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In this first of three papers we examine the use of niche concepts in ecology and especially in species distribution modelling ( SDM). This paper deliberately focuses on the lack of clarity found in the term 'niche'. Because its meanings are so diverse, the term niche tends to create confusion and requires constant qualification. The literature houses many idiosyncratic ideas of what the niche is, but few examples where niche is more explanatory than the terminologies of population and community ecology or the statistical methods used to implement SDM analyses. In many cases the original (and inspirational) concepts are not directly applicable to our modern applications (e.g. set theory). There are some conceptual limitations found in individual definitions of niche (e.g. the fundamental niche concept), so it is perhaps understandable why more neutral terminology is becoming popular in SDM. An examination of the literature reveals a wide range of uncritical use of niche terminology. Our findings in this paper do not necessarily support the position of niche as a universally useful concept. [ABSTRACT FROM AUTHOR]

The article focuses on the species-area relationship (SAR). It says that SAR is a essentially important pattern in the ecology along with the understanding of the processes that mold the form taken by every type of SAR that are important for both the conservation biogeography and ecological biogeography. It states that most considered type of SAR is whether the cumulative totals are calculated throughout a set of areas or whether the actual number of species are discovered in every area.

In their recent paper published in Science (2016, 351, 1437-1439), Chan et al. analysed 137 montane gradients, concluding that they found a novel pattern-a negative relationship between mean elevational range size of species and daily temperature variation, which was claimed as empirical evidence for a novel macrophysiological principle (Gilchrist's hypothesis). This intriguing possibility was their key conceptual contribution. Unfortunately, as we show, the empirical evidence was flawed because of errors in the analyses and substantial sampling bias in the data. First, we re-ran their analyses using their data, finding that their model should have been rejected. Second, we performed two additional re-analyses of their data, addressing biases and pseudoreplication in different ways, both times again rejecting the evidence claimed to support Gilchrist's hypothesis. These results overturn the key empirical findings of Chan et al.'s study. Therefore, the 'macrophysiological principle' should be regarded as currently remaining unsupported by empirical evidence. [ABSTRACT FROM AUTHOR]

Until recently, the high degree of diversity and endemism of the Guayana Highlands was explained within the frame of the refuge theory. Although this hypothesis is unsupported by recent palaeoecological evidence, no new diversification model has been proposed. This paper is a proposal based on the latest palynological findings that indicate a downward biotic migration ofc.1100 m altitude during glacials, and the subsequent interglacial upward shift, in response to colder and warmer climates, respectively. Therefore, during glacials, biotic mixing is expected in the lowlands, thus promoting sympatric speciation, hybridization and polyploidy. At the mountaintops, unknown cold-adapted taxa and páramo-like(?) communities are expected to have occurred, and vicariance prevailed. In the interglacials, many taxa have had the opportunity for ascending to the mountains again, allowing genetic interchange among their slopes and summits, while others would have been adapted to lowlands. The interglacial highland communities, where vicariance still predominated, experienced some extinction owing to habitat loss by upland displacement. According to this model, the successive alternation of glacials and interglacials resulted in a net increase of diversity and endemism, favoured by the complex topography and habitat heterogeneity, which allowed high niche diversification. This model has some similarities with the Andean and Amazon modes of diversification, but the special topographical characteristics of the Guayana region made it different in other fundamental aspects. The Guayana Highlands would have acted as a‘biodiversity pump’ for the surrounding inner and coastal lowlands, due to the repeated speciation and further spreading events, as a response to climate. Several working hypotheses are suggested in relation to the proposed model. The use of coordinated international multiproxy projects combining palaeoecology and genetic analysis of modern taxa is strongly encouraged for exploring these ideas. [ABSTRACT FROM AUTHOR]

Abstract Aim This paper reviews possible candidate models that may be used in theoretical modelling and empirical studies of species–area relationships (SARs). The SAR is an important and well-proven tool in ecology. The power and the exponential functions are by far the models that are best known and most frequently applied to species–area data, but they might not be the most appropriate. Recent work indicates that the shape of species–area curves in arithmetic space is often not convex but sigmoid and also has an upper asymptote. Methods Characteristics of six convex and eight sigmoid models are discussed and interpretations of different parameters summarized. The convex models include the power, exponential, Monod, negative exponential, asymptotic regression and rational functions, and the sigmoid models include the logistic, Gompertz, extreme value, Morgan–Mercer–Flodin, Hill, Michaelis–Menten, Lomolino and Chapman–Richards functions plus the cumulative Weibull and beta-P distributions. Conclusions There are two main types of species–area curves: sample curves that are inherently convex and isolate curves, which are sigmoid. Both types may have an upper asymptote. A few have attempted to fit convex asymptotic and/or sigmoid models to species–area data instead of the power or exponential models. Some of these or other models reviewed in this paper should be useful, especially if species–area models are to be based more on biological processes and patterns in nature than mere curve fitting. The negative exponential function is an example of a convex model and the cumulative Weibull distribution an example of a sigmoid model that should prove useful. A location parameter may be added to these two and some of the other models to simulate absolute minimum area requirements. [ABSTRACT FROM AUTHOR]

