Low bird diversity in the Fynbos plant diversity hotspot: Quaternary legacies in the current distributions of passerine birds

The Fynbos Biome or Cape Floristic Region is well‐known for its plant diversity. This diversity does not seem to carry over at higher trophic levels, and in particular in birds. Here, we analyzed the passerine bird assemblages of the Fynbos Biome at the quarter degree resolution with occupancy models and citizen science data. Multivariate analysis of distribution summary metrics revealed a gradient of specialist to generalist species, in which range‐restricted, specialist species responded positively to increases in number of competing species and included ancient lineages. Wide‐ranging, generalist species exhibited stronger affinities for the arid Karoo Biomes than for the other neighboring biome (Albany Thicket) and for the other mesic biomes in South Africa. Both results are explained by the Quaternary legacy hypothesis: the combined effects of habitat filtering, isolation by distance, and limited in situ diversification, acting throughout the Quaternary, and caused by the contrasting winter‐rainfall regime of the region and the low phylogenetic diversity and original adaptations of the plant assemblages.     

Integrating individual habitat choices and regional distribution of a biodiversity indicator and top predator

Aim Habitat selection studies have mainly focused on behavioural choices of individuals or on the habitat‐related regional distribution of a population, with little integration of the two approaches. This is despite the fact that traditional biogeography theory sees the geographical distribution of a species as the collective outcome of the adaptive habitat choices of individuals. Here, we integrate individual habitat choices with regional distribution through a bottom‐up Geographical Information System (GIS)‐based approach, by using a 9‐year data set on a large avian predator, the eagle owl (Bubo bubo L.). We further examine the potential population level and biodiversity consequences of this approach. Location The study was conducted in the Trento Region (central‐eastern Italian Alps) and in six other areas of the nearby Lombardia Region in the central Alps. Methods We used stepwise logistic regression to build a habitat suitability model discriminating between eagle owl territories and an equal number of random locations. The model was applied to the whole Trento region by means of a GIS so as to predict suitable habitat patches. The predicted regional distribution (presence–absence in 10‐km grid quadrats) was then compared with the observed one. Furthermore, we compared estimates of biodiversity in quadrats with and without eagle owls, so as to test whether the presence of this top predator may signal macro‐areas of high biodiversity. Results The logistic habitat suitability model showed that, compared with a random distribution, eagle owls selected low‐elevation breeding sites with high availability of prey‐rich habitats in their surroundings. Breeding performance increased with the availability of prey‐rich habitats, confirming the adaptiveness of the detected habitat choices. We applied the habitat suitability model to the 6200 km² study region by means of a GIS and found a close fit between the observed and predicted regional distribution. Furthermore, population abundance was positively related to the availability of habitat defined as suitable by the above analyses. Finally, high biodiversity levels were associated with owl presence and with the amount of suitable owl habitat, demonstrating that modelling habitat suitability of a properly chosen indicator species may provide key conservation information at the wider ecosystem level. Main conclusions Our bottom‐up modelling approach may increase the conservation‐value of habitat selection models, by (1) predicting local and regional distribution, (2) estimating regional population size, (3) stimulating further hypothesis testing, (4) forecasting the population effects of future habitat loss and degradation and (5) aiding in the identification and prioritization of high‐biodiversity areas.     

Assessing the vulnerability of species richness to anthropogenic climate change in a biodiversity hotspot

