Environmental and human factors influencing rare plant local occurrence, extinction and persistence: a 115-year study in the Mediterranean region

Aim Assessing whether environmental and human factors influenced the spatial distribution and the dynamics of regionally rare plant species since the late nineteenth century, and whether these spatial and temporal patterns of rare species occurrences differ according to their chorology (level of endemism and biogeographic affinity). Location An area extending over 6250 km² in the French Mediterranean Region. Methods We used two botanical surveys achieved in 1886 and in 2001, and considered species rare if occurring in only one or two sites in the study area. Each rare species was assigned to a group of endemism level (restricted endemic, non‐endemic), and of biogeographic affinity (Mediterranean, South/Central European, Mountain, Eurosiberian). A 1 × 1 km grid was applied to the study zone. Generalized linear models were developed to study the spatial distribution and the fate of rare species occurrences (local extinction vs. local persistence between 1886 and 2001), as a function of environmental and human variables. Multivariate analyses were used to test whether the spatial distribution and the fate of rare species occurrences differed according to their chorology. Results In 2001, rare species as a whole tended to occur at higher altitude, in zones dominated by semi‐natural open habitats, and where cultivated area had decreased in the last 30 years. Between 1886 and 2001, rare species were the most prone to local extinction in zones where human population density, cultivated area and livestock density had increased the most. Between 1886 and 2001, rare species had a higher probability of local persistence in zones of high altitude and steep slope, on basic bedrocks and with low cultivated area. Rare species with Mountain and Eurosiberian affinities occurred in marginal habitats in the study region, i.e. on gneiss‐micaschist bedrocks and at high altitudes, whereas Mediterranean and South/Central European rare species occupied more varied environmental conditions. Between 1886 and 2001, Eurosiberian rare species showed high rates of local extinction whereas Mediterranean rare species had a significantly higher probability of local persistence. Restricted endemic species mostly occurred in zones of high slope, low human population density, and where cultivated area had decreased in the last 30 years. Occurrences of restricted endemics remained significantly stable between 1886 and 2001. Main conclusions Environmental and land‐use changes that occurred over the twentieth century in the Mediterranean Basin had significant impacts on the spatial distribution and on the long‐term dynamics of rare species occurrences. Urbanization and recent agriculture intensification, occurring mainly in coastal plains and littoral zones, caused most local extinctions of rare species from 1886 to 2001. Local populations of Eurosiberian species, which reach their range limits in marginal zones of the Mediterranean, also appear to be highly vulnerable. Conversely, most restricted endemic species occur in habitats with harsh topography and low human disturbance and have a higher potential of local persistence.     

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

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

Forest composition in Mediterranean mountains is projected to shift along the entire elevational gradient under climate change

Aim Species distribution models have been used frequently to assess the effects of climate change on mountain biodiversity. However, the value and accuracy of these assessments have been hampered by the use of low‐resolution data for species distributions and climatic conditions. Herein we assess potential changes in the distribution and community composition of tree species in two mountainous regions of Spain under specific scenarios of climate change using data with a high spatial resolution. We also describe potential changes in species distributions and tree communities along the entire elevational gradient. Location Two mountain ranges in southern Europe: the Central Mountain Range (central west of the Iberian Peninsula), and the Iberian Mountain Range (central east). Methods We modelled current and future distributions of 15 tree species (Eurosiberian, sub‐Mediterranean and Mediterranean species) as functions of climate, lithology and availability of soil water using generalized linear models (logistic regression) and machine learning models (gradient boosting). Using multivariate ordination of a matrix of presence/absence of tree species obtained under two Intergovernmental Panel on Climate Change (IPCC) scenarios (A2 and B2) for two different periods in the future (2041–70 and 2071–2100), we assessed the predicted changes in the composition of tree communities. Results The models predicted an upward migration of communities of Mediterranean trees to higher elevations and an associated decline in communities of temperate or cold‐adapted trees during the 21st century. It was predicted that 80–99% of the area that shows a climate suitable for cold–wet‐optimum Eurosiberian coniferous and broad‐leaved species will be lost. The largest overall changes were predicted for Mediterranean species found currently at low elevations, such as Pinus halepensis, Pinus pinaster, Quercus ilex ssp. ballota and Juniperus oxycedrus, with sharp increases in their range of 350%. Main conclusions It is likely that areas with climatic conditions suitable for cold‐adapted species will decrease significantly under climate warming. Large changes in species ranges and forest communities might occur, not only at high elevations within Mediterranean mountains but also along the entire elevational gradient throughout this region, particularly at low and mid‐elevations. Mediterranean mountains might lose their key role as refugia for cold‐adapted species and thus an important part of their genetic heritage.     