Aim This paper has as its central aim the location of centres of species richness and endemism in the sub-Saharan African flora. Previous postulation of these centres has been based on an intuitive interpretation of distributional data; this paper provides a test of these centres. A second aim is to establish whether the two indices, richness and endemism, locate the same centres. Thirdly the relationship between species richness and endemism, and latitude and rainfall are explored. Location The study area includes much of sub-Saharan Africa, but excludes the species-poor southern margin of the Sahara and the Namib–Kalahari regions. Methods Analyses were based on 1818 species, scored on a 2.5 × 2.5 degree grid. Species richness was inferred from a simple grid-diversity count; endemism was determined by three measures: the number of species restricted to two grids, the sum of the inverse of the ranges of the component species of each grid, and the proportion of the species in each grid that have restricted ranges. Results The African flora shows a remarkably profound patterning, both in species richness and endemism. The two measures locate largely the same centres, although the rank order among them differs. These centres are: the Cape Floristic Region, East Coast, Congo-Zambezi watershed, Kivu, Upper and Lower Guinea. Richness is strongly related to maximum rainfall, but there are no obvious correlations between modern climate and endemism. Species richness and endemism north of the equator is much more concentrated into centres than south of the equator. Main conclusions There are strongly developed refugia in sub-Saharan Africa. North of the equator, these refugia are sharply delimited and rather small, separated by large areas of very low endemism. South of the equator endemism tends to be more generally distributed. Variation in species richness in sub-Saharan Africa can be explained largely by modern rainfall, while endemism may be related to palaeoclimatic fluctuations. Both species richness and endemism show a strong skewing towards the south, indicating that the fluctuations in the Sahara might have influenced the modern distribution of plants in Africa. [ABSTRACT FROM AUTHOR]

In a recent article (Dormann et al., 2012, Journal of Biogeography, 39, 2119-2131), we compared different approaches to species distribution modelling and depicted modelling approaches along an axis from purely 'correlative' to 'forward process-based' models. In their correspondence, Kriticos et al. (2013, Journal of Biogeography, doi:) challenge this view, claiming that our continuum representation neglects differences among models and does not consider the ability of fitted process-based models to combine the advantages of both process-based and correlative modelling approaches. Here we clarify that the continuum view resulted from recognition of the manifold differences between models. We also reinforce the point that the current trend towards combining different modelling approaches may lead not only to the desired combination of the advantages but also to the accumulation of the disadvantages of those approaches. This point has not been made sufficiently clear previously. [ABSTRACT FROM AUTHOR]

The discovery of new species of mammals in Europe is a rare event, but owing to recent progress in genetic methods used to survey current biodiversity, such discoveries have been accumulating during the last decades. The naming of these new taxa has important bearings in conservation, as this is the first step needed for them to be recognised by the scientific community but also legally. The naming of new animal species, however, needs to follow the strict rules of the International Code of Zoological Nomenclature in order to be available and to provide a stable basis for further taxonomic research. We report here a case where new names have been improperly proposed to designate distinctive lineages in the Natterer's bat species complex. As these new names do not follow several mandatory rules imposed by the Code, they are declared unavailable and are not to be used for further taxonomy studies. [ABSTRACT FROM AUTHOR]

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an 'ultimate goal of the niche' by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word 'niche'. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling. [ABSTRACT FROM AUTHOR]

By over-focusing on precise definitions, ecology has produced a confused idea of the niche concept. This, our second paper, develops a practical philosophy for the niche that approaches the concept at the correct level of abstraction. We deconstruct the niche into effect and response components and then reconstruct those parts into a general, visual schematic of the niche and ecology. Using this schematic we examine the relationship of particular niche ideas to ecology, and examine the relationship between niche and ecological sub-disciplines, particularly species distribution modelling ( SDM). This general description clarifies the duality of the niche concept, as both a facet of species and a facet of environments. Unclear use of these dual concepts can confuse the scientific approach, and our ideas about uncertainty and error. By misclassifying models as concepts, ecology has confused the niche. Our practical philosophy uses the current wealth of ecological and niche ideas as a panoramic view of a general niche concept. We argue that stitching the niche produces a concept that underpins straightforward ecological thinking. [ABSTRACT FROM AUTHOR]