Aim To compare theoretical approaches towards estimating risks of plant species loss to anthropogenic climate change impacts in a biodiversity hotspot, and to develop a practical method to detect signs of climate change impacts on natural populations. Location The Fynbos biome of South Africa, within the Cape Floristic Kingdom. Methods Bioclimatic modelling was used to identify environmental limits for vegetation at both biome and species scale. For the biome as a whole, and for 330 species of the endemic family Proteaceae, tolerance limits were determined for five temperature and water availability‐related parameters assumed critical for plant survival. Climate scenarios for 2050 generated by the general circulation models HadCM2 and CSM were interpolated for the region. Geographic Information Systems‐based methods were used to map current and future modelled ranges of the biome and 330 selected species. In the biome‐based approach, predictions of biome areal loss were overlayed with species richness data for the family Proteaceae to estimate extinction risk. In the species‐based approach, predictions of range dislocation (no overlap between current range and future projected range) were used as an indicator of extinction risk. A method of identifying local populations imminently threatened by climate change‐induced mortality is also described. Results A loss of Fynbos biome area of between 51% and 65% is projected by 2050 (depending on the climate scenario used), and roughly 10% of the endemic Proteaceae have ranges restricted to the area lost. Species range projections suggest that a third could suffer complete range dislocation by 2050, and only 5% could retain more than two thirds of their range. Projected changes to individual species ranges could be sufficient to detect climate change impacts within ten years. Main conclusions The biome‐level approach appears to underestimate the risk of species diversity loss from climate change impacts in the Fynbos Biome because many narrow range endemics suffer range dislocation throughout the biome, and not only in areas identified as biome contractions. We suggest that targeted vulnerable species could be monitored both for early warning signs of climate change and as empirical tests of predictions.     

Predicting the occurrence of rare Brazilian birds with species distribution models

Species distribution models (SDMs) yield reliable and needed predictions to identify regions that have similar environmental conditions and were used here to predict potential ranges of rare species to identify new localities were they might occur based on their occurrence probability (i.e. niche suitability). We modeled the potential distribution ranges of ten endangered or rare birds from the South American Cerrado biome, using four temperature- and four precipitation-related bioclimatic variables, three topographical variables, and nine different niche modeling methods for each species. We used an ensemble-forecasting approach to reach a consensus scenario to obtain the average distribution for each species based on the five best models generating a distribution map of each species. Model efficiency was related to sample size and not appropriate below ten independent spatial occurrences. The potential distributions of seven species revealed that their occurrence ranges might go beyond their known ranges, but that most of them seem to occur near the regions where they have already been reported. The models of only three species were considered unsatisfactory in helping identify their potential distribution. Models created maps with higher occurrence probability regions where rare Cerrado birds might occur. These range projections can potentially decrease the costs and improve the efficiency of future field searches. On methodological terms, the application of SDMs to predict species ranges should compare different modeling methods and evaluate the effect of sample size on their performance.     

Host range and distribution of small mammal fleas in South Africa,with a focus on species of medical and veterinary importance

The host range and distribution of flea species on rodents and insectivores across multiple vegetation types in South Africa were investigated. Habitat suitability for flea species considered as important vectors of disease in humans and domestic animals was modelled. Data originated from fleas that were recovered from small mammals captured at 29 localities during 2009–2013 and published literature searched for flea records. Climate‐based predictor variables, widely used in arthropod vector distribution, were selected and habitat suitability modelled for 10 flea vector species. A total of 2469 flea individuals representing 33 species and subspecies were collected from 1185 small mammals. Ten of each of the flea and rodent species are plague vectors and reservoirs, respectively. Multiple novel flea–host associations and locality records were noted. Three vector species were recorded from insectivores. Geographic distributions of flea species ranged from broad, across‐biome distributions to narrower distributions within one or two biomes. Habitat suitability models performed excellently for the majority of flea vectors and identified regions of summer and all‐year rainfall as representing suitable habitats for most vector species. Current knowledge of vector and disease ecology can benefit from similar sampling approaches that will be important not only for South Africa, but also for the sub‐region.     

Inferring biome associations of recent mammals from samples of temperate and tropical faunas: Paleoecological considerations