Elevational gradients in species abundance,assemblage structure and energy use of rainforest birds in the Australian Wet Tropics bioregion

Elevational patterns of species richness, local abundance and assemblage structure of rainforest birds of north‐eastern Australia were explored using data from extensive standardized surveys throughout the region. Eighty‐two species of birds were recorded with strong turnover in assemblage structure across the elevational gradient and high levels of regional endemism in the uplands. Both species richness and bird abundance exhibited a humped‐shaped pattern with elevation with the highest values being between 600 and 800 m elevation. While much of the variability in species richness could be explained by the species–area relationship, analyses of net primary productivity (NPP) and total daily energy consumption of the bird community (energy use) suggest that ecosystem energy flow or constraints may be a significant determinant of species richness. Species richness is positively correlated with local bird abundance which itself is closely related to total energy use of the bird community. We suggest the hypothesis that lower NPP limits bird abundance and energy use in the uplands (>500 m) and that low bird energy use and species richness in the lowlands is limited by a seasonal bottleneck in available primary productivity and/or a species pool previously truncated by an extinction filter imposed by the almost complete disappearance of rainforest in the lowlands during the glacial maxima. We suggest that some of the previously predicted impacts of global warming on biodiversity in the uplands may be partially ameliorated by increases in NPP because of increasing temperatures. However, these relationships are complex and require further data specifically in regard to direct estimates of primary productivity and detailed estimates of energy flow within the assemblage.     

Defining climate's role in ecosystem evolution: Clues from late quaternary mammals

Mammalian communities alter their taxonomic composition through time as the species composing them change their biogeographic range, become extinct, or evolve into new species. When taxonomic compositions change through these processes, inevitably the links between taxa and communities change too, resulting in evolution from one ecosystem into the next. Late Quaternary examples suggest that on a timescale encompassing a few thousand to a few hundred thousand years (the “multi‐millennial timescale"), climatic change is perhaps the most important driver of ecosystem evolution because it periodically forces biogeographic changes and extinction. Climatic change over this timescale, which essentially slips between “geological time”; and “ecological time”;, is not very closely in phase with population‐level evolution of a species analyzed for this study, the meadow vole Microtus pennsylvanicus; therefore climatic oscillations on the multi‐millennial timescale may not stimulate speciation much. Instead, speciation may contribute to ecosystem evolution independent of climatic change and over a longer time scale.     

Biogeographical zonation of the western Iberian peninsula on the basis of the distribution of earthworm species

We used TWINSPAN and CANOCO to investigate the biogeography of the western Iberian Peninsula on the basis of the distribution of earthworms among ninety areas of Galicia, Portugal, Asturias, León, Zamora, Salamanca, Cáceres, Badajoz and Huelva. This part of Iberia is clearly divisible into a Eurosiberian Region in the north and west and a Mediterranean Region in the south and east. For earthworm faunas, however, the limit between these regions is considerably further south than is conventionally accepted on the basis of Rivas Martinez's (1987) vegetation-type classification. Species character- istic of the Eurosiberian Region include Dendrobaena madeirensis, D. octaedra, Allolobophora caliginosa and various species of the genus Lumbricus . Within this region the earthworm fauna of Asturias is clearly distinct from that of Galicia and northern Portugal. Species characteristic of the Mediterranean Region include Allolobophora caliginosa , A. chlorotica and A. rosea , but inventories from this region are most easily identified by the absence or scarcity of those species characteristic of the Eurosiberian Region. Many areas show intermediate characteristics between the two major regions, and in some cases one region 'intrudes' into the other.     