Aim This paper has three aims: (1) to reconstruct the population history of a flightless silvicolous (forest) ground beetle in a region where strong anthropogenic activity has altered the connectivity of the landscape; (2) to estimate the effects of both contemporary and historical landscape structure on the genetics of populations; and (3) to investigate the reasons for clinal variation in one gene locus found in an earlier study carried out in the same geographical location. Location Münster (Westphalia), north-west Germany. Methods We investigated 26 populations of the ground beetle Carabus auronitens Fabricius, 1792 by analysing seven polymorphic microsatellite loci and an allozyme locus. Samples of at least 16 individuals per site were studied. These were obtained from dry pitfall traps placed at 23 sites and from three additional (refuge) populations. We used regression and correlation analyses to investigate the effects of both historical and contemporary landscape structure on the allele frequency distributions of the investigated loci. Spatial autocorrelation analysis was used to study possible clinal variations, and admixture rates were calculated in order to assess the genetic influence of populations from possible refuges. Possible reasons for the development of the cline were examined using simulation models. Results The allele frequency distributions at the investigated loci could not be explained by selection or isolation by distance. We found clinal variation in 50% of the investigated loci and our simulations indicated that this was unlikely to have developed by chance. Admixture rates show significant influences of the investigated refuge populations on the populations under study. Main conclusions The findings strongly suggest that the clinal variation is secondary. It results from recolonization of the area by C. auronitens from multiple refuges after anthropogenic landscape changes caused forest fragmentation and led to species isolation. [ABSTRACT FROM AUTHOR]

Aim This paper uses null model analysis to explore the pattern of species co-occurrence of terrestrial vertebrate fauna in fire-prone, mixed evergreen oak woodlands. Location The Erico–Quercion ilicis of the Mediterranean belt (50–800 m a.s.l.) in the Madonie mountain range, a regional park in northern Sicily (37°50′ N, 14°05′ E), Italy. Methods The stratified sampling of vertebrates in a secondary succession of recent burned areas (BA, 1–2 years old), intermediate burned areas (INT, 4–10 years old) and ancient burned areas (CNB, > 50 years old), plus forest fragments left within burned areas (FF, 1–2 years old) permitted the comparison of patterns of species co-occurrence using a set of separate presence/absence matrices. First, the breeding avifauna derived from standardized point counts was analysed using Stone & Roberts’ C-score, and by a null model algorithm (fixed/equiprobable). Secondly, the analysis was repeated using all vertebrate species recorded in the succession. Results Sixty-five species were recorded in the 2-year study period in the four sample treatments. Birds were found to make up the largest component (63%) of the recorded assemblage. The BA treatment had the lowest species richness, followed in order by the small, medium and large FFs, and then by the CNBs. For both analyses (birds and total vertebrates), the C-scores were quite small and not significantly different from those that could be expected by chance in the BA and INT burned areas; this indicates a random co-occurrence among vertebrates of those assemblages. Contrariwise, for both analyses in the CNBs, the C-scores were large and significantly different from the simulated indices, thereby indicating a non-random co-occurrence pattern (segregation) of vertebrates in the undisturbed woodlands. In addition, C-score values for the surviving FFs show a significant aggregation of species. Main conclusions The null model analyses highlighted a new aspect of fire disturbance in Mediterranean woodland ecosystems: the disruption in patterns of co-occurrence in the terrestrial vertebrate community. Wildfire alters community organization, inducing, for at least 10 years, a random aggregate of species. Communities re-assemble themselves, showing the occurrence of species segregation at least 50 years after fire. [ABSTRACT FROM AUTHOR]

Aim The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods The range-wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer programtcs. Nested clade analysis was conducted with the computer programceodis, and various parameters of genetic diversity were calculated and neutrality tested by the computer program DnaSP. Population differentiation was estimated using the programsarlequin andhapstep. The contribution of the populations to gene diversity and to allelic richness was calculated using the softwarecontrib. The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise FST for each population against the rest of the populations. Results Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low-temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north-central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean FST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north-central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern-edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes. [ABSTRACT FROM AUTHOR]

Aim This paper has two objectives. First, we examine how a variety of biotic, abiotic and anthropogenic factors influence the endemic and introduced arthropod richness on an oceanic island. Second, we look at the relationship between the endemic and introduced arthropod richness, to ask whether areas with high levels of endemic species richness deter invasions. Location The work was carried out on a young volcanic island, Terceira, in the Azores. Methods We used standard techniques to collect data on arthropod species richness. Environmental data were obtained from the CIELO climatic model and using GIS. The explanatory value of environmental variables on a small-scale gradient of endemic and exotic arthropod species richness was examined with generalized linear models (GLMs). In addition, the impact of both endemic and exotic species richness in the communities was assessed by entering them after the environmental variable(s) to see if they contributed significantly to the final model (the hierarchical method). Results Abiotic (climatic and geomorphological) variables gave a better explanation of the variation in endemic species richness, whereas anthropogenic variables explained most of the variation in introduced species richness. Furthermore, after accounting for all environmental variables, part of the unexplained variance in the endemic species richness is explained by the introduced species richness and vice-versa. That is, areas with high levels of endemic species richness had many introduced species. There is evidence of a somewhat inverse spatial distribution between a group of oceanic-type, forest-dwelling, endemic, relict arthropods and a group of more generalist endemic arthropods that are able to survive in disturbed marginal sites particularly rich in non-indigenous species. Main conclusions Richness of endemic species is mainly driven by abiotic factors such as a climatic axis (oceanic-type localities with lower temperatures and summer precipitations) and a binary variable CALD (location of sites in caldeiras or ravines), whereas richness of introduced species depends on disturbance related factors. However, after factoring out these major influences, there is a correlation between endemic and introduced richness, suggesting that – independent of the environmental and geographical factors that affect the distribution of endemic or introduced species – the richest endemic assemblages are more prone to invasion, due probably to a facilitation process. Inconclusive evidence suggests that non-indigenous species are limited to those sites under anthropogenic influence located mainly near forest edges, but the rate of expansion of those species to high-altitude, core pristine sites has still to be tested. [ABSTRACT FROM AUTHOR]