Reconstruction of past faunal assemblages is of primary concern to paleontologists because it yields important information concerning patterns of community structure, biogeography, and paleoclimatology. Unfortunately, the process of fossilization is serendipitous at best, resulting in fossil beds that only contain a sample of the extant fauna that existed at the time of fossilization. Herein, we examine the degree to which incomplete sampling of four well‐known small mammal faunas gives rise to uncertainty concerning the biome association of each site using neontological data from two tropical (Brazilian Cerrado and Gallery Forest) and two temperate (Kansas Prairie and Kentucky Mixed Deciduous‐coniferous Forest) areas. Two simulation approaches (variable and fixed sample sizes) were applied to each set of data to ascertain what proportion of the mammal fauna must be sampled before inferring the correct biome to which the fauna pertained. In the variable sample size approach, species were selected at random from the species pool until the sample correctly identified the biome from which the sample was obtained; this was repeated 200 times for each of the 4 sites. In the fixed sample size approach, a series of simulations were conducted in which each simulation had a fixed number of species, beginning at 2 and increasing at regular intervals until the entire fauna was included in the sample. The number of species required to correctly associate a site with the proper biome was highly variable for three of the four sites. As a result, the number of species required in a sample to be 95% certain of the biome association of Mixed Deciduous‐coniferous Forest, Prairie, and Gallery Forest sites represented a large proportion of the fauna in each case (78%, 88%, and 89%, respectively). In contrast, only 23% of the fauna needed to be sampled from the Cerrado site to obtain the same level of confidence. Adjusting the Cerrado analysis for the effect of endemic species only resulted in an inflation of this value to 33%. The effects of endemics in reducing the certainty of biome associations are only pronounced when sample sizes are small compared to the total species pool. The accuracy of estimating the correct biome association of a fauna is predicated upon the proportion of the fauna in the sample as well as the particular distributional patterns of the species that compose the fauna. Caution should be exercised when inferring the biome association of fossil sites because neither of these features of the sample are usually known. Moreover, even when these features are know, as in the neontological analyses, a large proportion of the fauna frequently is required to be confident of the correct biome association of the fauna. Results indicate that the body size of species found in a fossil assemblage or their ordinal taxonomic affinities can affect the probability of accurately deducing paleoenvironments. Smaller species, and members of the orders Rodentia or Insectivora, are more stenotopic than larger species, or members of the orders Artiodactyla and Carnivora. Fossil assemblages containing only members of the latter groups will consist of wide‐ranging species of broad habitat tolerance. Thus the paleoenvironment of such a fossil assemblage will be difficult to discern.     

Environmental correlates of anuran beta diversity in the Brazilian Cerrado

Evolutionary processes are known to influence contemporary patterns of biological diversity, yet disentangling the effects of current and historical drivers of biodiversity patterns remain challenging. We use spatial analyses of community dissimilarity to generate hypotheses about the current and historical processes underlying patterns of beta diversity in anuran species in the Brazilian Cerrado. Specifically, we use a generalized dissimilarity modeling (GDM) approach to model compositional dissimilarity of anuran species and endemics as a function of geographic separation and local (within‐Cerrado) environmental conditions. To gain insight about potential historical processes, we incorporate information from biomes adjacent to the Cerrado to investigate whether environmental conditions in neighboring areas can help explain patterns of beta diversity within the Cerrado. Patterns of anuran beta diversity of both endemics and all species in the Cerrado appear to be strongly influenced by local environmental gradients, with elevation as one of the most important variables in all models. However, in models using endemic species only, environmental conditions of adjacent biomes were related to beta‐diversity patterns, and more strongly so, than to total species models. These results suggest that phylogenetic niche conservatism within species groups that invaded the Cerrado from adjacent biomes may cause these species to be restricted to environmental conditions within the Cerrado that are most similar to the conditions in the adjacent biome where they originated. Time‐calibrated phylogenies of Cerrado endemics and studies of ancestral and current ranges of Cerrado species are needed to test this hypothesis.     

Geographical ecology and conservation of Eugenia L. (Myrtaceae) in the Brazilian Cerrado: Past,present and future

Human actions have caused the fragmentation of natural vegetation, habitat loss and climate change. The Cerrado, considered one of the global hotspots of diversity, has suffered great habitat loss due to these factors, which has been aggravated by the agricultural expansion that took place during the last 60 years. In this context, we chose species of the genus Eugenia L. (Myrtaceae) occurring in the Brazilian Cerrado to describe richness patterns and range loss, and determine conservation priorities for the Cerrado. Ecological niche models (ENMs) were applied to calculate the geographical range of each species in the past (Last Glacial Maximum – LGM, 21 000 years ago), present (PIP, representing current climatic conditions – 1760 years ago) and future (near future – NF, 2080–2100). These results were combined to calculate the richness of the group and also to estimate the range loss of these species in the future. Moreover, we evaluated the irreplaceability of areas for species conservation, aiming to maximize the biotic stability of Eugenia species. Our results showed that the highest species richness in the past was found in the southwestern region of the Cerrado and, currently, the richest regions are found in the central and southeastern areas. However, in the future, we predict a shift of the greatest values of richness towards the southeastern region, an area currently occupied by the Atlantic forest. Although areas with high conservation priorities were found scattered across the biome, this shift is worrisome due to the high fragmentation rate and intensive human occupation thoughout the Atlantic region. Thus, conservation efforts should focus on areas found within these limits.     

