The Mediterranean Basin (MB) is a species-rich biogeographical region with many endemic taxa. We analysed the historical patterns of temporal and geographical diversification of Mediterranean Blaps (Tenebrionidae), a diverse group of flightless beetles, estimated their date of origin and colonization of the MB, and tracked temporal changes in diversification rates.

Mediterranean Basin.

We reconstructed the phylogenetic relationships of Mediterranean Blaps using four mitochondrial genes and 47 morphological characters. Divergence-time estimates were investigated with a Bayesian relaxed clock approach that was calibrated with both fossil and geological constraints. Biogeographical analyses were performed using the dispersal–extinction–cladogenesis likelihood model associated with a stratified palaeogeographical scenario. Diversification rate analyses allowed the investigation of diversity dynamics through time as well as rate shifts during major Cenozoic climate events.

The Bayesian relaxed clock analysis suggests that Blaps first appeared in the MB about 28 Ma. The most likely scenario is that Mediterranean Blaps originated in the Arabian and north-east African regions and then dispersed progressively westwards and northwards, using temporary land bridges to colonize the northern shores of the MB. Island endemics are more likely to be the products of recent dispersals than of old vicariance events. Birth–death analyses suggest that diversification rates in the Miocene and Pliocene are consistent with a ‘museum model’, in which most of the extant diversity is best explained by a steady accumulation of lineages under constant diversification rates. Although major Cenozoic climatic events do not seem to have influenced the diversification of Mediterranean Blaps, a decrease in diversification rates was detected during the Pleistocene.

Our results suggest that Mediterranean Blaps lineages diversified between the Oligocene and the Pliocene, with current distribution patterns mostly accounted for by early vicariance and late dispersal events. Diversification rates were relatively constant through time, but decreased during Pleistocene glaciation cycles. This scenario may be applicable to other Mediterranean terrestrial animal taxa.

We investigated genetic divergence among two widespread eastern Australian orchids (Dendrobium sect. Dendrocoryne): Dendrobium speciosum and Dendrobium tetragonum. These orchids are endemic to mesic habitats, with distributional ranges that cross major geographical breaks associated with deep divergences in various fauna. We compared the biogeography of these orchids with other taxa and tested for congruence of divergence date estimations.

Eastern Australia, latitude 14° S to 34° S.

Phylogenetic relationships within each species were estimated using maximum parsimony based on sequences of internal transcribed spacer (ITS) regions of nuclear ribosomal DNA and the psbA–trnH spacer region of plastid DNA. Divergence dates were inferred by Bayesian relaxed-clock dating, calibrated on an early Miocene macrofossil, Dendrobium winikaphyllum from New Zealand.

Deep divergences were revealed within each species. Dendrobium speciosum includes three major geographical clades (deepest 2.6% ITS divergence): a northern Queensland clade, which occurs mainly to the north of the Black Mountain Corridor (BMC) in the Wet Tropics; a central Queensland clade; and a southern clade related to the central clade and separated from it by a dry corridor, the St Lawrence Gap (SLG). The central and northern lineages show overlap near the BMC. Divergence in this area is estimated to date from the Pliocene, possibly late Miocene, 4.3 (2.0–6.9) Ma, and at the SLG in the early Pleistocene, possibly late Pliocene, 2.0 (0.6–3.8) Ma. Dendrobium tetragonum also includes two clades, deeply divergent (3%) at the SLG, estimated as Pliocene in age but possibly latest Miocene, 3.7 (1.8–5.9) Ma.

Dendrobium orchids reveal significant divergence associated with geographical breaks in eastern Australia, the SLG and BMC, patterns broadly concordant with findings for fauna. We infer that divergences were driven by topographical and climatic conditions, with contraction and fragmentation of mesic biomes during periods of drying in the late Neogene.

In order to investigate the relative importance of ecological (habitat specialization) and biogeographical (speciation, geographical dispersal limitation) processes as causes of non-random spatial distribution of tree species in the mountain forests of Malesia, we analysed the elevational change in the taxonomic and phylogenetic diversity of tree assemblages in different biogeographical subregions.

Malesia (Borneo, Java, Sulawesi and the Philippines).

Tree inventory data of 12 old-growth forests from a wide elevational range (650–3080 m a.s.l.) were taxonomically harmonized and standardized (50 random draws of 245 individuals each per plot), and the phylogeny of 204 genera was resolved and scaled to its evolutionary origin. The taxonomic and phylogenetic diversities were calculated using effective generic measures, and the diversity patterns analysed by regression, ordination and classification.

The primary factor determining the diversity patterns of the tree assemblages was elevation, whereas the influence of region was surprisingly low. This results in common elevational patterns in taxonomic and phylogenetic community structure across western and central Malesia. The major clades of the contemporary mountain forest trees must therefore have evolved before the formation of the Malay Archipelago in its present form (sympatric speciation). Taxonomic richness and phylogenetic diversity exhibited opposite trends with elevation. Generic richness decreased linearly with elevation; the phylogenetic structure of high-elevation forests revealed overdispersion, indicating convergent trait evolution towards higher elevations, whereas the submontane and colline assemblages showed clustering with a considerable number of confamilials. The upper montane forests of Borneo and Sulawesi were characterized by the dominance of Southern Hemisphere conifers, which differentiated them from lower-elevation communities.

Our results indicate that ecological, evolutionary and biogeographical processes (environmental filtering, sympatry and long-distance dispersal) have shaped the contemporary community structure of Malesian mountain forests. Wallace's Line may represent a significant barrier between the lowland tree floras of Borneo and Sulawesi, but this is not true for those at higher elevations. The uniqueness of high-elevation forests in terms of their high phylogenetic diversity and of their unusual structure calls for a high priority in conservation programmes.

We still have limited understanding of the contingent and deterministic factors that have fostered the evolutionary success of some species lineages over others. We investigated how the interplay of intercontinental migration and key innovations promoted diversification of the genus Androsace.

Mountain ranges and cold steppes of the Northern Hemisphere.

We reconstructed ancestral biogeographical ranges at regional and continental scales by means of a dispersal–extinction–cladogenesis analysis using dated Bayesian phylogenies and contrasting two migration scenarios. Based on diversification analyses under two frameworks, we tested the influence of life form on speciation rates and whether diversification has been diversity-dependent.

We found that three radiations occurred in this genus, at different periods and on different continents, and that life form played a critical role in the history of Androsace. Short-lived ancestors first facilitated the expansion of the genus' range from Asia to Europe, while cushions, which appeared independently in Asia and Europe, enhanced species diversification in alpine regions. One long-distance dispersal event from Europe to North America led to the diversification of the nested genus Douglasia. We found support for a model in which speciation of the North American–European clade is diversity-dependent and close to its carrying capacity, and that the diversification dynamics of the North American subclade are uncoupled from this and follow a pure birth process.

The contingency of past biogeographical connections combined with the evolutionary determinism of convergent key innovations may have led to replicated radiations of Androsace in three mountain regions of the world. The repeated emergence of the cushion life form was a convergent key innovation that fostered radiation into alpine habitats. Given the large ecological similarity of Androsace species, allopatry may have been the main mode of speciation.

The coqui frog (Eleutherodactylus coqui) was introduced to the Hawai'ian archipelago in the late 1980s and became established as a widespread species on Hawai'i Island over a short timespan, suggesting that humans are facilitating their movement. To determine the importance of human facilitation, we assessed dispersal patterns and genetic structure of coqui populations using microsatellite data.

Hawai'i Island.

We obtained genotype data using seven microsatellites from coqui specimens collected from 25 populations on Hawai'i Island. The dispersal mechanism was examined using a Mantel test in GenAlEx and a genetic distance tree analysis in Phylip. Allelic diversity, measures of equilibrium, and genetic structure were analysed in GenAlEx and Arlequin. The correlation between genetic distance and geographical distance was used to distinguish between diffusion dispersal (positive correlation) and jump dispersal (zero or negative correlation).

The Mantel test for isolation by distance found no significant correlation between genetic and geographical distance (r² = 0.002, P = 0.4401). The genetic distance tree topology is consistent with this result and exhibited a pattern expected if population establishment occurred through jump dispersal. Migration rates were high (N_M = 4.228), inbreeding was high, genetic differentiation between populations was low, and significant genetic structure was detected among populations (4% of total variation, P < 0.002).

Genetic distance is not correlated with geographical distance, suggesting that humans are important facilitators of coqui dispersal. Migration rate was high, indicating that the rapid expansion of coquies on Hawai'i Island was human-facilitated, while high levels of inbreeding and significant genetic structure suggest low post-establishment dispersal. If this is the case, early detection of coqui populations will be crucial for management due to their propensity to be spread through human-facilitated jump dispersal, followed by slow rates of diffusion dispersal from these newly established populations.

The aim of this study was to investigate patterns of genetic isolation associated with populations in discrete habitat patches in a North American cold desert through analysis of the pallid dotted-blue butterfly, Euphilotes pallescens. This small butterfly is largely restricted to low-elevation habitats across the Great Basin. The apparent geographical isolation and reported morphological variation among E. pallescens populations makes this species an ideal candidate with which to investigate patterns of genetic isolation and diversification in this arid region.

Great Basin, western North America.

We used sequence data from nuclear and mitochondrial genes to investigate genetic diversity among E. pallescens populations, and among E. pallescens and a number of closely related Euphilotes species, using Bayesian phylogenetic analyses, as well as population genetic analyses. In conjunction with genetic variation, morphological variation was examined in the context of geographical and subspecific differentiation.

Our genetic and morphological analyses suggest a moderate amount of isolation among populations, consistent with the hypothesis of restricted gene flow among isolated dune habitats, and possibly associated with isolation in distinct Pleistocene refugia. The patterns of diversification within E. pallescens and among closely related species are complicated by discordance among phylogenetic reconstructions based on nuclear and mitochondrial genes. Discordance among gene genealogies suggests a complex evolutionary history, perhaps involving alternating periods of reticulation and divergence in isolation.

Although E. pallescens may be a vagile species, we find that persistence on isolated dunes in the Great Basin is associated with appreciable genetic and morphological differentiation among populations. However, genetic, morphological and taxonomic axes of variation are only partially in agreement. More generally, the discordance we find among genetic regions is consistent with the ascendant paradigm in phylogenetic reconstruction: gene genealogies often do not perfectly match species trees. Thus we present Euphilotes as a model for future biogeographical and phylogenetic reconstructions employing larger data sets of independent sequence markers.

To investigate the possibility of range expansion and diversification within the subterranean environment in a genus of troglobiont beetles of the family Leiodidae (Troglocharinus), which have a disjunct distribution between the Pyrenees and the Catalonian coast.

North-eastern Iberian Peninsula.

We sequenced 4 kb of five mitochondrial and two nuclear genes of 50 specimens of 12 of the 18 species of Troglocharinus, plus several outgroups. We reconstructed a phylogeny using Bayesian inference and maximum likelihood, estimated divergence times using Bayesian probabilities and an a priori evolutionary rate, compared the diversification of the main clades within the genus, and reconstructed their ancestral distribution using maximum likelihood.

We found strong support for the monophyly of Troglocharinus and the clades in each of the geographical areas, which diverged in the early Pliocene. The coastal clade was further divided into geographically well-defined lineages, separated by Quaternary deposits. The origin of the coastal clade was a single colonization in the early Pliocene from the central Pyrenees. The diversification of the Pyrenean clade followed a constant rate, while the diversification rate of the coastal clade significantly decreased through the Plio-Pleistocene transition.

Troglocharinus expanded its range from its ancestral area in the central Pyrenees to the coast of Catalonia and subsequently diversified, probably within the subterranean environment. Our favoured scenario is a stepping-stone migration, with possibly short-distance dispersals through the surface, along the eastern margin of the north-eastern Ebro basin. The range expansion took place in a narrow temporal window with favourable conditions between the early Pliocene and the onset of the Mediterranean climate by the mid-Pliocene. Surface dispersal was probably severely limited afterwards, as shown by the fragmentation of the coastal lineage.