In this paper we aim to show that proportional sampling can detect species–area relationships (SARs) more effectively than uniform sampling. We tested the contribution of alpha and beta diversity in ant communities as explanations for the SAR. Tropical forest remnants in Viçosa, Minas Gerais, Brazil (20 °45′ S, 42 °50′ W). We sampled 17 forest remnants with proportional sampling. To disentangle sampling effects from other mechanisms, species richness was fitted in a model with remnant size, number of samples (sampling effects) and an interaction term. A SAR was observed independent of the number of samples, discarding sampling effects. Alpha diversity was not influenced by remnant size, and beta diversity increased with remnant size; evidence to the fact that habitat diversity within remnants could be the dominant cause of the SAR. Such a relationship between beta diversity and remnant area may have also arisen due to the combined effects of territoriality and aggregation of ant species. The proposed model, together with proportional sampling, allowed the distinction between sampling effects and other mechanisms. [ABSTRACT FROM AUTHOR]

Aim: There has been growing interest in non‐cave subterranean habitats and their influence on the evolution of troglomorphic (i.e. 'subterranean adapted') species. Studies on the diversification of aquatic subterranean organisms in these habitats generally support the 'subterranean island' hypothesis, whereby isolated subterranean refuges lead to patterns of short‐range endemism. However, their terrestrial counterparts have received less attention. We aimed to elucidate the applicability of the 'subterranean island' hypothesis to terrestrial subterranean fauna through genetic analyses of two widespread troglomorphic cockroach species. To investigate the influence of subterranean biogeography, we also analysed a closely related species that inhabits 'classic' cave environments to represent a contrasting biogeographic comparison. Location: Pilbara region, Western Australia, and the Chillagoe‐Mungana Caves, Queensland (Australia). Taxa: Cave cockroach species: Nocticola cockingi, Nocticola quartermainei and Nocticola australiensis. Methods: We used DArTseq to generate genome‐wide SNPs in 78 samples, and Sanger sequencing to generate 16S mtDNA data. We then applied various population genomic analyses to characterize the distribution of genetic diversity within the three study species. Results: We identified distinct genetic clusters within the two Pilbara species; however, there appeared to be a notable lack of discernible population differentiation across large parts of their range (>135 km), opposing the subterranean island hypothesis. The highest level of population differentiation in the three study species was between the two caves in Queensland, ~3 km apart. Main Conclusions: The Pilbara subterranean habitat appeared to be conducive to gene flow across relatively large distances, contrasting high levels of endemism observed in other subterranean taxa within the region. The disparate patterns of gene flow among the Pilbara and Queensland study species emphasize the significance of differing subterranean habitats on patterns of dispersal and vicariance. These inferences will inform conservation genetic management of these species, and may help elucidate the evolutionary paradox of widespread subterranean fauna. [ABSTRACT FROM AUTHOR]

Aim: The Nearctic is a complex patchwork of habitats and geologic features that form barriers to gene flow resulting in phylogeographic structure and speciation in many lineages. Habitats are rarely stable over geologic time, and the Nearctic has undergone major climatic changes in the past few million years. We use the common kingsnake species complex to study how climate, geography, and history influence lineage formation over a large, complex landscape. Location: Nearctic/North America. Taxon: Common kingsnake, Lampropeltis getula, species complex. Methods: We analysed genome‐wide sequence data from 51 snakes spanning the majority of the species complex's range. We used population clustering, generalized dissimilarity modelling and coalescent methods to identify the number of genetic clusters within the L. getula complex, infer the environmental correlates of genetic differentiation, and estimate models of divergence and gene flow among lineages. Results: We identified three major lineages within the L. getula complex and further continuous spatial structure within lineages. The most important ecological correlates of genetic distance in the complex are related to aridity and precipitation, consistent with lineage breaks at the Great Plains/Desert ecotone and the Cochise filter barrier. Lineages are estimated to have undergone multiple rounds of isolation and secondary contact, with highly asymmetric migration occurring at present. Main conclusions Changing climates combined with a large and geologically complex landscape have resulted in a mosaic of discrete and spatially continuous genetic structure. Multiple rounds of isolation and secondary contact as climate fluctuated over the past ~4.4 My have likely driven the evolution of discrete lineages that maintain high levels of gene flow. Continuous structure is strongly shaped by aridity and precipitation, suggesting roles for major precipitation gradients in helping to maintain lineage identity in the face of gene flow when lineages are in geographic contact. [ABSTRACT FROM AUTHOR]

