nacella (Mollusca: Patellogastropoda). Location Southern Ocean. Methods We used multi-locus time-calibrated phylogeny of Nacella at the scale of the whole Southern Ocean to elucidate the underlying processes involved in the origin and diversification of the genus. Results Divergence-time estimates suggest that soon after its origin during the mid-Miocene (c. 12.5 Ma), Nacella separated into two main lineages currently distributed in (1) South America and (2) Antarctica and the sub-Antarctic islands. We identified two pulses of diversification, during the late Miocene (8 to 5.5 Ma) and the Pleistocene (< 1 Ma). Main conclusions Major periods of climatic and oceanographical change strongly affected the biogeography of Nacella and demonstrate both the long- and short-term influence of the Antarctic Circumpolar Current across the Southern Ocean. Our analyses support the validity of all currently recognized Nacella species and reveal a new South-American lineage. This work constitutes the most detailed molecular-based study of an ecologically important, near-shore invertebrate Southern Ocean group and in so doing contributes to the improved understanding of the underlying patterns and processes in the origin and diversification of marine benthic fauna across this globally important region.

Cretaceous West Gondwana vicariance shaped giant water scavenger beetle biogeography

Abstract: Aim We tested the hypothesis that ancient vicariance in giant water scavenger beetles shaped their current distribution. Location Worldwide except Antarctica. Methods We inferred a molecular phylogenetic hypothesis for the tribe Hydrophilini using probabilistic methods based on broad geographical and taxonomic sampling. We used fossil-based molecular dating and likelihood model-based ancestral range estimation to reconstruct the biogeography of this clade. Results Our results suggest that the tribe originated in the Cretaceous about 120 Ma with a most likely ancestral range in the Gondwanan fragment comprising continental Africa and South America. We infer an ancient vicariance following this early origin, consistent with the split of these two large landmasses in the mid-Cretaceous. The rest of the biogeographical history of the group is shaped by dispersal events throughout the Cenozoic. Main conclusions The biogeographical history of hydrophiline water beetles is consistent with the hypothesis of West Gondwana vicariance, although an origin in either Africa or South America is a likely alternative. Although the early cladogenesis of this clade might have been shaped by the opening of the Atlantic Ocean, subsequent biogeographical evolution is mainly driven by dispersal events.

Historical and contemporary correlates of snake biogeographical subregions in the Atlantic Forest hotspot

Abstract: Aim Snake faunal dissimilarity within tropical forests is not well characterized, nor are the factors underlying these patterns. Our aim was to disentangle the ecological and historical factors driving biogeographical subregions (BSR) for snakes. Location Brazilian Atlantic Forest (BAF). Methods We compiled 274 snake inventories to build a species-by-site matrix and used unconstrained ordination and clustering techniques to identify the number of snake BSR. We applied an interpolation method to map axes of compositional variation over the whole extent of the BAF, and then classified the compositional dissimilarity according to the number of snake BSR identified a priori. We used multinomial logistic regression models and deviance partitioning techniques to investigate the influence of contemporary climatic stability, productivity, topographic complexity, and historical climate shifts in explaining the BSR. Results We identified 198 snake species organized into six BSR, three of them located along the BAF coast and the other three predominantly inland BSR. Climatic stability made the largest contribution to explaining the variability in snake BSR, followed by productivity and historical variation in climate. Topography was important only if historical variation in climate was excluded from the analysis. Main conclusions The highest rates of snake endemism within BAF were in the coastal BSR, as compared to the inland BSR that are mostly composed of open habitat specialists. Our findings suggest that the topographic complexity of the BAF acts on snake distributions not as a physical barrier, but rather as a climatic barrier, providing historical climate refuges for species living along altitudinal gradients. Overall, the predominance of climatic stability and historic variation in climate in explaining snake BSR reinforces the importance of thermoregulatory constraints in shaping the distribution of tropical ectotherm species.