Conservation strategies need predictions that capture spatial community composition and structure. Currently, the methods used to generate these predictive maps generally focus on deterministic processes and omit stochasticity and other uncertainty in model outputs. Here we present a novel approach to model the means and variance of assemblage properties.

The western Swiss Alps.

We propose a new approach to processing probabilistic predictions derived from stacked species distribution models (S-SDMs) in order to predict and assess the uncertainty in predictions of community properties. We compare the utility of our novel approach with that of a traditional threshold-based approach. We used data sampled in 2009 and 2010 from 192 sites in total for mountain butterfly communities spanning a large elevational gradient as a case study and evaluated the ability of our approach to model the species richness and phylogenetic diversity of communities within an ensemble forecasting framework.

Our approach allowed mapping of the variability in species richness and phylogenetic diversity projections, in addition to the mean, for 78 butterfly species. S-SDMs reproduced the observed decrease in phylogenetic diversity and species richness with elevation, a consequence of environmental filtering. The prediction accuracy of community properties varied along environmental gradients: at low elevations, variability was higher for predictions of species richness while it was the opposite for phylogenetic diversity.

The use of our probabilistic approach to process species distribution model outputs in order to reconstruct communities provides an improved picture of the range of possible assemblage realizations under similar environmental conditions given modelling uncertainty, and helps to inform managers of the usefulness of modelling results.

Our aim was to map the climate dependence of tree species distributions (probability of occurrence) and forest growth (net primary productivity) by comparing the congruence and incongruence between correlative and process-based modelling approaches.

Iberian Peninsula, south-western Europe.

We used forest inventory data for three widespread tree species (Quercus ilex, Pinus halepensis and Pinus sylvestris) to model climatic suitability with an ensemble of seven correlative species distribution models (using biomod). We then simulated forest net primary productivity (NPP) as a surrogate of forest growth for forests of each species using an ecophysiological process-based model (gotilwa+) along a gradient of climatic suitability. The spatial distribution of the growth estimates was then compared with that of the suitability estimates, and robust regression was used to classify regions in terms of model congruence.

Quercus ilex and P. sylvestris both showed a positive relationship between forest NPP and climatic suitability. The main discrepancies were found in the north of the peninsula, where there was high potential forest growth but low climate suitability. Low forest-growth estimates in areas of high suitability only appeared for P. sylvestris in southern montane regions. Pinus halepensis always showed a negative relationship between estimated growth and climatic suitability. The analysis of other ecophysiological parameters (mean leaf life and leaf area index) suggests that this tree species has different physiological strategies that allow differential growth rates in areas of low suitability.

We found that the relationship between estimated growth and distribution varies strongly in different areas and species. Mapping the incongruences between the predicted climatic suitability and growth allowed us to identify regions where other factors (e.g. biotic interactions) may be more significant than the physiological limits on growth. We show that new insights into species distributions can be gained from mapping the differences between correlative and process-based models.

We reconstructed the biogeographical and evolutionary history of Saltator by producing a robust phylogenetic hypothesis that we used to evaluate the geographical origins of this genus, and assessed the potential influence of major Neotropical biogeographical features on the origin of lineages within this assemblage (i.e. phylogroups).

Neotropics.

Our phylogenetic reconstruction is based on newly sequenced mitochondrial DNA data representing all known species of Saltator. This phylogenetic hypothesis was then used to define phylogenetic structure and to assess divergence times for these clades. Phylogroups were assigned to unique biogeographical regions allowing us (1) to perform ancestral biogeographical analyses (using rasp) to reconstruct ancestral areas for all nodes within our topology, and (2) to examine the geography of speciation and evolutionary history of Saltator.

The novel phylogenetic relationships in Saltator showed that this tanager clade originated and diversified in South America in the mid-Miocene (c. 13 Ma), ultimately yielding three distinct clades composed of a minimum of 26 phylogroups. A positive correlation was found between phylogenetic distance and co-occurrence (percentage range overlap) for Saltator.

Our evolutionary scenario for Saltator is consistent with a radiation initiated by uplift of the Andes during the last 10 million years. The biogeography of Saltator and the large number of phylogroups recovered suggest that an allopatric mode of speciation is the major driver in the evolutionary history of this group of tanagers.

Top-down (climatic) controls of fire occurrence are expected to homogenize fire regimes in a given area over long (millennial) temporal scales. Previous investigations in south-eastern British Columbia have shown that bottom-up (local site) factors can override long-term climate as a dominant control. Here, we examine the interactions between fire regime controls using five 5000-year-long lake sediment records.

All lakes are located in separate watersheds within a 550-km² region of Engelmann spruce–subalpine fir forest in the Columbia Mountains, British Columbia, Canada.

Sedimentary macroscopic (> 150 μm) charcoal analysis was used to produce local fire history records. Fire events were identified by decomposing the charcoal concentration series using the program CharAnalysis. We analysed the temporal coherence of the reconstructed fire events and the distributions of the fire return intervals at all sites and pooled sites by their north-facing or south-facing aspect.

Since 5000 cal. yr bp, fire frequency was highest between 4250 and 2750 cal. yr bp and lowest from 750 cal. yr bp to the present. Median fire return intervals were shorter on the warmer and drier south-facing slopes (135–190 years) and longer on the cooler and moister north-facing slopes (226–241 years). Significant synchrony existed between sites with similar aspect, but no synchrony was found at sites with opposing aspect, providing evidence for the importance of bottom-up controls. Smoothed fire frequencies suggested that the influence of aspect varied throughout the period and that the importance of aspect could be overridden by other controls. The asynchrony between sites with opposite aspects suggests that local conditions for fire are important spatial controls on the fire regime.

Aspect is an important bottom-up control of fire regimes in mid-elevation forests and its influence varies through time. The variability of climate–fire–vegetation interactions in the region needs to be investigated to understand the importance of top-down and bottom-up controls.

Across eastern Australia, mountain ranges (the Great Dividing Range) and river catchments (the Murray–Darling Basin) are likely to have shaped the phylogeographical structure of many species. We address how such processes have influenced the phylogeography of the lace monitor, Varanus varius, a large mobile lizard.

Eastern and south-eastern Australia.

Phylogeographical hypotheses were tested using up to 90 museum and field-collected samples from across the entire species' range; a 671-bp region of the mtDNA gene ND4 was sequenced and all individuals were genotyped (eight microsatellite loci).

Maximum-likelihood analysis of sequence data revealed three geographically separate clades, with divergences estimated to have occurred during the Pleistocene. The south-eastern clade showed an expansion pattern from northern refugia and dispersal appears to have occurred along the Murray–Darling river system. Microsatellite analyses support mtDNA clades but indicate secondary contact in the Hunter Valley, New South Wales.

Our results indicate that phylogeographical structure and contemporary gene flow in Varanus varius is shaped by dispersal capacity, geographical barriers and the presence of ancient river corridors. Indeed, only the most significant geological (McPherson Range) and habitat barriers (Burdekin Gap) appear to limit gene flow in this species. The expansion of the clade on the western side of the Great Dividing Range suggests that ancient riparian corridors have facilitated extensive gene flow. Our study highlights the importance of understanding a species' ecological dynamics when examining broad-scale evolutionary patterns.

To establish a spatial and temporal framework within which we can begin to investigate the role of geography in the evolution of Pomacanthus species. This study examines the phylogenetic relationships among Pomacanthus species, tests whether the degree of sympatry among sister taxa correlates with their age, and explores potential modes of diversification.

Pan-tropical coral reef systems.

Three gene regions (12S rRNA, 16S rRNA and nuclear S7) from all 13 Pomacanthus species were used in conjunction with fossil calibration to reconstruct a chronogram. IUCN maps were used to evaluate geographical range overlap. Various age–range correlation (ARC) analyses were used to test for a correlation between range overlap and node age. Range-size symmetry and node age were also examined.

Biogeographical splits within the phylogeny corroborated key biogeographical events well, suggesting a potential role for allopatric speciation in the evolutionary history of the genus. ARC analyses suggested that speciation leading to sympatry is widespread in Pomacanthus, with 80% of sister species showing complete or substantial (> 85%) range overlap. No significant relationship between degree of sympatry and node age was recovered, which demonstrates that, for this group, exceptional sympatry is not necessarily a result of relatively old lineages. Range-size symmetry analysis was consistent with models of peripatric speciation within a finite area.

We present evidence consistent with allopatric speciation, while our ARC results are consistent with simulations of sympatric speciation, with the possibility of peripheral budding having led to the richness of sympatric species in the West Indian Ocean. We discuss how these processes can affect the interpretation of temporal and spatial analyses, and provide a basis for future investigations into the processes driving speciation.

The aim of this study was to assess the impact of pre-Quaternary tectonics and orogeny relative to that of Pleistocene climate change on diversification within the Pseudouroctonus minimus complex, a group of vaejovid scorpions with stenotopic habitat requirements.

South-western North America (United States and Mexico).

Multilocus sequence data (1899 base pairs from two mitochondrial and two nuclear genes) were generated from 65 samples of scorpions in the minimus complex. Phylogeographical structure within the minimus complex was explored using model-based phylogenetic methods and a general mixed Yule coalescent model to identify independent geographical clusters. A time-calibrated multilocus species tree was reconstructed using a multispecies coalescent approach. Ancestral areas were estimated at divergence events across the tree using a probabilistic Bayesian approach.

Extensive geographical structure was evident within two well-supported clades. These clades probably diverged over 25 million years ago (Ma), based on estimated mean divergence dates, followed by 14 divergences in the Miocene (25–5 Ma) and 4 divergences in the Pliocene and Pleistocene (< 5 Ma). The ancestral origin of the minimus complex was reconstructed to be across California and the Mexican Highlands. The Chihuahuan Desert was colonized twice from the Mexican Highlands, and one dispersal event occurred from the Mexican Highlands back to California.

Spatial and temporal patterns of evolution in the minimus complex support predictions that stenotopy promoted pre-Quaternary diversification. Miocene and Pliocene geomorphology, perhaps in concert with climate change, induced allopatric divergence across the heterogeneous landscape of south-western North America. Stenotopic scorpions such as the minimus complex provide a model for exploring correlations between Earth history and biological diversification.

Little is known about factors affecting the elevational and longitudinal zonation of tropical Andean stream communities. We investigated epilithon, macroinvertebrate and fish assemblages along a 4100-m elevational–longitudinal gradient in an Andean headwater of the Amazon Basin. We interpret our results within the context of environmental factors, emphasizing temperature, as well as ecological theory relating shifts in metazoan functional feeding groups to shifts in basal resources along the fluvial continuum.

Arazá-Inambari-Madre de Dios watershed, south-eastern Peru.

We sampled water physicochemistry, epilithon and macroinvertebrate diversity and abundance, and fish diversity at 18 main-stem and 14 tributary sites from high puna grasslands (4300 m a.s.l.) to Amazon Basin lowlands (200 m a.s.l.).

Water physicochemical parameters and the taxonomic and ecological structure of invertebrate and fish assemblages displayed mostly nonlinear responses to elevation: water temperature and percentage of macroinvertebrate taxa identified as leaf shredders had U-shaped responses; dissolved oxygen and percentage of macroinvertebrate taxa identified as grazers had hump-shaped responses. Epilithon richness increased slightly with elevation whereas macroinvertebrate and fish richness decreased.

Elevational gradients in physicochemical parameters are insufficient to explain abrupt and nonlinear shifts in community taxonomic and functional structure. Rather, trophic interactions, including predation and longitudinal turnover in basal food resources, seem to exert a stronger influence on the distributions of Andean aquatic organisms. A steep elevational decline in relative taxonomic diversity of leaf-shredding (versus algae-grazing) insects supports the hypothesis that temperature affects the functional composition of insect assemblages via its influence on microbial decomposition rates. This relationship, and the distributions of several insect and fish species across narrow elevational bands, suggests that Andean stream communities may be sensitive to global warming. Placer mining and road building impacts have already altered stream community structure, including the absence of many benthic species from low-elevation habitats.