Aim: We evaluated the relative importance of geographical and environment variables for taxonomic, phylogenetic and functional β‐diversity of phyllostomid bats along the entire Amazon biome and specifically in the lowlands. Location: Amazon biome. Taxon: Chiroptera. Methods: We carried out a bibliographic review and compiled a wide and unprecedented database of 106 phyllostomid bat species at 102 sites throughout the Amazon biome. For all possible pairs of sites in both datasets, we estimated the Jaccard pairwise dissimilarity, that is, β‐diversity, considering its three dimensions—taxonomic, phylogenetic and functional—for its two components—turnover (substitution of species) and differences in species richness. The association between dissimilarity measurements and geographical and environment variables was assessed using multiple regressions on distance matrices (MRM). Results: We found that turnover and differences in species richness had similar contributions to the taxonomic β‐diversity. However, for phylogenetic and functional β‐diversity, lineages and functions richness differences contribute slightly more than turnover for total β‐diversity. In the lowlands, species, lineages and functions richness differences were slightly higher than turnover for all diversity dimensions. When accounting for all the sites, elevation was the main predictor of phyllostomid bats' taxonomic, phylogenetic and functional turnover. For lowland sites, ecoregions was the main (but relatively weak) predictor associated with all β‐diversity dimensions. Main conclusions: Analysis of filtering sites according to elevation revealed that species in the Amazonian lowlands are taxonomically and phylogenetically different from species in the Andes, and present taxonomic, phylogenetic and functional redundancy between assemblages. When accounting for the whole range of distribution of bats, results showed the predominant effect of elevation over other geographical and environmental predictors. This indicates that the diversity of good dispersers such as bats is more affected by specialisation along environment and climatic gradients than by geographical barriers throughout the Amazon biome. [ABSTRACT FROM AUTHOR]

Aim: The Antarctic Circumpolar Current imparts significant structure to the Southern Ocean biota. The Antarctic Polar Front is a major barrier to dispersal, with separate species (or sometimes intraspecific clades) normally occurring either side of this feature. We examined the biogeographic structure of an apparent exception to this rule in a widespread genus of the Southern Ocean, the periwinkle snail, Laevilitorina. Location: Southern Ocean. Taxon: Littorinidae, Laevilitorininae, Laevilitorina. Methods: Using 750 specimens from 16 Southern Ocean Laevilitorina populations across >8000 km, we analysed mitochondrial COI and nuclear 28S sequences to uncover the evolutionary history of these marine near‐shore snails. We utilized multi‐locus phylogenetic reconstructions, species‐delimitation analyses, divergence‐time estimations and geometric morphometrics. Results: Molecular data revealed that the widespread nominal species L. caliginosa comprises seven species‐level clades, all supported by morphological data, whereas the Antarctic nominal species L. antarctica, L. claviformis and L. umbilicata are conspecific. Six "caliginosa" clades are restricted to southern South America, but one lineage extends from Antarctica to distant sub‐Antarctic islands on both sides of the APF. Geometric morphometrics also identified significant differences among these clades, but uncoupled from genetic differentiation. Main conclusions: The apparent trans‐APF distribution of the poorly dispersing Laevilitorina caliginosa is largely illusory: this taxon consists of at least seven discrete species, only one of which has a trans‐APF distribution. Similar to most Laevilitorina species, the remaining six "caliginosa" clades are narrow endemics. Biogeographical patterns in Laevilitorina reflect the role of vicariance associated with geological processes together with recent long‐distance dispersal events. Laevilitorina originated near the Eocene/Oligocene boundary and diversified during the Miocene and the Pliocene. Laevilitorina is not a cryptic‐species complex: speciation was accompanied by hitherto unrecognized morphological differentiation. This study represents the most detailed molecular work on Southern‐Ocean littorinids and reveals unforeseen diversity across this globally important region. [ABSTRACT FROM AUTHOR]

Aim To illustrate problems in the methods proposed by B. Vilenkin and V. Chikatunov to study levels of endemism and species–area relationships. Location The study used data on the distribution of tenebrionid beetles (Coleoptera, Tenebrionidae) on the Aegean Islands (Greece). Methods A total of 32 islands and 170 taxa (species and subspecies) were included in this study. Levels of endemism were evaluated both as the proportion of endemic taxa, and according to the methods proposed by Vilenkin and Chikatunov, which are based on the number of non-endemic taxa and various relationships with area. A model of the species–area relationship proposed by these authors was also analysed. Results The number of endemic taxa was positively correlated with the number of taxa with different distribution types, but this positive correlation did not influence the estimation of the level of endemism. In fact, the commonly used estimate of endemicity as a percentage was strongly correlated with the endemism values calculated according to the method of Vilenkin and Chikatunov. The usual power function fitted the species–area relationship as well as the most complicated method of Vilenkin and Chikatunov. Main conclusions As hypothesized by Vilenkin and Chikatunov, the number of endemic taxa was influenced both by the number of taxa of other biogeographical ranks, and by an island's area. However, explanations for the positive relationship between the number of endemic taxa and taxa of different biogeographical ranks are equivocal. Importantly, this relationship did not necessarily influence the level of endemism, which could be expressed adequately by percentages. The method proposed by Vilenkin and Chikatunov to estimate the species–area relationship cannot be clearly justified on theoretical grounds and is of questionable practical utility. [ABSTRACT FROM AUTHOR]