Ants on a mountain: spatial, environmental and habitat associations along an altitudinal transect in a centre of endemism

Mountains are biodiversity hotspots and provide spatially compressed versions of regional and continental variation. They might be the most cost effective way to measure the environmental associations of regional biotic communities and their response to global climate change. We investigated spatial variation in epigeal ant diversity along a north–south elevational transect over the Soutpansberg Mountain in South Africa, to see to what extent these patterns can be related to spatial (regional) and environmental (local) variables and how restricted taxa are to altitudinal zones and vegetation types. A total of 40,294 ants, comprising 78 species were caught. Ant richness peaked at the lowest elevation of the southern aspect but had a hump-shaped pattern along the northern slope. Species richness, abundance and assemblage structure were associated with temperature and the proportion of bare ground. Local environment and spatially structured environmental variables comprised more than two-thirds of the variation explained in species richness, abundance and assemblage structure, while space alone (regional processes) was responsible for <10%. Species on the northern aspect were more specific to particular vegetation types, whereas the southern aspect’s species were more generalist. Lower elevation species’ distributions were more restricted. The significance of temperature as an explanatory variable of ant diversity across the mountain could provide a predictive surrogate for future changes. The effect of CO₂-induced bush encroachment on the southern aspect could have indirect impacts complicating prediction, but ant species on the northern aspect should move uphill at a rate proportional to their thermal tolerance and the regional increases in temperature. Two species are identified that might be at risk of local extinction.     

Gradients in stream fish assemblages across a Mediterranean landscape: contributions of environmental factors and spatial structure

1. Despite wide recognition that fish assemblages are influenced by factors operating over a range of spatial scales, little effort has been devoted to quantifying large‐scale variation and the multiscale dependencies of assemblage patterns and processes. This is particularly true for Mediterranean streams, where seasonally predictable drying‐up may lead to a strong association between assemblage attributes and large‐scale factors affecting the distribution of population sources and extinction likelihood. 2. The contribution of large‐scale factors to stream fish assemblage variation was quantified across a Mediterranean landscape, in south‐west Portugal. Fish abundance and species composition were estimated at 166 sites across third‐ to sixth‐order streams, in March–July 1998. Variance partitioning by redundancy analyses was used to analyse assemblage variation against three sets of predictor variables: environmental (catchment position, and geomorphic and hydrological factors), large‐scale spatial trends and neighbourhood effects. 3. Environmental variables and spatial trends accounted for 34.6% of the assemblage variation across the entire region, and for 36.6 and 57.8% within the two largest catchments (Mira and Seixe). Neighbourhood effects were analysed at the catchment scale, increasing the explained variation to 56.1% (Mira) and 70.7% (Seixe). 4. A prevailing environmental gradient was reflected in an increase in the abundance of all species and size‐classes in relation to catchment position, with more fish present in larger streams and in downstream reaches. Variables describing geomorphic and hydrological settings were less important in explaining assemblage variation. 5. Spatial trends always accounted for the smallest fraction of assemblage variation, and they were probably associated with historical barriers to fish dispersal. The strong neighbourhood effects may be related to spatially autocorrelated habitat conditions, but they are also a likely consequence of fish emigration/extinction and colonisation processes. 6. These results emphasise that a substantial proportion of fish assemblage variation in Mediterranean streams may be explained by large‐scale factors, irrespective of microhabitats and local biotic interactions. It is suggested that this pattern results to a large extent from the seasonal drying‐up, with the summer shortage of surface water limiting fish occurrence in headwaters, and consequently the key core areas for fish concentrating in larger streams and tributaries adjacent to large streams because of neighbourhood effects.     