We analysed range-wide chloroplast DNA (cpDNA) variation in a clade of North American goldenrods (Solidago subsect. Humiles) to infer its biogeographical history and evolution. Our objectives were to: (1) examine the structuring of cpDNA diversity in this widespread species complex, (2) reconstruct Pleistocene refugia and post-glacial migration of the study species, and (3) test hypotheses relating to the frequency of polyploidization. We expected the glacial history of Solidago to differ markedly from that of temperate trees and forest understorey plants.

North America (Canada, continental USA, Mexico).

1466 bp of chloroplast intergenic spacer DNA (cpDNA) were sequenced from 368 individuals representing 72 populations of subsect. Humiles, which consists of the widespread Solidago simplex and four geographically restricted species. Estimates of N_ST and G_ST were compared as a test of phylogeographical structure, and spatial analysis of molecular variance (SAMOVA) was used to examine cpDNA variation. Rarified haplotype diversity and chromosome diversity (ploidy levels) were used to infer locations of glacial refugia and post-glacial expansion, and to determine origins of polyploidy, respectively.

A total of 46 haplotypes were recovered. While there was significant phylogeographical structure (N_ST > G_ST), cpDNA variation was not strongly partitioned across species boundaries, geography or ploidy levels, and six haplotypes were shared among species. The highest haplotype diversity was located in western North America, followed by the south-eastern USA and the formerly glaciated Great Lakes region.

Solidago simplex recolonized formerly glaciated eastern North America from refugia in western North America and near the perimeter of the ice margin. The south-eastern USA had only limited involvement in recolonization of these northern regions. The geographical disjunction and scattered positions of polyploids in the haplotype network provide evidence of multiple polyploid origins within S. simplex, and the restriction of endemic, polyploid taxa to post-glacial habitats provides evidence of Holocene polyploid speciation. The results highlight polyploidization as a source of adaptive genetic variation and speciation in novel and post-glacial habitats.

To investigate how marine barriers shaped the demographic history of Atlantic seahorses (Syngnathidae: Hippocampus).

Atlantic Ocean.

Range-wide sampling (n = 390) at mitochondrial and up to five nuclear DNA loci was carried out across the Hippocampus erectus species complex (H. erectus from the Caribbean/North America, H. patagonicus from South America and H. hippocampus from Europe and West Africa). Multi-species coalescent and approximate Bayesian computation (ABC) frameworks were used to estimate support of competing biogeographical hypotheses and demographic parameters, including lineage divergence times, effective population sizes and magnitudes of population size change.

We identified four distinct lineages within the H. erectus complex. A posterior probability of 0.626 and corresponding Bayes factors ranging from 3.68 to 11.38 gave moderate to strong support for a basal divergence between South American populations of H. patagonicus and Caribbean/North American populations of H. erectus coincident with the inter-regional freshwater outflow of the Amazon River Barrier (ARB). Estimates of historical effective population sizes and divergence times indicate that European and West African populations of H. hippocampus expanded after colonization from a more demographically stable Caribbean/North American H. erectus.

Our findings of trans-Atlantic colonization followed by isolation across a deep oceanic divide, and isolation across a freshwater barrier, may demonstrate a contrast in marine divide permeability for this group of rafters. Demographic inference supports the establishment of an ancestral population of the H. erectus complex in the Americas, followed by the ARB splitting it into Caribbean/North and South American lineages at a time of increased sedimentation and outflow. Our estimates suggest that following this split, colonization occurred across the Atlantic via the Gulf Stream currents with subsequent trans-Atlantic isolation. These results illustrate that rafting can be a means of range expansion over large distances, but may be insufficient for sustaining genetic connectivity across major barriers, thereby resulting in lineage divergence.

The distribution of vulnerable marine ecosystems in the deep sea is poorly understood. This has led to the emergence of modelling methods to predict the occurrence of suitable habitat for conservation planning in data-sparse areas. Recent global analyses for cold-water corals predict a high probability of occurrence along the slopes of continental margins, offshore banks and seamounts in the north-eastern Atlantic, but tend to overestimate the extent of the habitat and do not provide the detail needed for finer-scale assessments and protected area planning. Using Lophelia pertusa reefs as an example, this study integrates multibeam bathymetry with a wide range of environmental data to produce a regional high-resolution habitat suitability map relevant for marine spatial planning.

Irish continental margin (extended continental shelf claim).

Maximum entropy modelling was used to predict L. pertusa reef distribution at a spatial resolution of 0.002°. Coral occurrences were assembled from public databases, publications and video footage, and filtered for quality. Environmental predictor variables were produced by re-sampling of global oceanographic data sets and a regional ocean circulation model. Multi-scale terrain parameters were computed from multibeam bathymetry.

Suitable habitat was predicted on mound features and in canyon areas along a narrow band following the slopes of the Irish continental margin, the Rockall Bank and the Porcupine Bank. Standard deviation of the seabed slope (54%), temperature (28%) and bottom shear stress (9%) were the most important variables to predict coral distribution.

This is the first regional coral habitat suitability modelling study to incorporate full coverage multibeam bathymetry in the deep sea. The use of high-resolution environmental data and quality-controlled distribution data significantly reduces habitat overestimation demonstrated by global-scale analyses and produces detailed maps to support marine protected area network design. The strong response of the corals to local-scale terrain variability highlights the need to protect the seabed from anthropogenic impacts that may reduce its complexity, such as bottom trawling.

For many deep-sea fisheries, there is an urgent management requirement for information on the presence of vulnerable marine ecosystems (VMEs). Gathering deep-sea data using conventional techniques can be expensive and time-consuming. One way to provide a relatively rapid assessment of VME presence is to use data from fisheries by-catch and historical scientific observations. Our aim was to predict suitable habitat for octocorals around South Georgia and to estimate the extent to which octocoral habitat is currently protected by fisheries management measures. In addition, we attempted to determine the types of terrain in which octocorals and fishing activities occur.

South Georgia, sub-Antarctic.

A terrain map of South Georgia was created using Benthic Terrain Modeler (BTM). Georeferenced octocoral data were combined with environmental layers to create an octocoral habitat suitability map using ecological niche factor analysis (ENFA).

Most octocoral by-catch samples originated from narrow crest (an area representing shelf break and moraines) and steep (continental) slope terrains. Calcite saturation state and apparent oxygen utilization (AOU) were the most influential environmental parameters in determining highly suitable octocoral habitat. The ENFA model highlighted shelf-break areas to be highly suitable habitat for octocorals and that 38% of this habitat around South Georgia lies within areas currently protected by fisheries management; a further 20% is below the 2000-m fishing depth, meaning effectively that 58% of predicted highly suitable octocoral habitat is currently protected. Although these results indicate protection levels for octocoral habitat well above international standards/targets, the fishery remains active within a relatively concentrated shelf area at 700–2000 m, potentially having a large impact on the 42% of highly suitable octocoral habitat predicted to lie at these depths.

This research demonstrates the potential for using fisheries by-catch data to create habitat suitability maps that can inform fisheries management and future research.

While there is a huge macroecological and biogeographical literature addressing endemism, very little has been done to systematically study lineages that are widely distributed across the globe. Our aim here was to list and analyse those lineages of terrestrial tetrapod vertebrates found in 60–90% of the world, loosely termed here as cosmopolitan.

Global.

Two sets of geographical units and three occupancy criteria were used to list, analyse and map cosmopolitan lineages and their sister lineages.

Among the 83 lineages identified, 2 were represented by amphibians, 9 by reptiles, 13 by mammals, and the remainder by birds, of which 12 were passerines and 47 were non-passerines. All these lineages are present in parts of Southeast Asia, most of them throughout much of Eurasia and Africa, but fewer in South America and very few in Australia. Only three of the lineages (all reptiles) are likely to exemplify vicariance or early dispersal-driven cosmopolitanism, the rest having attained world-wide distribution via extensive, geologically recent dispersal. The distribution of sister lineages indicates that many cosmopolitan lineages probably originated in the savanna regions of Africa, some in Southeast Asia, and fewer in tropical America.

Cosmopolitan distributions in tetrapods are primarily the result of dispersal, with large body size and the ability to fly being two key correlates of rapid global colonization. We argue that a cosmopolitan lineage framework in biogeographical and ecological studies could add great depth to the understanding of evolutionary success, and would be highly relevant to the field of invasion biology.

Quaking aspen (Populus tremuloides) has the largest natural distribution of any tree native to North America. The primary objectives of this study were to characterize range-wide genetic diversity and genetic structuring in quaking aspen, and to assess the influence of glacial history and rear-edge dynamics.

North America.

Using a sample set representing the full longitudinal and latitudinal extent of the species’ distribution, we examined geographical patterns of genetic diversity and structuring using 8 nuclear microsatellite loci in 794 individuals from 30 sampling sites.

Two major genetic clusters were identified across the range: a south-western cluster and a northern cluster. The south-western cluster, which included two subclusters, was bounded approximately by the Continental Divide to the east and the southern extent of the ice sheet at the Last Glacial Maximum to the north. Subclusters were not detected in the northern cluster, despite its continent-wide distribution. Genetic distance was significantly correlated with geographical distance in the south-western but not the northern cluster, and allelic richness was significantly lower in south-western sampling sites compared with northern sampling sites. Population structuring was low overall, but elevated in the south-western cluster.

Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the south-western cluster may result from distinct gene pools separated during the Pleistocene and reunited following glacial retreat, similar to patterns found in other forest tree species in the western USA. In aspen, populations in the south-western portion of the species range are thought to be at particularly high risk of mortality with climate change. Our findings suggest that these same populations may be disproportionately valuable in terms of both evolutionary potential and conservation value.

Broad-scale patterns in the distribution of phytophagous arthropods have been explained by species turnover due to host plant, environment, geographical distance and historical biogeography. In this study, variability due to plant species turnover was eliminated by focusing on the arthropods utilizing a single widely distributed plant species, Parkinsonia aculeata L. (Leguminosae: Caesalpinioideae). This enabled us to examine the effects of geography and climate on arthropod species turnover.

Neotropics (USA to Argentina).

A statistical approach was used to determine whether arthropod assemblages across the range of P. aculeata differed significantly between biogeographical areas. We determined whether host-specific arthropods have more restricted ranges, contributing to higher species turnover. Finally, generalized dissimilarity modelling (GDM) was used to correlate significant differences in assemblages between biogeographical provinces with environmental differences and geographical separation.

Phytophagous arthropod assemblages differed significantly between biogeographical areas. Most herbivores had a small geographical distribution. We did not detect higher species turnover for host-specific species. The GDM model explained 21.8% of the variance in species assemblages. Of the variables examined, climate and geographical distance were both better predictors of variation in phytophagous arthropod assemblages on P. aculeata than biogeographical areas, with climate the better predictor of the two.

Observed patterns in turnover of the phytophagous insect fauna of P. aculeata are consistent with expected broad-scale responses to historical processes and climatic variation. Climate and geography explain similar proportions of compositional dissimilarity, and most species, regardless of host-specificity, have restricted geographical ranges. The statistically significant differences observed between arthropod assemblages in different biogeographical provinces are likely to be caused by a combination of niche-based processes and to some extent dispersal limitation. Although variability due to host plant has been eliminated in the current study, there remains no simple explanation for broad-scale patterns in the distribution of phytophagous arthropods.

We investigated the hypothesis that body size evolution of mammals is strongly influenced by ecological interactions, resulting in evolutionary divergence in body size in species-rich (e.g. mainland) biotas, and convergence on the size of intermediate but absent species in species-poor (e.g. insular) biotas.

Mediterranean palaeo-islands.

We assembled data on temporal variation in body size of palaeo-insular mammals and associated variation in ecological characteristics (colonization or extirpation of mammalian competitors and predators) for 19 species of fossil, non-volant mammals across four large (> 3640 km²) islands ranging between the late Miocene and Holocene. These are the only fossil species for which fine-detailed time series are available at present.