AbstractAim Estimates of endemic and non-endemic native vascular plant species in each of the three Western Australian Botanical Provinces were made by East in 1912 and Beard in 1969. The present paper contains an updated assessment of species endemism in the State. Location Western Australia comprises one third of the continental Australian land mass. It extends from 13° to 35° S and 113° to 129° W. Methods Western Australia is recognized as having three Botanical Provinces (Northern, Eremaean and South-West) each divided into a number of Botanical Districts. Updated statistics for number of species and species endemism in each Province are based on the Census of Western Australian Plants data base at the Western Australian Herbarium (onwards). Results The number of known species in Western Australia has risen steadily over the years but reputed endemism has declined in the Northern and Eremaean Provinces where cross-continental floras are common. Only the isolated South-West Province retains high rates of endemism (79%). Main conclusions With 5710 native species, the South-West Province contains about the same number as the California Floristic Province which has a similar area. The Italian mediterranean zone also contains about this number but in a smaller area, while the much smaller Cape Floristic Region has almost twice as many native species. The percentage of endemic species is highest at the Cape, somewhat less in south-western Australia and less again in California. Italy, at 12.5%, has the lowest value. Apart from Italy, it is usual for endemism to reach high values in the largest plant families. In Western Australia, these mainly include woody sclerophyll shrubs and herbaceous perennials with special adaptations to environmental conditions. While those life forms are prominent in the Cape, that region differs in the great importance of herbaceous families and succulents, both of which are virtually absent from Western Australia. In California and Italy, most endemics are in families of annual, herbaceous perennial and soft shrub plants. It is suggested that the dominant factor shaping the South-West Province flora is the extreme poverty of the area’s soils, a feature that emphasizes sclerophylly, favours habitat specialization and ensures relatively many local endemic species. [ABSTRACT FROM AUTHOR]

Aim: The centre‐periphery hypothesis (CPH) states that peripheral populations exhibit lower genetic diversity, abundance and size, and higher differentiation compared to central populations, due to a decline in environmental suitability towards range margins. Here, we tested if neutral genetic diversity and functional leaf trait diversity fit the predicted patterns of the CPH. Location: Cerrado, Brazil. Taxon: Qualea grandiflora (Vochysiaceae) and Annona crassiflora (Annonaceae). Methods: Variation in eight functional leaf traits and nine or eight microsatellite loci were analysed in 37 populations (777 individuals) of Q. grandiflora and 21 populations (397 individuals) of A. crassiflora. We tested CPH using three distinct centres of species' range: geographical (centre of species' geographic occurrence), historical (centre of species' refugia) and ecological (centre of species' current suitability areas). Generalised linear regressions were performed between genetic diversity and differentiation, coefficients of variation and means of leaf metamer traits of populations and their distances from each centre. Results: A decrease in allele richness was observed from central towards peripheral populations for ecological (both species) and geographical centres (Q. grandiflora). Overall, the results for both species pointed to a decrease in metamer vigour towards marginal populations, pattern consistent with a decrease in environmental suitability towards periphery as predicted by CPH. Besides geographical and ecological centres, leaf traits fitted CPH considering historical centre. Main Conclusions: Results for leaf traits and genetic diversity of two phylogenetically distant species indicate the consistency of the CPH for Cerrado species. Our results highlight the importance of considering distinct centres and a great number of populations along species' range to better determinate the processes underlying the distribution of genetic diversity and functional traits. The low genetic diversity and metamer vigour in marginal populations can explain the Cerrado endemism of studied species and suggest that the ongoing climatic changes can be critical for their survival. [ABSTRACT FROM AUTHOR]

The article focuses on the long-term effects of forest fragmentation. A research paper by H.L. Vasconcelos and his colleagues examined the long-term effects of forest fragmentation on Amazonian ant communities. They found that fewer ant species per plot and fewer rare species were supported by fragments. The number of species occurring in fragments and continuous forest were almost similar. The effects of fragmentation can be understood by understanding the differences and similarities between forest and habitat.