How local extinction changes rarity: an example with Sonoran Desert fishes

That spatially rare species may be predisposed to extinction is a common tenet of ecology. However, the opposite side of the relationship – how extinction alters spatial rarity – remains little explored. We used an extensive biodiversity database to contrast patterns of spatial rarity of a biogeographic assemblage of native Sonoran fishes before and after an extensive, decades-long wave of extirpations. Focusing on 25 fish species native to the Lower Basin of the Colorado River, we analyzed two key aspects of spatial rarity: 1) species range sizes (expressed as kilometers of stream reach occupied) and 2) species' co-occurrence patterns. Native fish species that were spatially rare historically suffered disproportionate losses in occurrences. However, endemic species did not suffer increased losses relative to non-endemic (but still native) species of comparable rarity. Species' geographic range sizes were concordant through time, with spatially rare species remaining rare after extensive extirpations relative to species that were historically more widespread. In contrast, extirpations greatly disrupted patterns of species co-occurrence on both local and regional scales. Over 50% of the species pairs that historically co-occurred (in the same 5  km reach) no longer co-occur anywhere in the Lower Basin, and species pairs that infrequently co-occurred in historic times suffered greater proportional losses than did more widely co-occurring pairs. Such changes in the relationship between spatial rarity and species richness deserve attention because they inhibit conservation planning (decreasing the efficiency of reserve design) and reduce interaction diversity altering opportunities for long-term co-evolutionary change.     

Biogeographic patterns in major marine realms: function not taxonomy unites fish assemblages in reef,seagrass and mangrove systems

We examine the effects of different biogeographic histories on assemblage composition in three major marine habitats in two biogeographically distinct marine realms. Specifically, we quantify the taxonomic and functional composition of fish assemblages that characterise coral reef, seagrass and mangrove habitats, to explore the potential effects of biogeographic history and environment on assemblage composition. The three habitats were surveyed in the Caribbean and on the Great Barrier Reef using a standardised underwater visual census method to record fish size and abundance data. The taxonomic composition of assemblages followed biogeographic expectations, with realm‐specific family‐level compositions. In marked contrast, the functional composition of assemblages separated habitats regardless of their biogeographic locations. In essence, taxonomy characterises biogeographic realms while functional groups characterise habitats. The Caribbean and Indo‐West Pacific have been separated for approximately 15 million years. The two realms have different taxonomic structures which reflect this extended separation, however, the three dominant shallow‐water marine habitats all retain distinct functional characteristics: seagrass fishes are functionally similar regardless of their taxonomic composition or biogeographic location. Likewise, for coral reefs and mangroves. The results emphasise the advantages and limitations of taxonomic vs. functional metrics in evaluating patterns. Taxonomy primarily reflects biogeographic and evolutionary history while functional characteristics may better reflect ecological constraints.     

Contribution of rarity and commonness to patterns of species richness in biogeographic transitions regions: Woody plants of Uruguay

There is a growing body of evidence suggesting that widespread (i.e. common) rather than geographically restricted species (i.e. rare) shape the overall distribution patterns of species richness. This is a non‐intuitive fact, given that local and regional assemblages are normally composed by numerous rare species and few common ones. We evaluated here the primacy of common species in a biogeographic transition zone, where rarity has frequently a higher incidence. We analysed the geographical variability of trees and shrubs in Uruguay, located in a transitional zone between prairie and forest biomes, to assess the relative contribution of rare and common species to the generation of richness patterns. The distribution of 301 species of the native woody assemblage of Uruguay was mapped over the national grid system (302 quadrants of approximately 22 × 30 km), using published data and herbarium records. The overall assemblage was segregated into four subassemblages in function of species distribution (quartiles). Species richness in the four quartiles was positively correlated with overall richness, but common species (quartile 3) showed the highest level of correlation. Then, we ranked species from the most widespread to the most restricted (common‐to‐rare) and from the most restricted to the most widespread (rare‐to‐common). Along each stage of the sequences we obtained a series of species richness patterns for increasing numbers of species. Correlating the species richness pattern for each subassemblage of both sequences with that of the full assemblage, we also found higher correlations in the common‐to‐rare sequence. We conclude the Uruguayan woody plants assemblage has a very large number of rare species as expected for a transitional biogeographical zone, but it was the common species that contributed most to the overall pattern of species richness. We propose the low contribution of rare species is explained by the most interspecific variability in ecological determinants within the assemblage of rare species. Therefore the spatial covariance among rare species is low, and so is the relationship with overall species richness.     