Our results are consistent with predictions based on an ecological interactions hypothesis of body size evolution. Following colonization (or first appearance in the insular fossil record) small mammals (such as mice, shrews and pikas) tended to increase in body size. These trends, however, ceased or were reversed following colonization of the focal islands by mammalian predators or competitors.

While body size evolution is likely to be influenced by a variety of characteristics of the focal islands (e.g. climate, area, isolation and habitat diversity) and species (e.g. diet, resource requirements and dispersal abilities), temporal trends for palaeo-insular mammals indicated that the observed trends for any particular species, island and climatic regime may be strongly influenced by interactions among species. Ultimately, invasion of a competitor often leads to the extinction of the native, insular species.

To test the ‘naturalness’, or integrity as a biogeographical unit, of the Caribbean subregion.

A wide geographical range in the Caribbean (32° N, 115° W; 10° S, 56° W). As units of analysis, 43 biogeographical provinces were used: 24 assigned to the Caribbean subregion, and 19 provinces situated north and south of this subregion, which were used as outgroup areas.

We analysed 895 plant and animal taxa distributed in the Caribbean. We used parsimony analysis of endemicity with progressive character elimination (PAE-PCE) to identify generalized tracks and nodes, and parsimony analysis of paralogy-free subtrees to infer their historical relationships.

We obtained 10 generalized tracks and five nodes from the panbiogeographical analysis and 14 most parsimonious general area cladograms from the cladistic biogeographical analysis. In general terms, the results of both analyses are congruent, reflecting a similar history of vicariant events in the Caribbean area.

Panbiogeographical and cladistic biogeographical analyses reflected a similar history of vicariant events in the Caribbean: the Caribbean subregion as it is currently defined does not represent a ‘natural’ biogeographical unit; the Isthmus of Tehuantepec might not represent a conspicuous biogeographical barrier; and the biogeographical relevance of the Isthmus of Panama exceeds the last 3 million years, which is the time it has operated as a connection between North and South America.

Diversification and rapid radiation are well documented in lacertid lizards. Niche conservation is frequently observed among related taxa, whereby niches will not change much during speciation events. Here, we investigate the relationship between environmental niche divergence and phylogenetic relatedness in a widespread group of green lizards, the Lacerta trilineata group.

Eastern Mediterranean, Anatolia and adjacent regions.

A dated phylogeny based on three mitochondrial genes was contextualized using species distribution models of all genetically identified lineages in the Lacerta trilineata group. Based on this analysis, ancestral climatic niche occupancy was reconstructed using niche occupancy profiles. Niche divergence among lineages was quantified by computing multivariate niche overlaps.

All taxa are associated with humid areas, but there is extensive variation in their climatic niche breadths and positions, which accord with the main phylogenetic split in the group. Our results suggest divergent niche evolution within subclades and convergent evolution among clades, which implies only a limited degree of niche conservatism regarding annual variations in temperature and precipitation. In contrast, niche axes – mainly reflecting precipitation patterns of the coldest quarter – show a greater difference among clades than within clades, and therefore a higher degree of niche conservatism.

Based on estimated divergence times between taxa and geological events in Anatolia, our results can be explained by fragmentation of the range of a hypothetical ancestral species, resulting in different adaptations of subclades either to humid continental climates or to more Mediterranean climates. Our study highlights deviations from classical niche conservatism theory due to significant niche shifts among sister taxa.

Recent advances in the availability of species distributional and high-resolution environmental data have facilitated the investigation of species richness–environment relationships. However, even exhaustive distributional databases are prone to geographical sampling bias. We aim to quantify the inventory incompleteness of vascular plant data across 2377 Chinese counties and to test whether inventory incompleteness affects the analysis of richness–environment relationships and spatial predictions of species richness.

China.

We used the most comprehensive database of Chinese vascular plants, which includes county-level occurrences for 29,012 native species derived from 4,236,768 specimen and literature records. For each county, we computed smoothed species accumulation curves and used the mean slope of the last 10% of the curves as a proxy for inventory incompleteness. We created a series of data subsets with different levels of inventory incompleteness by excluding successively more under-sampled counties from the full data set. We then applied spatial and non-spatial regression models to each of these subsets to investigate relationships between the species richness of subsets and environmental factors, and to predict spatial patterns of vascular plant species richness in China.

Log₁₀-transformed numbers of records and documented species were strongly correlated (r = 0.97). In total, 91% of Chinese counties were identified as under-sampled. After controlling for inventory incompleteness, the overall explanatory power of environmental factors markedly increased, and the strongest predictor of species richness switched from elevational range to annual wet days. Environmental models calibrated with more complete inventories yielded better spatial predictions of species richness.

Our results indicate that inventory incompleteness strongly affects the explanatory power of environmental factors, the main determinants of species richness obtained from regression analyses, and the reliability of environment-based spatial predictions of species richness. We conclude that even large distributional databases are prone to geographical sampling bias, with far-reaching implications for the perception of and inferences about macroecological patterns.

To produce a dynamic model of tree line position and habitat suitability for temperate and warm temperate forests, with high spatial and temporal resolution from the Last Glacial Maximum to the present, using an approach based on the quasi-constant altitudinal difference between the tree line altitude (TLA) and the equilibrium line altitude (ELA) of glaciers.

Central Mediterranean.

Data sets of current tree line position and ELA were integrated and five different scenarios of tree line shifts were simulated at a millennial scale. The model was parameterized using a dense palynological data set (964 time points, representing 121 pollen sampling sites). The simulated tree line fluctuations were compared with those of the boreal forest reconstructed using field data from the southern Alps.

The reconstructed evolution of TLA yielded good results for the interval of tree line formation (correct assignment rate: lower limit = 98.29%; upper limit = 94.29%) and the best-fitting scenario within each millennium tree line (combined scenarios: AUC ± 2 SD = 0.877 ± 0.047; Kappa ± 2 SD = 0.651 ± 0.100). There was also strong agreement between the simulated and the reconstructed tree line fluctuations for both the timing and magnitude of tree line shift.

Although all the analyses support the hypothesis of a quasi-constant difference between TLA and ELA, we found a major relative upward shift of the tree line position within the interval of tree line formation, probably due to the increase in both precipitation and atmospheric CO₂ concentration since the onset of the Bølling–Allerød Interstadial. Palaeodistribution maps may be useful for drawing inferences about the biogeography of single temperate and warm temperate species or for recolonization simulations; however, model-based inferences will need to account for several variables, including local climate variability, fire and herbivore disturbance, and lack of complete spatial association between modelled forests and species of interest.

The relative importance of long-distance dispersal versus vicariance in determining the distribution of lichen-forming fungi remains unresolved. Here, we examined diversity and distributions in a cosmopolitan lichen-forming fungal species complex, Rhizoplaca melanophthalma sensu lato (Ascomycota), across a broad, intercontinental geographical distribution. We sought to determine the temporal context of diversification and the impacts of past climatic fluctuations on demographic dynamics within this group.

Antarctica, Asia, Europe, North America and South America.

We obtained molecular sequence data from a total of 240 specimens of R. melanophthalma s.l. collected across five continents. We assessed the monophyly of candidate species using individual gene trees and a tree from a seven-locus concatenated data set. Divergence times and relationships among candidate species were evaluated using a multilocus coalescent-based species tree approach. Speciation probabilities were estimated using the coalescent-based species delimitation program bpp. We also calculated statistics on molecular diversity and population demographics for independent lineages.

Our analyses of R. melanophthalma s.l. collected from five continents supported the presence of six species-level lineages within this complex. Based on current sampling, two of these lineages were found to have broad intercontinental distributions, while the other four were limited to western North America. Of the six lineages, five were found on a single mountain in the western USA and the sixth occurred no more than 200 km away from this mountain. Our estimates of divergence times suggest that Pleistocene glacial cycles played an important role in species diversification within this group. At least three lineages show evidence of recent or ongoing population expansion.

We investigate first whether fire regimes resulting from the combination of climate change and fire-fighting policy may affect species distributions in Mediterranean landscapes, and second to what extent distributional dynamics may be constrained by the spatial legacy of historical land use.

Catalonia (north-eastern Spain).

We modelled the distributional responses of 64 forest and open-habitat bird species to nine fire-regime scenarios, defined by combining different levels of climate change and fire suppression efficiency. A fire-succession model was used to stochastically simulate land-cover changes between 2000 and 2050 under these scenarios. We used species distribution models to predict habitat suitability and occupancy dynamics under either no dispersal or full dispersal assumptions.

Under many simulated scenarios, the succession from shrubland to forest dominated over the creation of new low-vegetation areas derived from wildfires. Consequently, open-habitat specialists were the group most affected by losses of suitable habitat. Fire regimes obtained under scenarios including high fire suppression efficiency resulted in a larger number of bird species experiencing reductions in their distribution area.

Anthropogenic factors, such as historical land-use change and fire suppression, can drive regional distribution dynamics in directions opposite to those expected from climatic trends. This raises the question of what drivers and interactions should be given priority in the prediction of biodiversity responses to global change at the regional scale.

The objectives of this study were to elucidate the phylogenetic origins and phylogeographical history of Ligularia hodgsonii, which exhibits a disjunct distribution between south-western–central China and Japan.

China and Japan.

Three chloroplast DNA (cpDNA) spacer regions (trnQ–5′rps16, trnL–rpl32 and psbA–trnH) were sequenced in 280 individuals of L. hodgsonii isolated from 29 natural populations, including 23 from China and 6 from Japan. Phylogenetic inference was performed using MrBayes and beast analyses. Statistical dispersal–vicariance analysis (S-DIVA) was utilized to resolve the biogeographical events in L. hodgsonii, and to clarify the origin of the species’ disjunct distribution.

Genetic variation in cpDNA revealed 19 unique haplotypes among populations. A high degree of genetic diversity (H_T = 0.913) and a significant level of differentiation (G_ST = 0.933, N_ST = 0.989) were detected. Different haplotypes from continental and island populations were analysed, and the degree of genetic diversity observed within each of the two regions was similar. S-DIVA analysis supported the occurrence of a vicariance event between the continental and island areas.

Based on S-DIVA analysis, the non-overlapping cpDNA haplotypes and similar genetic diversity levels in continental and island populations, we conclude that the disjunct distribution of L. hodgsonii is the result of vicariance. Molecular dating suggests that the separation between populations on the islands of Japan (northern Honshu and Hokkaido) and mainland Asia occurred during the middle to late Pleistocene. Following divergence, L. hodgsonii populations probably underwent severe range contraction into multiple isolated refugia during the Last Glacial Maximum, when conditions were colder and drier than at present.

Thermophilic species persisted in southern refugia during the cold phases of the Pleistocene, and expanded northwards during warming. These processes caused genetic imprints, such as a differentiation of genetic lineages and a loss of genetic diversity in the wake of (re)colonization. We used molecular markers and species distribution models (SDMs) to study the impact of range dynamics on the common wall lizard, Podarcis muralis, from southern refugia to the northern range margin.

Parts of the Western Palaearctic.

We genotyped 10 polymorphic microsatellites in 282 individuals of P. muralis and sequenced the mitochondrial DNA (mtDNA) cytochrome b gene to study the genetic structure, divergence times and ancestral distributions. Furthermore, we generated SDMs for climate scenarios for 6 and 21 ka derived from two different global circulation models.

We detected two major mtDNA lineages – a western France clade (Pyrenees to Brittany), and an eastern France clade (southern France to Germany, Belgium and Luxembourg). This split was dated to c. 1.23 Ma. The latter clade was divided into two subclades, which diverged c. 0.38 Ma. Genetic diversity of microsatellites within each clade was nested and showed a significant loss of genetic diversity from south to north, a strong pattern of allele surfing across nearly all loci, and an increase in genetic differentiation towards the northern range margin. Results from SDMs suggest that southward range retraction during the late glacial period split the distribution into geographically distinct refugia.