Aim: Environmental and spatial factors are broadly recognized as important predictors of beta diversity patterns. However, the scale at which beta diversity patterns are evaluated will affect the outcoming results. For example, studies at larger scales will usually find spatial processes as the main predictor of beta diversity patterns. In this study, we evaluate how beta diversity patterns change when analyses are conducted at different scales by reducing the scale of analysis in a hierarchical manner. Location: Atlantic Forest biome. Taxon: Chiroptera. Methods: Information on the occurrence of 59 bat species were obtained from the Atlantic Bats and Species Link database. We partitioned beta diversity into its two components (nestedness and turnover), and calculated these indexes hierarchically: the biome in its entirety (all ecoregions); between larger regions (north, central and south); and between ecoregions within each region. We performed a Generalized Dissimilarity Model (GDM) to identify and predict the turnover of bat species in the Atlantic Forest based on geo‐climatic predictors. We obtained 19 geo‐climatic data from AMBDATA, an environmental dataset based on different data sources commonly used in species distribution modelling. Results: We found that turnover was the main component influencing a latitudinal gradient when the biome was analysed in its entirety. However, when the scale of the analysis was reduced, we found that species loss (nestedness component) had a large effect in determining beta diversity dissimilarity. We also found that nestedness was the main pattern explaining beta diversity dissimilarity along a longitudinal gradient. Main conclusions: Beta diversity patterns changed with the scale of analysis, which indicates that bat species composition does not follow the same pattern throughout the Atlantic Forest. This corroborates the importance of analysing beta diversity patterns at different scales to understand how environmental dissimilarity across geographical space can influence species distribution patterns. [ABSTRACT FROM AUTHOR]

Aim: Knowledge of species responses to past environmental change provides a basis to predict and mitigate the outcomes of future environmental change. While paradigm studies of comparative phylogeography have surveyed dissimilar taxa as a means to identify generalities of species responses to past environmental change, the fact that such taxa are dissimilar also raises the chances that any shared patterns reflect coincident responses from different processes ('phylogeographic convergence'). Here we advocate for and demonstrate the value of examining closely related, ecologically similar co‐distributed species in comparative phylogeographic studies aimed at inferring the environmental processes driving distributional change. Closely related species with similar environmental requirements represent valid phylogeographic replicates, meaning that shared historical distributional responses can more confidently be attributed to the operation of the same process ('phylogeographic parallelism'). Location: Tasmania, temperate south‐east Australia. Taxa: We compared phylogeographic patterns observed in two closely related, co‐distributed skink species (Carinascincus) sharing similar ecological and physiological tolerances. Methods: Using mitochondrial and nuclear DNA, we reconstructed relationships between populations across the known range of C. metallicus and compared it with those of C. ocellatus. We also compared dated phylogenies inferred using Bayesian approaches, and analyses of population structure and genetic diversity. Results: We found remarkably similar geographic patterns of genetic diversity in these two species, suggesting they responded similarly to Plio‐Pleistocene climate cycling. We infer that glacial cold and aridity forced these species into similar lowland refugial regions throughout Tasmania and the Bass Strait Islands. Main conclusions: Examining phylogeographic patterns in closely related, ecologically similar co‐distributed species allows for confident inference of mechanisms driving historical distributional changes. This is an important step towards generating robust predictions of species responses to future environmental change. [ABSTRACT FROM AUTHOR]

Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that 'species' within the biome are often composed of cryptic species. In order to identify biodiversity hotspots more robustly and across multiple dimensions we integrate functional, spatial and new phylogeographic data for the Cerrado lizard fauna by (a) mapping the spatial patterns of species and phylogenetic diversity; and (b) using endemism measures to identify areas of unique diversity. We then quantify the extent to which existing protected areas represent the diversity. Location: Brazilian savanna (Cerrado). Methods: We generated species distribution models using distribution records for all Cerrado lizard species. These, combined with mitochondrial DNA phylogenies and natural history data, allowed us to map species richness, phylogenetic and functional diversity and phylogenetic and weighted endemism. Phylogenetic endemism maps were then cross‐referenced against protected areas to calculate the amount of evolutionary history preserved within these areas. Results: The central region of the Cerrado, a vast and climatically stable plateau, stands out as important under all biodiversity metrics. Including evolutionary relationships in biodiversity assessment, we detected four regional hotspots with high concentration of spatially restricted evolutionary diversity. Protected areas cover only 10% of the Cerrado area and hold 11.64% of the summed phylogenetic endemism of all lizards in the biome. Main Conclusions: We highlighted both stable (Chapada dos Veadeiros and Serra do Espinhaço plateaus) and environmentally heterogenous regions (Araguaia and Tocantins valleys) as hotspots of evolutionary diversity. The creation and/or manipulation of areas for conservation are essential for the conservation and survival of the rich and endemic lizard fauna of the Cerrado. [ABSTRACT FROM AUTHOR]