Twenty years of understorey bird extinctions from Amazonian rain forest fragments: consistent trends and landscape-mediated dynamics

Aim We analysed presence/absence data for understorey bird species in rain forest fragments sampled from 1979 through 2001. Here we consider extinctions between 1992, when most fragments had been isolated for at least 8 years, and 2001. Our objectives were to determine whether high extinction rates documented soon after isolation continued through up to 20 years after isolation, and to examine fragment size and landscape effects on extinction. Location Biological Dynamics of Forest Fragments Project, near Manaus, Brazil. Methods Through 1992, birds were surveyed with standardized mist net sampling in ten 1‐ to 100‐ha fragments. We repeated the mist net protocol in 2000–01. We also added remote taping of the dawn chorus and tape playback surveys for species captured in 1991–92 but not in 2000–01. Results Between 1992 and 2001, 37 species went extinct in at least one fragment. As expected, extinction rate decreased with increasing fragment size. Over 30% of species went extinct in 1‐ha fragments, compared to about 5% in 100‐ha fragments. Extinction followed a predictable pattern: most species lost from 100‐ha fragments between 1992 and 2001 had already gone extinct in smaller fragments before 1992. Despite extinctions, fragments gained species between 1992 and 2001, apparently due to species moving through the developing second growth matrix. Fragments surrounded by old second growth had lower extinction rates than predicted based on fragment size alone. Main conclusions Sequential extinctions occurred for at least 20 years. Some additional species previously lost from smaller fragments may continue to go extinct in 100‐ha fragments. At the same time, species assemblages in 1‐ and 10‐ha fragments mostly reflect second‐growth dynamics by 20 years after isolation. High species loss predicted from the first few years after isolation has not occurred, almost certainly because of recolonization.     

The Mediterranean Sea as a ‘cul‐de‐sac’ for endemic fishes facing climate change

The Mediterranean Sea is a hotspot of biodiversity, and climate warming is expected to have a significant influence on its endemic fish species. However, no previous studies have predicted whether fish species will experience geographic range extensions or contractions as a consequence of warming. Here, we projected the potential future climatic niches of 75 Mediterranean Sea endemic fish species based on a global warming scenario implemented with the Mediterranean model OPAMED8 and a multimodel inference, which included uncertainty. By 2070–2099, the average surface temperature of the Mediterranean Sea was projected to warm by 3.1 °C. Projections for 2041–2060 are that 25 species would qualify for the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List, and six species would become extinct. By 2070–2099, 45 species were expected to qualify for the IUCN Red List whereas 14 were expected to become extinct. By the middle of the 21st century, the coldest areas of the Mediterranean Sea (Adriatic Sea and Gulf of Lion) would act as a refuge for cold‐water species, but by the end of the century, those areas were projected to become a ‘cul‐de‐sac’ that would drive those species towards extinction. In addition, the range size of endemic species was projected to undergo extensive fragmentation, which is a potentially aggravating factor. Since a majority of endemic fishes are specialists, regarding substratum and diet, we may expect a reduced ability to track projected climatic niches. As a whole, 25% of the Mediterranean Sea continental shelf was predicted to experience a total modification of endemic species assemblages by the end of the 21st century. This expected turnover rate could be mitigated by marine protected areas or accelerated by fishing pressure or competition from exotic fishes. It remains a challenge to predict how these assemblage modifications might affect ecosystem function.     