The strong genetic differentiation mirrors the effects of long-term isolation of P. muralis in multiple refugia. Post-glacial recolonization of Northern Europe has taken place from two distinct refugia, most probably along river systems (Rhône, Rhine, Moselle) and along the Atlantic coastline, with subsequent nested elimination of genetic diversity and increasing genetic differentiation at the northern range margin.

Knowledge of mammal community composition across large areas is critical to the reconstruction of biogeographical trends in past ecosystems where mammalian fossils serve as palaeoecological proxies. We employed ‘ecometrics’ (taxon-free trait analysis) to compare fossil communities of the Italian Plio-Pleistocene across space and time. We tested the hypotheses that ecometric traits characterizing fossil mammal communities differ between time bins, and that they exhibit geographical correlations.

Peninsular Italy, excluding islands (Sardinia and Sicily).

We explored selected ecometric traits (body weight, biomass, hypsodonty and brachial index) in 69 local fossil assemblages at the scale of nine palaeocommunities (PCOMs), and at the broader scale of ‘mammal age’, or biochronological unit, to which they belong: Villafranchian, Galerian or Aurelian. Principal components analysis, MANOVA and linear discriminant analysis were used to describe differences in the PCOM and mammal age ecospaces. We also tested for the effects of latitude and longitude on the ecometric variables and mapped their distributions during individual mammal ages.

Spatial analysis suggested that neither latitude nor longitude relate meaningfully to any of the ecological parameters under consideration. However, PCOMs in each biochronological interval were successfully discriminated using ecometric traits, with the exception of the localities from Triversa and Pirro, which bore more resemblance to the younger Aurelian localities. The mammal ages were more clearly distinct.

Communities differ from one another particularly in relation to both the average body weight of herbivores and the entire mammalian fauna and the biomass of prey species. This is probably related to a climatic cooling trend that occurred between the Pliocene and Pleistocene and resulted in the evolution of larger forms. Hypsodonty trends are identified and we support hypsodonty as a valuable ecometric trait, but only at larger temporal scales.

Our aim was to elucidate the effect of mass extinctions on inferred crown ages of terrestrial clades endemic to ancient islands. We thereby assessed the potential for mass extinction events, such as the Zealandian marine incursion episode in the Oligocene, to skew the interpretation of the evolutionary history of clades of various sizes.

Simulation study focusing on New Zealand.

Clades of various sizes were simulated under a birth–death model with variable parameters for diversification, invoking a prolonged extinction event, using the R package TreeSim. We measured the scaled root shift J between actual (i.e. first cladogenetic event) and inferred (i.e. most recent common ancestor of extant taxa) clade divergence times in simulated phylogenies incurred by extinction processes.

A pulse of extinction followed by a prolonged period of low cladogenetic potential – modelled after the geological history of Zealandia in the Oligocene – produced large root shifts in clades of all sizes. Small clades with high net diversification rates were especially prone to belying pre-Oligocene history. In simulations invoking mass extinctions wherein a pre-extinction root was retained, phylogenies of extant taxa were characterized by anti-sigmoidal log lineage-through-time plots that mimicked an upturn in diversification rate after the extinction period.

Non-selective mass extinctions can engender large discrepancies in actual and inferred root ages, particularly in small, old clades. The evolutionary histories of lineages that survive mass extinctions are difficult to distinguish from scenarios of rapid radiation. This outcome challenges previous interpretations of post-Oligocene crown ages for clades endemic to New Zealand as sufficient evidence for rejecting a pre-Oligocene evolutionary history. As a corollary, our results suggest that the extant size of a particular clade is the foremost indicator of its potential for historical biogeographical inference. We therefore review the hypothesis of the total submersion of Zealandia, highlighting empirical cases of lineages with demonstrable pre-Oligocene history that refute the hypothesis of total submersion.

Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution.

Indo-Pacific, Red Sea, Arabian/Persian Gulf.

Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus.

Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder.

The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations.

Metacommunity theories attribute different relative degrees of importance to dispersal, environmental filtering, biotic interactions and stochastic processes in community assembly, but the role of spatial scale remains uncertain. Here we used two complementary statistical tools to test: (1) whether or not the patterns of community structure and environmental influences are consistent across resolutions; and (2) whether and how the joint use of two fundamentally different statistical approaches provides a complementary interpretation of results.

Grassland plants in the French Alps.

We used two approaches across five spatial resolutions (ranging from 1 km × 1 km to 30 km × 30 km): variance partitioning, and analysis of metacommunity structure on the site-by-species incidence matrices. Both methods allow the testing of expected patterns resulting from environmental filtering, but variance partitioning allows the role of dispersal and environmental gradients to be studied, while analysis of the site-by-species metacommunity structure informs an understanding of how environmental filtering occurs and whether or not patterns differ from chance expectation. We also used spatial regressions on species richness to identify relevant environmental factors at each scale and to link results from the two approaches.

Major environmental drivers of richness included growing degree-days, temperature, moisture and spatial or temporal heterogeneity. Variance partitioning pointed to an increase in the role of dispersal at coarser resolutions, while metacommunity structure analysis pointed to environmental filtering having an important role at all resolutions through a Clementsian assembly process (i.e. groups of species having similar range boundaries and co-occurring in similar environments).

The combination of methods used here allows a better understanding of the forces structuring ecological communities than either one of them used separately. A key aspect in this complementarity is that variance partitioning can detect effects of dispersal whereas metacommunity structure analysis cannot. Moreover, the latter can distinguish between different forms of environmental filtering (e.g. individualistic versus group species responses to environmental gradients).

We used newly identified fossil specimens to reconstruct the Quaternary distributions of five Microtus species (Rodentia: Arvicolinae) from the Pacific coast of the United States. We used these distributions to test the hypothesis that when projected onto past, alternative climate surfaces, species distribution models (SDMs) created using only climate variables are concordant with the empirical data of fossil Microtus species occurrences.

Specimens from 11 fossil localities in California, Oregon and Nevada were identified and evaluated.

Geometric morphometrics and discriminant analyses were used to identify fossil Microtus specimens. Using a maximum-entropy modelling approach, the best model for all five species was selected using the Akaike information criterion. Nineteen bioclimate variables were used to create SDMs for the five Microtus species using both Community Climate System Model (CCSM) and Model for Interdisciplinary Research on Climate (MIROC) models.

We confidently identified 144 Microtus fossils, including the first fossil specimens of Microtus oregoni and Microtus townsendii. SDMs reconstructed approximately half the extralimital fossil occurrences (i.e. those found outside the present-day range). Those species with extralimital occurrences not reconstructed have niche models primarily influenced by precipitation variables. The two species whose extralimitals were well predicted occupy indistinguishable climatic niches.

The ranges of Pacific coast Microtus species have undergone substantial regional contractions since the Last Glacial Maximum (LGM; 21 ka). Inconsistencies between LGM SDMs and Quaternary fossil ranges indicate potential problems with LGM precipitation reconstructions, although interspecific interactions are also likely to contribute to these differences. Overall, the study highlights the need for further, detailed, species-level palaeodistributions to put recent observations in a broader temporal context and examine the effectiveness of SDMs coupled with climate models for predicting range dynamics under scenarios of climate change.

Previous work on the tidepool copepod Tigriopus californicus revealed a curious case of incipient speciation at the southern end of the species' range in Baja California, Mexico. The present study expands on the geography of this pattern and tests for congruence between reproductive and phylogenetic patterns.

The Pacific coast of North America, from central Baja California to south-eastern Alaska (27–57° N), including the full range of T. californicus.

Primary techniques included mating experiments (> 4000 crosses), phylogeny reconstruction (mitochondrial cytochrome c oxidase subunit I) and screening of single nucleotide polymorphisms (SNPs, 42 loci). Analyses used > 8000 copepods for the mating experiments, 86 copepods for the phylogeny and 41 copepods for the SNP assays. Phylogenies were constructed using Bayesian, maximum likelihood and maximum parsimony methods.

Populations were found to fall into three reproductive groups: northern and southern groups that were reproductively isolated from each other, and an intermediate group that could serve as a conduit for gene flow. The northern and intermediate populations fell into one clade while all southern populations fell into a second clade. These two clades are now separated by less than 12 km at latitude 29.35° N. Nuclear SNP data for a subset of locations confirmed striking divergence between populations on either side of this boundary. The second (southern) clade was further subdivided into two clades separated by the lagoon region of Guerrero Negro (latitude 28° N).

Reproductive assays and molecular data (both mitochondrial and nuclear) reveal a sharp break at 29.35° N, a region with no obvious barriers to dispersal, with no evidence for mixing across this narrow transition zone. Results also showed a milder break at the Guerrero Negro Lagoon (28° N), a location where breaks have been reported for other taxa.

The extent and diversity of invertebrate aerial dispersal both on remote islands and in polar regions has long been of interest to biogeographers. We therefore monitored the airborne dispersal of insects and other micro- and macroinvertebrates to and on Macquarie Island in order to assess (1) the magnitude and composition of local aerial dispersal activity by the island's invertebrate fauna, and (2) the potential for exotic arrival and establishment.

Macquarie Island.

Two robust wind-traps were run year-round on Macquarie Island from 1991 to 1994 to collect airborne insects and other micro- and macroinvertebrates.

More than 3000 invertebrates were caught in these traps over the sampling period in the most comprehensive aerial survey of subantarctic invertebrates to date. Representatives of seven orders of Insecta were captured: Psocoptera, Thysanoptera, Hemiptera, Coleoptera, Diptera, Lepidoptera and Hymenoptera. Other taxa captured included other arthropods (Arachnida and Collembola) but also terrestrial Gastropoda. Evidence of possible long-distance dispersal (LDD) was limited to two exotic catches (one species of Collembolon, and one species of Thysanoptera). The abundance and composition of indigenous invertebrates caught in the traps indicates that the frequency of short-distance dispersal (SDD) movements on the island far exceeds that which had previously been realized.

More than half the total catch (53%) was of flightless (i.e. passively dispersed) invertebrates, with 84% of them flightless in one of the two traps. The extent of passive dispersal movements is consistent, with most invertebrates being widely distributed at a whole-island scale. Aerial dispersal may act as a conduit for non-indigenous arrivals but this occurs infrequently. Other explanations for exotic species in traps are equally likely. The implications of these findings are discussed in relation to terrestrial invertebrate biogeography.

Our aims were to infer the roles of ecology and geology in the adaptive radiation, historical biogeography, and diversification dynamics of the native Hawaiian leafhoppers (Hemiptera: Cicadellidae: Nesophrosyne).

The Hawaiian Archipelago.

A six gene molecular data set for 191 Nesophrosyne species was used to reconstruct relationships in absolute time with relaxed Bayesian methods. Dated phylogenetic hypotheses were used to reconstruct historical biogeography and host plant associations. Phylogenetic clustering methods were implemented to examine the structuring of Nesophrosyne species according to island. Lineage diversification dynamics were inferred using the γ-statistic and birth–death likelihood methods.

Nesophrosyne split from a common ancestor with its sister genus 4.5 million years ago (Ma), with a basal divergence in Hawaii 3.2 Ma. Historical biogeographical reconstructions reveal a Kauai origin for the genus and complex island colonization patterns. Ancestral host plant associations reconstruct Urticaceae and Rubiaceae at the root, with host transitions resulting in host-specific clades. Only species endemic to Kauai are significantly clustered with respect to the whole phylogeny; however, species show significant terminal level clustering for the four main high islands. Diversification rates in Nesophrosyne show an initial burst in net speciation rate with a subsequent decline.

Nesophrosyne colonized the Hawaiian Islands after the formation of Kauai. Host plant arrival times and insect–insect competition may have been important in shaping diversification patterns. The plant families Urticaceae and Rubiaceae played critical roles in the early diversification of Nesophrosyne. Island geography imposed significant barriers to gene flow, leading to extensive allopatric speciation and intra-island diversification. A high initial net speciation rate was associated with host plant transitions, and the formation and establishment of Nesophrosyne on multi-volcano islands (e.g. Oahu and Maui Nui). Net diversification rates exhibit a diversity-dependent decline, corresponding to the end phase of island formation.