Aim: Determine the relative influence of geographical distance, environmental differences, and host species composition on the similarity of bat fly species composition. Location: Neotropics. Taxon: Bats (Chiroptera: Phyllostomidae) and bat flies (Diptera: Streblidae). Methods: Abundance data on bats and ectoparasites were obtained from published studies. The relative influences of environmental variation (annual precipitation, temperature seasonality, elevation, and NDVI), host species composition, and geographic distance on parasite community composition were analysed with Generalized Dissimilarity Modelling and variance partitioning. Additionally, we evaluated the influence of these environmental variables and geographic distance on host species composition. Results: Our model explains 45.3% of the variance in the dissimilarity of bat fly species. Host species composition had the most significant influence on bat fly species composition across communities, followed by environmental effects. Variance partitioning showed that host species composition explained 14.9% and environmental characteristics explained 10.3% of the variance in bat fly species dissimilarity. Geographical distance alone had a negligible effect as it accounted for only 0.007% of the variance in bat fly species composition. Host species composition was mainly influenced by geographic distance (18.0%) and secondarily by environmental variables (9.8%). The most important environmental variables influencing parasite and host species composition were annual precipitation and temperature seasonality, respectively. Main Conclusions: The lack of relationship between geographical distance and bat fly species composition may reflect either the high mobility or the high dispersal capacity of bat flies, or a combination of these. Alternatively, it could reflect a taxonomic artefact. Environmental differences seem to directly affect bat flies, as opposed to affecting them indirectly through their impact on the hosts. Our results support the fundamental role that host species composition plays in determining the species composition of highly host‐specific parasites. However, we argue that host specificity is not the only trait impacting ectoparasite species composition. [ABSTRACT FROM AUTHOR]

Aim: Temporal dynamics of biodiversity along tropical elevational gradients are unknown. We studied seasonal changes of Lepidoptera biodiversity along the only complete forest elevational gradient in the Afrotropics. We focused on shifts of species richness patterns, seasonal turnover of communities and seasonal shifts of species' elevational ranges, the latter often serving as an indicator of the global change effects on mountain ecosystems. Location: Mount Cameroon, Cameroon. Taxon: Butterflies and moths (Lepidoptera). Methods: We quantitatively sampled nine groups of Lepidoptera by bait‐trapping (16,800 trap‐days) and light‐catching (126 nights) at seven elevations evenly distributed along the elevational gradient from sea level (30 m a.s.l.) to timberline (2,200 m a.s.l.). Sampling was repeated in three seasons. Results: Altogether, 42,936 specimens of 1,099 species were recorded. A mid‐elevation peak of species richness was detected for all groups but Eupterotidae. This peak shifted seasonally for five groups, most of them ascending during the dry season. Seasonal shifts of species' elevational ranges were mostly responsible for these diversity pattern shifts along elevation: we found general upward shifts in fruit‐feeding butterflies, fruit‐feeding moths and Lymantriinae from beginning to end of the dry season. Contrarily, Arctiinae shifted upwards during the wet season. The average seasonal shifts of elevational ranges often exceeded 100 m and were even several times higher for numerous species. Main conclusions: We report seasonal uphill and downhill shifts of several lepidopteran groups. The reported shifts can be driven by both delay in weather seasonality and shifts in resource availability, causing phenological delay of adult hatching and/or adult migrations. Such shifts may lead to misinterpretations of diversity patterns along elevation if seasonality is ignored. More importantly, considering the surprising extent of seasonal elevational shifts of species, we encourage taking account of such natural temporal dynamics while investigating the global climate change impact on communities of Lepidoptera in tropical mountains. [ABSTRACT FROM AUTHOR]

Aim: To define the major biogeographical regions and transition zones for freshwater fish species. Taxon: Strictly freshwater species of actinopterygian fish (i.e. excluding marine and amphidromous fish families). Methods: We based our bioregionalization on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11,295 species in 2,581 basins. On the basis of this dataset, we generated a bipartite (basin‐species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions. Results: Our bioregionalization scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino‐Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic). Main conclusions: Our results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater‐specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10–20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions. [ABSTRACT FROM AUTHOR]

Aim: Current species distributions are shaped by present and past biotic and abiotic factors. Here, we assessed whether abiotic factors (habitat availability) in combination with past connectivity and a biotic factor (body mass) can explain the unique distribution pattern of Southeast Asian mammals, which are separated by the enigmatic biogeographic transition zone, the Isthmus of Kra (IoK), for which no strong geophysical barrier exists. Location: Southeast Asia. Taxon: Mammals. Methods: We projected habitat suitability for 125 mammal species using climate data for the present period and for two historic periods: mid‐Holocene (6 ka) and last glacial maximum (LGM 21 ka). Next, we employed a phylogenetic linear model to assess how present species distributions were affected by the suitability of areas in these different periods, habitat connectivity during LGM and species body mass. Results: Our results show that cooler climate during LGM provided suitable habitat south of IoK for species presently distributed north of IoK (in mainland Indochina). However, the potentially suitable habitat for these Indochinese species did not stretch very far southwards onto the exposed Sunda Shelf. Instead, we found that the emerged landmasses connecting Borneo and Sumatra provided suitable habitat for forest dependent Sundaic species. We show that for species whose current distribution ranges are mainly located in Indochina, the area of the distribution range that is located south of IoK is explained by the suitability of habitat in the past and present in combination with the species body mass. Main conclusions: We demonstrate that a strong geophysical barrier may not be necessary for maintaining a biogeographic transition zone for mammals, but that instead a combination of abiotic and biotic factors may suffice. [ABSTRACT FROM AUTHOR]