Identifying hotspots for biodiversity management using rank abundance distributions

Aim Identification of biodiversity hotspots has typically relied on species richness. We extend this approach to include prediction to regional scales of other attributes of biodiversity based on the prediction of Rank Abundance Distributions (RADs). This allows us to identify areas that have high numbers of rare species and areas that have a rare assemblage structure. Location Continental slope and shelf of south‐western Australia, between 20.5 and 30° S and depths of 100–1500 m. Methods We use a recently developed method to analyse RADs from biological surveys and predict attributes of RADs to regional scales from spatially abundant physical data for demersal fish and invertebrates. Predictions were made for total abundance (N), species richness (S) and relative evenness at 147,996 unsampled locations using data from two spatially limited surveys. The predictions for S and relative evenness were then independently split into categories, creating a bivariate distribution. The RAD categories are mapped spatially between 20.5 and 30° S to depths of 1500 m to allow identification of areas with rare species and assemblage structure across this region. Results Rank abundance distributions for demersal fish vary with large scale oceanographic patterns. Peaks in abundance and unevenness are found on the shelf break. The bivariate distributions for richness and evenness for both fish and invertebrates show that all assemblage structures are not equally likely. The RAD categories identify regions that have high numbers of rare species and areas with unique assemblage structure. Main conclusions Predicted RADs over large regions can be used to identify biodiversity hotspots in more detail than richness alone. Areas of rare species and rare assemblage structure identified from fish and invertebrates largely overlap, despite the underlying data coming from two different data sets with two different collection methods. This approach allows us to target conservation management at species that would otherwise be missed.     

Taxonomic and biological trait differences of stream macroinvertebrate communities between mediterranean and temperate regions: implications for future climatic scenarios

Streams in mediterranean regions have highly seasonal discharge patterns, with predictable torrential floods and severe droughts. In contrast, discharge is less variable in temperate regions and intermittent flow conditions are uncommon. Hydroclimatic models predict that climate change would increase frequency and severity of floods and droughts across Europe, thus increasing the proportion of streams with mediterranean characteristics in actually temperate areas. Correspondingly, understanding actual ecological differences between mediterranean and temperate streams may help to anticipate large‐scale ecological impacts of climate change. Given that large‐scale factors determine local community composition, we hypothesized that climatic differences between mediterranean and temperate regions should affect the taxonomic and biological trait composition in streams. We assembled the abundance of stream macroinvertebrate genera of 265 sites each from the Mediterranean Basin and from temperate Europe and linked these abundances to published information on 61 categories of 11 biological traits reflecting the potential of resilience from and resistance to disturbances. Although regional taxonomic richness was higher in the mediterranean than in the temperate region, local taxonomic richness and diversity did not significantly differ between regions. Local trait richness and diversity were significantly higher in the mediterranean region. Both local taxonomic and trait‐community composition differed between regions, but the former varied much more than the latter, highlighting that climate change could produce large changes in the taxonomic but rather weak changes in the trait composition. The mediterranean region was characterized by macroinvertebrates with higher dispersion and colonization capabilities, suggesting that species loss in the temperate region, by extinction or northward emigration of taxa, would be compensated for by immigration of southern mediterranean taxa. Thus, climate change would likely have stronger implications for the local conservation of taxa than for the trait composition of stream macroinvertebrate communities.     

Ecological communities are vulnerable to realistic extinction sequences

Loss of species will directly change the structure and potentially the dynamics of ecological communities, which in turn may lead to additional species loss (secondary extinctions) due to direct and/or indirect effects (e.g. loss of resources or altered population dynamics). Furthermore, the vulnerability of food webs to repeated species loss is expected to be affected by food web topology, species interactions, as well as the order in which species go extinct. Species traits such as body size, abundance and connectivity might determine a species’ vulnerability to extinction and, thus, the order in which species go primarily extinct. Yet, the sequence of primary extinctions, and their effects on the vulnerability of food webs to secondary extinctions, when species abundances are allowed to respond dynamically, has only recently become the focus of attention. Here, we analyse and compare topological and dynamical robustness to secondary extinctions of model food webs, in the face of 34 extinction sequences based on species traits. Although secondary extinctions are frequent in the dynamical approach and rare in the topological approach, topological and dynamical robustness tends to be correlated for many bottom–up directed, but not for top–down directed deletion sequences. Furthermore, removing species based on traits that are strongly positively correlated to the trophic position of species (such as large body size, low abundance, high net effect) is, under the dynamical approach, found to be as destructive as removing primary producers. Such top–down oriented removal of species are often considered to correspond to realistic extinction scenarios, but earlier studies, based on topological approaches, have found such extinction sequences to have only moderate effects on the remaining community. Thus, our result suggests that the structure of ecological communities, and therefore the integrity of important ecosystem processes could be more vulnerable to realistic extinction sequences than previously believed.     