Spatial and temporal variations in the composition of freshwater invertebrate assemblages may be useful indicators of past climate change and help us to predict species responses to future climate change. The objective of this study was to understand the relationship between climate variables and fossil Cladocera assemblages in lake sediments along a contemporary climate gradient from hemiboreal to subarctic ecoregions in Finland and throughout the Holocene climate succession.

Seventy-three small shallow lakes across a climate gradient from hemiboreal (60° N) to subarctic (70° N) Finland and a case study lake, Lake Arapisto, in south boreal Finland.

Fossil cladoceran assemblages were analysed from the surface sediments of 73 lakes to investigate their association with climate, using ordination techniques (detrended correspondence analysis and redundancy analysis) and generalized linear modelling (GLM). The long-term variation of the abundance of specific climate-sensitive cladoceran species was then analysed in a sediment core from a boreal lake and compared with a chironomid-based Holocene temperature reconstruction from an adjacent lake.

Mean July air temperature was identified as a significant variable in explaining species distribution across the spatial climate gradient. This result, together with GLMs that recognized several climate-sensitive species, indicates that certain cladoceran taxa may be useful indicators of climate. For example, the planktonic Bosmina longirostris and the phytophilous Graptoleberis testudinaria were more abundant in the warm southern lakes, in contrast to the benthic Alona affinis and Alona intermedia, which were typical for the cold northern lakes. The surface-sediment inferences were supported by the core analysis from Lake Arapisto, because species associated with cold lakes increased in abundance during the cold early Holocene, and species associated with warm lakes thrived during the Holocene Thermal Maximum and Anthropocene.

The spatio-temporal distribution of Cladocera is regulated by regional climate, and therefore the species–climate relationships in space and time can be used to interpret past, present and future distributional patterns under a changing climate.

We assessed the generality of the island rule in a database comprising 1593 populations of insular mammals (439 species, including 63 species of fossil mammals), and tested whether observed patterns differed among taxonomic and functional groups.

Islands world-wide.

We measured museum specimens (fossil mammals) and reviewed the literature to compile a database of insular animal body size (S_i = mean mass of individuals from an insular population divided by that of individuals from an ancestral or mainland population, M). We used linear regressions to investigate the relationship between S_i and M, and ANCOVA to compare trends among taxonomic and functional groups.

S_i was significantly and negatively related to the mass of the ancestral or mainland population across all mammals and within all orders of extant mammals analysed, and across palaeo-insular (considered separately) mammals as well. Insular body size was significantly smaller for bats and insectivores than for the other orders studied here, but significantly larger for mammals that utilized aquatic prey than for those restricted to terrestrial prey.

The island rule appears to be a pervasive pattern, exhibited by mammals from a broad range of orders, functional groups and time periods. There remains, however, much scatter about the general trend; this residual variation may be highly informative as it appears consistent with differences among species, islands and environmental characteristics hypothesized to influence body size evolution in general. The more pronounced gigantism and dwarfism of palaeo-insular mammals, in particular, is consistent with a hypothesis that emphasizes the importance of ecological interactions (time in isolation from mammalian predators and competitors was 0.1 to > 1.0 Myr for palaeo-insular mammals, but < 0.01 Myr for extant populations of insular mammals). While ecological displacement may be a major force driving diversification in body size in high-diversity biotas, ecological release in species-poor biotas often results in the convergence of insular mammals on the size of intermediate but absent species.

Why are some species geographically restricted? Ecological explanations suggest that endemic species may have restricted distributions because limited phenotypic variability results in narrow niches. However, studying variability of traits independently may not fully explain the interactions within and between complex phenotypes and environments. Here, we hypothesize that endemic species are restricted to a narrow range of habitats due to strong phenotypic integration (i.e. strong correlations among traits), strong environmental integration (i.e. strong correlations among the environments occupied) and strong correlations among trait–environment combinations.

The Kerguelen Islands, sub-Antarctic.

We measured flowering phenology, multiple morphological characters, and species distribution along three abiotic environmental gradients (elevation, soil moisture and soil salinity) in 14 plant species whose distributions range from strictly endemic to cosmopolitan.

We found that for individual species, trait means and variances were independent of endemism, but that endemics occupied higher and less variable microhabitats. However, phenotypic integration, environmental integration along the three gradients, and the strength of trait–environment correlations all increased with the level of species endemism.

Higher levels of integration within and between phenotypes and environments are associated with more restricted geographical ranges in the species studied. In endemic species phenotypic integration may explain range contraction during the taxon cycle and reduce the ability to adapt to novel microhabitats formed as a result of environmental change.

To assess statistically the relative importance of climate and human impact on forest composition in the late Holocene.

Estonia, boreonemoral Europe.

Data on forest composition (10 most abundant tree and shrub taxa) for the late Holocene (5100–50 calibrated years before 1950) were derived from 18 pollen records and then transformed into land-cover estimates using the REVEALS vegetation reconstruction model. Human impact was quantified with palaeoecological estimates of openness, frequencies of hemerophilous pollen types (taxa growing in habitats influenced by human activities) and microscopic charcoal particles. Climate data generated with the ECBilt-CLIO-VECODE climate model provided summer and winter temperature data. The modelled data were supported by sedimentary stable oxygen isotope (δ¹⁸O) records. Redundancy analysis (RDA), variation partitioning and linear mixed effects (LME) models were applied for statistical analyses.

Both climate and human impact were statistically significant predictors of forest compositional change during the late Holocene. While climate exerted a dominant influence on forest composition in the beginning of the study period, human impact was the strongest driver of forest composition change in the middle of the study period, c. 4000–2000 years ago, when permanent agriculture became established and expanded. The late Holocene cooling negatively affected populations of nemoral deciduous taxa (Tilia, Corylus, Ulmus, Quercus, Alnus and Fraxinus), allowing boreal taxa (Betula, Salix, Picea and Pinus) to succeed. Whereas human impact has favoured populations of early-successional taxa that colonize abandoned agricultural fields (Betula, Salix, Alnus) or that can grow on less fertile soils (Pinus), it has limited taxa such as Picea that tend to grow on more mesic and fertile soils.

Combining palaeoecological and palaeoclimatological data from multiple sources facilitates quantitative characterization of factors driving forest composition dynamics on millennial time-scales. Our results suggest that in addition to the climatic influence on forest composition, the relative abundance of individual forest taxa has been significantly influenced by human impact over the last four millennia.

Our aims are: (1) to highlight the power of dynamic occupancy models for analysing species range dynamics while accounting for imperfect detection; (2) to emphasize the flexibility to model effects of environmental covariates in the dynamics parameters (extinction and colonization probability); and (3) to illustrate the development of predictive maps of range dynamics by projecting estimated probabilities of occupancy, local extinction and colonization.

Switzerland.

We used data from the Swiss breeding bird survey to model the Swiss range dynamics of the European crossbill (Loxia curvirostra) from 2000 to 2007. Within-season replicate surveys at each 1 km² sample unit allowed us to fit dynamic occupancy models that account for imperfect detection, and thus estimate the following processes underlying the observed range dynamics: local extinction, colonization and detection. For comparison, we also fitted a model variant where detection was assumed to be perfect.

All model parameters were affected by elevation, forest cover and elevation-by-forest cover interactions and exhibited substantial annual variation. Detection probability varied seasonally and among years, highlighting the need for its estimation. Projecting parameter estimates in environmental or geographical space is a powerful means of understanding what the model is telling about covariate relationships. Geographical maps were substantially different between the model where detection was estimated and that where it was not, emphasizing the importance of accounting for imperfect detection in studies of range dynamics, even for high-quality data.

The study of species range dynamics is among the most exciting avenues for species distribution modelling. Dynamic occupancy models offer a robust framework for doing so, by accounting for imperfect detection and directly modelling the effects of covariates on the parameters that govern distributional change. Mapping parameter estimates modelled by spatially indexed covariates is an under-used way to gain insights into dynamic species distributions.

Spatial extent is inherently related to the potential roles of the main mechanisms structuring metacommunities. We examined the effects of varying spatial extent (ecological province, region and subregion) on the environmental and spatial components of variation in lake macrophyte communities. We also studied these effects separately for three macrophyte functional groups.

The US state of Minnesota.

We examined average and heterogeneity differences in macrophyte community composition and environmental variation among the subregions of Minnesota using canonical analysis of principal coordinates (CAP) and homogeneity of multivariate dispersion (PERMDISP), respectively. We further used partial redundancy analysis (pRDA) to decompose variation in macrophyte community composition between environmental variables and spatial location at each spatial extent and geographical region. Spatial variables were derived using principal coordinates of neighbour matrices (PCNM) analysis.

CAP and PERMDISP analyses showed that the subregions differed both in average community composition and in the heterogeneity of community composition for all macrophyte taxa, for emergent and submerged macrophytes, but not for non-rooted macrophytes. We did not, however, find significant differences in overall environmental heterogeneity among the subregions. Variation partitioning using pRDAs showed that species sorting is more important than spatial processes for macrophytes, although these patterns were relatively weak. There was, however, much regional specificity, with the environmental and spatial fractions of community composition varying widely at different spatial extents, among different geographical regions and among functional groups. Contrary to our initial expectations, we did not find increasing spatial structuring and decreasing environmental control with increasing spatial extent.

Our findings indicate that, in macrophyte metacommunities, the relative contribution of spatial processes and environmental control varies rather unpredictably with spatial extent and geographical region. Our findings are thus of importance in advancing metacommunity ecology by showing that drawing wide-ranging conclusions based on a single spatial extent or a single geographical region may be unwise.

Africa is renowned for the current abundance and diversity of its large mammals. The aim of this study was to assess distinctions evident in the functional composition of continental large herbivore faunas during the late Pleistocene before extinctions depleted the megafauna outside Africa.

The African large herbivore fauna was compared with that formerly inhabiting South America, Australia, North America, Eurasia and tropical Asia during the late Pleistocene.

Pleistocene faunas were reconstructed from the literature in terms of their relative body size composition, grazer/browser contributions and taxonomic representations, omitting forest and island species.

Although the three southern continents were closely similar in the overall species richness of large herbivores that they supported during the late Pleistocene, South America had a predominance of very large herbivores, while most of Australia's mammalian herbivores were relatively small and those of Africa were intermediate. Africa had many more grazers, especially in the size range 100–1000 kg, than other continents. The South American pattern resembled that in North America and Eurasia, while Africa and Australia diverged in different ways.

Neither the total extent of savannas in each continent nor the morphological features enabling bovid radiation seemed adequate on their own to explain the greater richness of macrograzers in Africa. Africa is characterized by the widespread occurrence of arid/eutrophic savannas, which are unrepresented in other continents. The prevalence of savanna is partly attributable to the high elevation of interior eastern and southern Africa, associated with relatively low rainfall, and to the comparatively high soil fertility, related to volcanic influences. This promoted an abundance and diversity of medium-sized grazing ruminants unrivalled elsewhere. Indigenous grasses in South America and Australia are less well adapted to withstand severe grazing than the African grasses introduced to support livestock. The locally high abundance of African ungulates presented conditions that facilitated the adaptive transition by early hominins from plant-gatherers to meat-scavengers.

We review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess fine-scale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area of endemism.

The Pilbara region, Western Australia.

Literature is summarized, including the history of Pilbara landscapes and climate, and previous biogeographical work. We used mitochondrial DNA phylogenetic datasets of seven co-distributed gecko (diplodactyline and gekkonine) lineages to assess the monophyly of Pilbara lineages, and concordance with geological and habitat divisions.