Geographic shifts in climatically suitable areas and loss of genetic variability in Dipteryx alata ("Baru" Tree; Fabaceae)

Many species are expected to suffer strong shifts in their geographic ranges due to climate changes in the next 50 years, with severe consequences for biodiversity patterns and population structure. We used here an ensemble forecast approach for obtaining species' range in which multiple species distribution models and climatic models were combined to model loss of genetic variability in Baru, Dipteryx alata (Fabaceae), an economically important Neotropical tree native to the Cerrado of Brazil. We estimated a series of genetic parameters (number of alleles per locus, expected heterozygosity under Hardy-Weinberg equilibrium and mutation-drift equilibrium) for this species based on eight microsatellite loci. We then recalculated these parameters assuming that local populations in areas of low future environmental suitability will go extinct. All genetic parameters remained approximately constant up to a 50% threshold of climatic suitability in the future; after this critical threshold there is an abrupt reduction in all parameters, although the magnitude of shift is only about 10% of current values, on average. Thus, despite the shifts in geographic range and climatically suitable areas towards southeastern Brazil, our analyses do not predict a strong loss of genetic diversity in D. alata because of the broad tolerance of this species, which ensures large future ranges, contrasting with other Cerrado species that have been analyzed in a similar manner.     

Model‐based integration of observed and expert‐based information for assessing the geographic and environmental distribution of freshwater species

Freshwater ecosystems harbor specialized and vulnerable biodiversity, and the prediction of potential impacts of freshwater biodiversity to environmental change requires knowledge of the geographic and environmental distribution of taxa. To date, however, such quantitative information about freshwater species distributions remains limited. Major impediments include heterogeneity in available species occurrence data, varying detectability of species in their aquatic environment, scarcity of contiguous freshwater‐specific predictors, and methods that support addressing these issues in a single framework. Here we demonstrate the use of a hierarchical Bayesian modeling (HBM) framework that combines disparate species occurrence information with newly‐developed 1 km freshwater‐specific predictors, to account for imperfect species detection and make fine‐grain (1 km) estimates of distributions in freshwater organisms. The approach integrates a Bernoulli suitability and a Binomial observability process into a hierarchical zero‐inflated Binomial model. The suitability process includes point presence observations, records of site visits, 1 km environmental predictors and expert‐derived species range maps integrated with a distance‐decay function along the within‐stream distance as covariates. The observability process uses repeated observations to estimate a probability of observation given that the species was present. The HBM accounts for the spatial autocorrelation in species habitat suitability projections using an intrinsic Gaussian conditional autoregressive model. We used this framework for three fish species native to different regions and habitats in North America. Model comparison shows that HBMs significantly outperformed non‐spatial GLMs in terms of AUC and TSS scores, and that expert information when appropriately included in the model can provide an important refinement. Such ancillary species information and an integrative, hierarchical Bayesian modeling framework can therefore be used to advance fine‐grain habitat suitability predictions and range size estimates in the freshwater realm. Our approach is extendable in terms of data availability and generality and can be used on other freshwater organisms and regions.     