Amphibian Diversity and Threatened Species in a Severely Transformed Neotropical Region in Mexico

Many regions around the world concentrate a large number of highly endangered species that have very restricted distributions. The mountainous region of central Veracruz, Mexico, is considered a priority area for amphibian conservation because of its high level of endemism and the number of threatened species. The original tropical montane cloud forest in the region has been dramatically reduced and fragmented and is now mainly confined to ravines and hillsides. We evaluated the current situation of amphibian diversity in the cloud forest fragments of this region by analyzing species richness and abundance, comparing assemblage structure and species composition, examining the distribution and abundance of threatened species, and identifying the local and landscape variables associated with the observed amphibian diversity. From June to October 2012 we sampled ten forest fragments, investing 944 person-hours of sampling effort. A total of 895 amphibians belonging to 16 species were recorded. Notable differences in species richness, abundance, and assemblage structure between forest fragments were observed. Species composition between pairs of fragments differed by an average of 53%, with the majority (58%) resulting from species replacement and the rest (42%) explained by differences in species richness. Half of the species detected are under threat of extinction according to the International Union for Conservation of Nature, and although their distribution and abundance varied markedly, there were also ubiquitous and abundant species, along with rare species of restricted distribution. The evident heterogeneity of the ten study sites indicates that to conserve amphibians in a mountainous region such as this one it is necessary to protect groups of fragments which represent the variability of the system. Both individually and together cloud forest fragments are very important to conservation because each remnant is inhabited by several threatened species, some of them at imminent risk of extinction.     

Does mobility explain variation in colonisation and population recovery among stream fishes?

1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly. 2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2‐year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best‐supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next‐best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species. 3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre‐removal samples were also abundant in post‐removal samples. 4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small‐scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent.     

Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time

Predicting future species extinctions from patterns of past extinctions or current threat status relies on the assumption that the taxonomic and biological selectivity of extinction is consistent through time. If the driving forces of extinction change through time, this assumption may be unrealistic. Testing the consistency of extinction patterns between the past and the present has been difficult, because the phylogenetically explicit methods used to model present-day extinction risk typically cannot be applied to the data from the fossil record. However, the detailed historical and fossil records of the New Zealand avifauna provide a unique opportunity to reconstruct a complete, large faunal assemblage for different periods in the past. Using the first complete phylogeny of all known native New Zealand bird species, both extant and extinct, we show how the taxonomic and phylogenetic selectivity of extinction, and biological correlates of extinction, change from the pre-human period through Polynesian and European occupation, to the present. These changes can be explained both by changes in primary threatening processes, and by the operation of extinction filter effects. The variable patterns of extinction through time may confound attempts to identify risk factors that apply across time periods, and to infer future species declines from past extinction patterns and current threat status.     

Species–area relationship within benthic habitat patches of a tropical floodplain river: An experimental test

The curvilinear relationship between species richness and habitat area (species–area relationship (SAR)) is a fundamental ecological pattern. The relationship is often viewed from a long‐term perspective across relatively large spatial scales, reflecting a balance between immigration and extinction dynamics. We explored whether predictions of SAR also manifest over short time periods (days) in benthic habitat patches of a dynamic floodplain river where littoral faunal assemblages are continuously assembled and disassembled with changing water levels. We examined the relationship of patch size with faunal abundance (i.e. fish and aquatic invertebrates), taxonomic richness, trophic group richness and overall assemblage composition. Strong taxa–area relationships emerged despite the relatively short experimental time period (21 days); larger patches had more taxa and trophic groups. For the smallest patches, taxonomic richness was especially sensitive to abundance of individuals; abundance of individuals was a less important predictor of taxonomic and trophic group richness for the largest patches. Despite the relatively short time frame for study within this temporally dynamic ecosystem, our findings indicate a strong SAR for fishes and macroinvertebrates inhabiting patchy habitats in the littoral zone of this tropical river.