The Pilbara harbours taxa genetically distinct from their non-Pilbara relatives, despite close geographical proximity of populations. This is emphasized at the eastern and southern margins of the Pilbara, where habitat gradients are pronounced. In contrast, the northern margin, where sandy substrates of the Pilbara meet the dunes of the northern deserts, exhibits little genetic differentiation. Within the Pilbara, diversification patterns are idiosyncratic and may reflect species-specific ecological differences. However, a repeated north/south partitioning of genetic diversity is evident across taxa. An additional emerging pattern is an east/west genetic division in the northern Pilbara, which may relate to major drainage divides and geological discontinuities associated with east and west Pilbara terrains.

The Pilbara is an area of exceptionally high biotic diversity and endemism. The broader biogeographical patterns revealed in our molecular analyses are consistent with those recently identified using species richness patterns of invertebrates. Future studies of additional taxa using multiple molecular markers will provide the means to test and refine the biogeographical hypotheses presented here. Understanding the biogeography of the Pilbara and the partitioning of genetic diversity across the ancient and heterogeneous landscape is of paramount importance in the face of rapidly expanding economic and developmental pressures.

To determine and compare the taxonomic identity and diversity of root nodule and rhizospheric microbial symbionts associated with Acacia pycnantha Benth. in its native (Australian) and invasive (South African) ranges, and to establish whether these associations are general or host specific.

The native range of A. pycnantha in Australia and invasive ranges in South Africa and Western Australia.

Bacteria were isolated from root nodules collected from 18 populations of A. pycnantha. Repetitive element polymerase chain reaction (REP-PCR) fingerprinting was used to assess overall bacterial diversity and clustering. Molecular phylogenies for a subset of isolates representing major REP-PCR clades were reconstructed using maximum parsimony and Bayesian phylogenetic analyses of the nuclear 16S–23S rRNA intergenic spacer (IGS), 16S rRNA, and the symbiotic nodA genes.

Twelve clusters were identified from the REP-PCR analysis; 11 included isolates from both the native range in Australia and invasive range in South Africa, while one cluster comprised only Australian isolates. Six rhizobial species were found in association with A. pycnantha: Bradyrhizobium japonicum, Rhizobium gallicum, R. lusitanum, R. miluonense, R. multihospitium and R. tropici. We also identified three plant-growth promoting bacteria isolated from root nodules of A. pycnantha: Burkholderia caledonica, B. graminis and B. phytofirmans. Phylogenetic analysis of the IGS gene retrieved clades containing symbionts from both Australia and South Africa while others comprised only South African taxa, suggesting the introduction of bacterial lineages from Australia to South Africa. Our phylogeographic analysis of the nodA gene confirmed that A. pycnantha was co-introduced with its symbionts to South Africa.

Acacia pycnantha is a promiscuous legume, associated with at least six different rhizobial symbionts, and forms associations with plant-growth promoting rhizosphere bacteria from the genus Burkholderia. In the invasive range of A. pycnantha in South Africa, nodules contained some symbionts of South African origin while other symbionts appear to have been co-introduced from Australia. Acacia pycnantha is associated with a wider suite of symbionts in its invasive than native range.

Our study aimed to identify and explore the main factors that influence tree recruitment of multiple species at a regional scale across peninsular Spain, an understanding of which is essential for predicting future forest species composition in the face of ongoing environmental change. The study focused on the dynamics of the key transition phase from saplings to adult trees.

The forests of peninsular Spain.

We used the extensive network of plots sampled in two consecutive Spanish national forest inventories (> 30,000 plots) to identify the factors that determine regeneration patterns of the 10 most abundant forest species of Spain at relatively large temporal (c. 10 years) and spatial scales (across Spain): five coniferous species of Pinus (pines) and five broadleaved species of the genera Fagus and Quercus. We fitted separate generalized linear models for the pine species and the broadleaved species to assess the response of sapling abundance and ingrowth rate to the spatial variability of climate (temperature, water availability and recent warming), forest structure (tree density, understorey and overstorey canopy cover, and basal area change) and disturbances (previous forest logging, wildfires and grazing).

Mean sapling abundance was four times higher for broadleaved species than for pines, while mean annual ingrowth was twice as high. Sapling abundance and ingrowth rate were mainly determined by stand structure, both in pines and broadleaved trees. The direct effects of disturbances and climate were comparatively smaller, and there was no detectable effect of recent warming.

The higher values of ingrowth rate of broadleaved species can be explained by their ability to maintain a higher sapling bank due to their greater shade tolerance. This differential response of pines and broadleaved species to canopy closure suggests a probable increase in broadleaved species at the expense of pines. This transition could occur earlier in stands with faster canopy closure dynamics. Spatially explicit, mixed-species demographic models incorporating both the ingrowth and the tree mortality components are needed for predicting the composition of future forests.

Various coral reef organisms display distinct gradients in taxonomic turnover throughout the tropical Pacific Ocean. Marine macrophytes are one of the most dominant and ecologically important benthic components of tropical reefs, yet little is known about the ecological biogeography of the macrophyte assemblages throughout this biodiverse region. This study assessed: (1) the geographical clustering of macrophyte assemblages in the tropical Pacific; (2) the environmental/geographical factors that best explain the observed patterns in taxon richness and taxon composition; and (3) the validity of large-scale biogeographical hypotheses with respect to the distribution of macrophyte assemblages.

Coral reefs of 39 US Pacific islands.

Surveys of reef macrophytes for all 39 Pacific islands were conducted from 2004 to 2007. Rank-order data of quadrats were transformed to proportional abundance data in order to compute site averages for each of the 84 macrophyte categories. Further data analysis employed taxon accumulation curves, generalized additive models, and multivariate techniques.

Pacific macrophyte assemblages displayed consistently higher within-archipelago similarities than between-archipelago similarities, which is reflected in pronounced differences in functional group composition between archipelagos. The maximum land elevation, maximum seasonal sea surface temperature, reef extent, and longitude of the investigated islands were the predictor variables that best described the similarities in macrophyte assemblage structure among islands. Maximum land elevation and reef extent, however, were the two predictor variables that best explained macrophyte richness per island.

Macrophyte assemblages of the Pacific Islands cluster in geographical groups, indicative of the importance of evolutionary factors related to dispersal and speciation. Whereas macrophyte assemblage structure is governed by both local (habitat diversity and availability) and regional (geographical and environmental descriptors related to oceanic isolation and latitude) variables, the macrophyte richness of these islands is defined primarily by local habitat diversity and availability. Biogeographical patterns of marine macrophyte assemblages in the tropical Pacific deviate from those of other well-studied marine organisms.

It is hypothesized that the ecological niches of polyploids should be both distinct and broader than those of diploids – characteristics that might have allowed the successful colonization of open habitats by polyploids during the Pleistocene glacial cycles. Here, we test these hypotheses by quantifying and comparing the ecological niches and niche breadths of a group of European primroses.

Europe.

We gathered georeferenced data of four related species in Primula sect. Aleuritia at different ploidy levels (diploid, tetraploid, hexaploid and octoploid) and used seven bioclimatic variables to quantify niche overlap between species by applying a series of univariate and multivariate analyses combined with modelling techniques. We also employed permutation-based tests to evaluate niche similarity between the four species. Niche breadth for each species was evaluated both in the multivariate environmental space and in geographical space.

The four species differed significantly from each other in mono-dimensional comparisons of climatological variables and occupied distinct habitats in the multi-dimensional environmental space. The majority of the permutation-based tests either indicated that the four species differed significantly in their habitat preferences and ecological niches or did not support significant niche similarity. Furthermore, our results revealed narrower niche breadths and geographical ranges in species of P. sect. Aleuritia at higher ploidy levels.

The detected ecological differentiation between the four species of P. sect. Aleuritia at different ploidy levels is consistent with the hypothesis that polyploids occupy distinct ecological niches that differ from those of their diploid relative. Contrary to expectations, we find that polyploid species of P. sect. Aleuritia occupy narrower environmental and geographical spaces than their diploid relative. These results on the ecological niches of closely related polyploid and diploid species highlight factors that potentially contribute to the evolution and distribution of polyploid species.

The relationship between changes in body form (limb reduction and body elongation) and geographical range size was investigated across 68 species of Lerista, a species-rich clade of Australian scincid lizards that exhibits extensive interspecific variability in both body form and range size.

Lerista occurs across the entire Australian mainland, with diversity concentrated in arid and semi-arid regions.

Geographical range size was estimated directly from c. 14,000 museum specimens using bioclimatic modelling in MaxEnt. Body form was quantified using principal components analysis of morphometric variables. Comparative analyses testing for a correlation between these two variables used a full Bayesian approach that accounts for uncertainties in trait optimization as well as in tree topology and branch lengths.

A serpentine body form (elongated with reduced limbs) was significantly associated with smaller geographical range size, in both phylogenetically corrected and uncorrected analyses – but only if species from single localities (whose ranges could not be modelled using the above methods) were excluded.

These results suggest a general predictive relationship between body form and geographical range size in lizards: elongate, limb-reduced lizards tend to exhibit more restricted geographical ranges that may reflect reduced dispersal ability and may also predispose them to greater vulnerability of extinction.

As data accumulate, a multi-taxon biogeographical synthesis of the Mojave Desert is beginning to emerge. The initial synthesis, which we call the ‘Mojave Assembly Model’, was predominantly based on comparisons of phylogeographical patterns from vertebrate taxa. We tested the predictions of this model by examining the phylogeographical history of Hadrurus arizonensis, a large scorpion from the Mojave and Sonoran deserts.

Mojave and Sonoran deserts, United States and Mexico.

We sequenced mitochondrial cytochrome c oxidase subunit I (COI) data from 256 samples collected throughout the range of H. arizonensis. We analysed sequence data using a network analysis, spatial analysis of molecular variance (SAMOVA), and a Mantel test. We then used a molecular clock to place the genetic patterns in a temporal framework. We tested for signals of expansion using neutrality tests, mismatch distributions and Bayesian skyline plots. We used Maxent to develop current and late-glacial species distribution models from occurrence records and bioclimatic variables.

Phylogenetic and structure analyses split the maternal genealogy basally into a southern clade along the coast of Sonora and a northern clade that includes six lineages distributed in the Mojave Desert and northern Sonoran Desert. Molecular dating suggested that the main clades diverged between the late Pliocene and early Pleistocene, whereas subsequent divergences between lineages occurred in the middle and late Pleistocene. Species distribution models predicted that the distribution of suitable climate was reduced and fragmented during the Last Glacial Maximum.

Genetic analyses and species distribution modelling suggest that the genetic diversity within H. arizonensis was predominantly structured by Pleistocene climate cycles. These results are generally consistent with the predictions of Pleistocene refugia for arid-adapted taxa described in the Mojave Assembly Model, but suggest that a northern area of the Lower Colorado River Valley may have acted as an additional refugium during Pleistocene glacial cycles.

Niche modelling is increasingly used to predict species' geographical distributions or to infer the evolutionary or ecological processes that constrain them, but relatively few studies have examined the ecological processes governing the distributions of parasites. Among such processes, niche divergence is frequently invoked to explain species range variation. Here, we test whether the geographical distributions of two lineages of Leucocytozoon (Haemosporida) avian parasites are linked to climatic conditions and whether niche divergence can explain their geographical separation.

Réunion, Mascarene archipelago, south-western Indian Ocean.

Leucocytozoon prevalence data were obtained by PCR screening of avian blood samples. Prevalence data and 20 environmental layers were used to build species distribution models (SDMs). SDMs were built by averaging the predictions of five different models: random forests (RF), generalized linear models (GLM), generalized additive models (GAM), multivariate adaptive regression splines (MARS) and support vector machines (SVM). Niche identity and background tests were used to test for a role of niche divergence in explaining parasite distributions.

The geographical ranges of the two lineages of Leucocytozoon under study showed little overlap. Species distribution modelling suggested that niche divergence may explain the spatial variation observed in Leucocytozoon distribution, implying that the geographical separation of parasites is linked to environmental conditions. The variables that best explained parasite distribution were all related to precipitation patterns.

As precipitation cannot directly affect endosymbiotic Leucocytozoon parasites, we suggest that the geographical separation of Leucocytozoon lineages is the result of an underlying geographical structure in the dipteran vectors that transmit these parasites. This illustrates the need to consider the ecology of vectors when predicting the distribution of vector-borne parasites. Our study also shows that different parasite lineages, contained within broadly defined parasitic taxa, may have very different ecologies, and that these differences should be taken into account when attempting to understand the ecological determinants of parasite distribution and disease emergence.

To analyse spatial and temporal patterns of dispersal events in the euapioids (Apiaceae subfamily Apioideae).

Worldwide, with an emphasis on the Northern Hemisphere.

A phylogeny of euapioids was inferred from 1194 nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) sequences using Bayesian methods. The reconstruction of ancestral areas was performed simultaneously with phylogenetic inference using a Markov discrete phylogeographical model with Bayesian stochastic search variable selection (BSSVS). Routes with significant non-zero migration rates were identified using Bayes factors. For each significant track and each tree, the distribution of dispersals in time was scored and the asymmetry of dispersals was evaluated.

The root of the euapioid umbellifers was reconstructed at c. 44.51 Ma (95% highest posterior density interval: 39.11–51.55 Ma). The Eastern Asiatic Region was reconstructed as the most probable ancestral area for the root of the tree. Seventeen migration routes have significant non-zero migration rates. Five of these tracks represent long-distance transoceanic routes: (1) western Eurasia–North America, (2) Eastern Asiatic Region–North America, (3) Australia–Neotropical Kingdom, (4) Australia–Neantarctic, and (5) Neotropical Kingdom–sub-Saharan Africa. Most dispersal events occurred among the areas that comprise the major diversification centres of apioid umbellifers: western Eurasia and the Mediterranean, Irano-Turanian and Eastern Asiatic regions. The floristic exchange among these regions was more or less symmetrical in all directions and continuous in time. The exchange between North America and the Eastern Asiatic Region was asymmetrical; the asymmetry of dispersals between western Eurasia and North America was less pronounced and not statistically significant. Floristic exchange was significantly asymmetrical for the Nearctic–Neotropical Kingdom, Nearctic–Neantarctic, western Eurasia–sub-Saharan Africa, and western Eurasia–Siberia migration tracks.

The observed dispersal pattern – intense and symmetrical within the same climatic zone versus scarce and often unidirectional between climatic zones or along long-distance transoceanic tracks – suggests that both the availability of suitable habitats and geographical barriers have played crucial roles in determining the present distribution of euapioid umbellifers.

Our aims were to determine the pattern of genetic variation in the endemic shrub Nolina parviflora, and to evaluate the influence of the geological history of the Trans-Mexican Volcanic Belt (TMVB) and nearby mountainous regions on plant population divergence.

Trans-Mexican Volcanic Belt, Sierra Madre Occidental, Sierra Madre Oriental and Sierra Madre del Sur mountain ranges in Mexico.

Twenty-eight populations (210 individuals) were sequenced for one nuclear (rpb2) and two chloroplast (trnL–F and psbA–trnH) DNA markers. Intraspecific phylogenetic relationships among haplotypes were reconstructed, and molecular dating, population genetic analyses and group testing were performed on the data. Isolation-by-distance analysis was conducted for the populations spanning the distribution of the species.

Twenty-four chloroplast marker haplotypes and 36 rpb2 haplotypes were recovered from the populations sampled. The combined marker phylogeny indicates the presence of two well-supported clades within the N. parviflora populations. Clade 1 includes populations from Jalisco and Zacatecas and Clade 2 comprises the remaining populations. We found an east–west geographical pattern of chloroplast DNA (cpDNA) haplotype distribution, indicating a lack of gene flow between these two regions. Divergence time estimates indicate an Oligocene to mid-Miocene divergence between Nolina and Dasylirion. Divergence estimates for Clade 1 are from the mid-Miocene to early Pleistocene, and for Clade 2 from the early Miocene to mid-Pliocene. Values of cpDNA G_ST (0.702) indicate a strong population structure and differentiation. A spatial analysis of molecular variance indicates 11 groups among the sampled populations and detects various well-supported geographical barriers.

Divergence time estimates suggest a correlation between the time of divergence between distinct N. parviflora populations and periods of uplift in the TMVB. We infer that the orogeny of this mountain range played an important role in driving the diversification of plant populations in central Mexico by creating topographical barriers that limited gene flow.

We test three alternative hypotheses for the disjunct Mediterranean–southern African distribution of endophagous weevils within the genera Rhinusa and Gymnetron (Coleoptera: Curculionidae): (1) a Palaearctic origin with dispersal to southern Africa; (2) a southern African origin with dispersal to the Palaearctic; and (3) a widespread ancestral distribution fragmented by vicariance. Divergence times are estimated to provide an approximate temporal framework for the evolution of the group and to evaluate potential palaeogeographical scenarios.

Southern Africa, the Mediterranean region, the Palaearctic and eastern Africa.

Freshly collected and dry, pinned samples of weevils were used as a source of DNA. Prior genetic information was used to identify short phylogenetically informative amplicons within the 16S ribosomal RNA gene (16S). Phylogenetic reconstructions using Bayesian and maximum likelihood analyses of mitochondrial and nuclear DNA sequence data and molecular dating techniques were used to infer the biogeographical history of Rhinusa and Gymnetron species. A statistical approach to dispersal–vicariance analysis (s-diva) was used to further assess biogeographical hypotheses.

Successful polymerase chain reaction amplification of targeted short 16S DNA sequences (150 bp) from dry, pinned specimens provided for increased species sampling of Rhinusa and Gymnetron by 230%, greatly expanding species representation from southern Africa. Phylogenetic reconstructions and s-diva analyses support a southern African origin for Rhinusa and Gymnetron species. Divergence time estimates suggest southern African and Palaearctic lineages diverged c. 11.6–7.4 Ma.

Rhinusa and Gymnetron represent a complex of lineages with a shared evolutionary history of range expansions from southern Africa into the Palaearctic. Our results support a late Miocene vicariance scenario, most likely as a result of repeated desertification. The use of prior genetic information to identify short phylogenetically informative amplicons offers a useful approach for molecular phylogenetic analyses incorporating archival material.

We test whether populations of the Mesoamerican azure-crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification.

Mexico.

We sequenced the mitochondrial ATPase-6 and ATPase-8 genes and the control region of 130 individuals collected throughout the range of the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed.

The data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300–75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent-based test indicated that selection is driving the observed morphological differentiation.

Our findings implicate the Isthmus of Tehuantepec as a permeable barrier driving recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent-based test, suggest that selection has been strong enough to counteract the effects of gene flow.

Biogeographical patterns within three classes, the Echinoidea, Bivalvia and Gastropoda, were investigated in Antarctic, sub-Antarctic and cold-temperate areas based on species occurrence data. Faunal similarities among regions were analysed to: (1) test the robustness of the biogeographical patterns previously identified in bivalves and gastropods; (2) compare them with the biogeographical patterns identified for echinoids; and (3) evaluate the reliability of the biogeographical provinces previously proposed, depending on the taxa and taxonomic levels analysed.

The Southern Ocean, sub-Antarctic islands and cold-temperate areas south of 45° S latitude at depths of < 1000 m.

Taxonomic similarities among 14 bioregions were analysed using a non-hierarchical clustering method, the bootstrapped spanning network (BSN) procedure. Taxonomic similarities were analysed within the three classes at species and genus levels.

The previously identified large-scale biogeographical entities are clarified. Echinoid and bivalve faunas are structured mainly according to three faunal provinces: (1) New Zealand, (2) southern South America and sub-Antarctic islands, and (3) Antarctica. Gastropod faunas group into five provinces: (1) New Zealand, (2) southern South America, (3) east sub-Antarctic islands, (4) West Antarctica, and (5) East Antarctica. Strong faunal relationships between bioregions perfectly match the flows of the Antarctic Circumpolar and Antarctic Coastal currents. Moreover, the legacy of the climatic and palaeoceanographic history of Antarctica is revealed by trans-Antarctic faunal affinities, thereby strongly supporting hypotheses of past marine seaways that would have connected both the Amundsen–Bellingshausen area to the Weddell Sea and the Weddell Sea to the Ross Sea.

A significant advantage of the BSN procedure lies in the possibility of identifying both biogeographical groupings and transitional areas; that is, both strong connections and groupings between bioregions. The method has also proved to be efficient for identifying potential faunal exchange pathways and dispersal routes, both present and past, by fitting networks to oceanographic and palaeogeographical maps.

Phylogeographical ‘breaks’ often occur at biogeographical province boundaries, suggesting common causative factors. Cape Hatteras, North Carolina, on the US Atlantic coast, separates water masses of sharply differing temperature and divides the Virginian and Carolinian provinces, but has not often been detected as a phylogeographical break. We studied the black sea bass, Centropristis striata (Linnaeus, 1758), a species with philopatric adults but long-lived planktonic larvae. An earlier study of only two Atlantic populations, and lower-resolution mitochondrial RFLP markers, showed strong separation between the Gulf of Mexico and the Atlantic, but not across Cape Hatteras.

Over 300 adults were collected from populations from the Gulf of Mexico, the US south Atlantic (North Carolina south of Cape Hatteras, the east coast of Florida, and South Carolina), and the US mid-Atlantic (North Carolina north of Cape Hatteras, Virginia, Delaware, New Jersey and Massachusetts).

We sequenced the mitochondrial control region, analysed DNA sequence and haplotype frequency differentiation and haplotype networks, and performed coalescent analyses of population sizes and migration rates.

Sequences formed three clusters – Gulf of Mexico, south Atlantic and mid-Atlantic – the Atlantic clusters being divided at Cape Hatteras. Analyses of molecular variance (AMOVA) showed that 31% of sequence variation was between populations on opposite sides of Cape Hatteras, while only 5% was between populations on the same side, yet migrate analysis detected asymmetric migration across the Cape, greater from north to south than in the opposite direction. A transitional population with roughly equal frequencies of south and mid-Atlantic haplotypes occupied a narrow stretch between Cape Hatteras and the Virginia border.

Strong barriers to gene flow exist between the Gulf of Mexico and the Atlantic, and across Cape Hatteras. Adult migratory and spawning behaviours that separate mid-Atlantic and south Atlantic populations, limited larval exchange, and selection imposed by thermal gradients are each potentially responsible. In addition, these data indicate that fishery stocks of black sea bass north and south of Cape Hatteras are genetically distinct, supporting their separate management.

A river hierarchy model has been proposed for stream-dwelling taxa, where genetic structure is expected to reflect geographical proximity and connectivity of river systems. However, many exceptions and deviations from this model have been detected. The present study tested three biogeographical hypotheses (River Hierarchy, Palaeoriver Systems and Interdrainage Dispersal) to assess how a recently identified galaxiid, Galaxias sp. ‘nebula’, came to have a wide distribution across multiple currently isolated river systems in the Cape Floristic Region of South Africa.

Seventeen river systems in the Cape Floristic Region at the southern tip of Africa.

We analysed mitochondrial cytochrome c oxidase subunit I and cytochrome b sequences from across the entire distribution of Galaxias sp. ‘nebula’ and compared divergence times between populations with known geological and climatic events to explain the observed geographical patterns of genetic diversity.

The data revealed historical divergence between the Olifants, Berg and southward-draining river systems. The phylogeographical analyses revealed that range expansion occurred across currently isolated river systems, with some haplotypes being shared between geographically distant river systems. Molecular dating revealed recent divergence times between populations from isolated river systems (c. 4000–1,200,000 years ago).

The phylogeographical pattern of Galaxias sp. ‘nebula’ indicates that drainage basin boundaries have historically not played a dominant long-term role in structuring this lineage. River captures are not widespread and frequent enough to explain the observed genetic patterns. Galaxias sp. ‘nebula’ has been able to disperse between proposed palaeoriver systems. Interdrainage dispersal via episodic freshwater connections during periods of increased rainfall during the Pleistocene and Holocene epochs seems to have played an important role in allowing this lineage to attain and maintain its wide contemporary distribution.