Status of succulent shrubs in the southern Namib Desert, Succulent Karoo Biome

The ratio of dead to alive succulent shrubs as an indicator of turnover was investigated to test whether the accepted notion of rapid turnover rates and cyclic succession in the Succulent Karoo Biome are applicable in the southern Namib. Based on counts of dead and alive plants, twelve species in two habitat types were investigated. These short‐term data which could not incorporate recruitment rates or changes over time, generated, however, some hypotheses. (i) Rapid turnover rates are likely not supported by all succulent plants at the Succulent Karoo Biome's northern boundary. With the exception of one species, mortality rates in succulent shrubs across a range of plant functional types were lower than reported in other parts of the biome. (ii) Sand plains appeared to support some transient species, indicating that there may be differences in vegetation dynamics between habitats. (iii) Species of different plant functional types showed no differences in ratio of dead to alive plants related to habitat. These species may have broad ecological tolerance limits and are perhaps less affected by changes in their environment. (iv) Shrubby Mesembryanthemaceae have high turnover rates and hence a short live span in the investigated area, but are longer lived than elsewhere in the Succulent Karoo Biome. As these hypotheses have implications for management and conservation of succulent species in this global biodiversity hotspot, a detailed evaluation of vegetation turnover, balancing mortality versus recruitment, should be investigated over a longer time span.     

Integrative Study of Brazilian Anurans: Geographic Distribution,Size, Environment,Taxonomy, and Conservation

Most megadiversity regions lack basic wild animal diversity information such as species lists. This absence of basic knowledge restricts the development and effectiveness of conservation action plans, which are urgently needed for animal groups such as amphibians, the most threatened vertebrate group in the world. In this study, we estimated Brazilian anuran diversity based on species range distribution shapes and evaluated factors that likely affect species lists, such as current taxonomy knowledge, current number of specimens collected in each region, biome characteristics, and anuran size (snout–vent length). We were able to demonstrate differences among the distributional patterns of species within each biome and each Brazilian federative state and among certain factors that influence their diversity, such as latitudinal variation. In this integrative study, we provide zoogeographic information about the richest (in terms of anuran biodiversity) country in the world (at least 849 described species, about 60% of which are endemic), which may be fundamental to future conservation actions in Brazil.     

Conserving the Brazilian semiarid (Caatinga) biome under climate change

The Caatinga is a semiarid biome of the northeast of Brazil with only 1?% of its territory currently conserved. The biome’s biodiversity is highly threatened due to exposure to land conversion for agricultural and cattle ranch. Climate forecasts predict increases in aridity, which could pose additional threats to the biome’s biodiversity. Here, we ask if the remnants of natural vegetation in Caatinga biome, where endemic terrestrial vertebrate species occur, are likely to retain more climatic suitability under climate change scenarios than other less pristine areas of the biome. In order to assess changes in climate suitability across individual species ranges, ensemble forecasting was used based on seven bioclimatic envelope models, three atmosphere–ocean general circulation models, and two greenhouse emission gas scenarios for 2020, 2050, and 2080. We found that most species will gain climatic suitability in the natural vegetation remnants of the Caatinga. Such gains are even greater than the expected to occur within random sets of areas with size similar to the natural vegetation remnants. Our results suggest that natural vegetation remnants will likely play a role of climate refuges for endemic vertebrate species, so efforts should be concentrated in these regions.     

Shifts in potential geographical distribution of Pterocarya stenoptera under climate change scenarios in China

Climate change poses a serious threat to biodiversity. Predicting the effects of climate change on the distribution of a species' habitat can help humans address the potential threats which may change the scope and distribution of species. Pterocarya stenoptera is a common fast‐growing tree species often used in the ecological restoration of riverbanks and alpine forests in central and eastern China. Until now, the characteristics of the distribution of this species' habitat are poorly known as are the environmental factors that influence its preferred habitat. In the present study, the Maximum Entropy Modeling (Maxent) algorithm and the Genetic Algorithm for Ruleset Production (GARP) were used to establish the models for the potential distribution of this species by selecting 236 sites with known occurrences and 14 environmental variables. The results indicate that both models have good predictive power. Minimum temperature of coldest month (Bio6), mean temperature of warmest quarter (Bio10), annual precipitation (Bio12), and precipitation of driest month (Bio14) were important environmental variables influencing the prediction of the Maxent model. According to the models, the temperate and subtropical regions of eastern China had high environmental suitability for this species, where the species had been recorded. Under each climate change scenario, climatic suitability of the existing range of this species increased, and its climatic niche expanded geographically to the north and higher elevation. GARP predicted a more conservative expansion. The projected spatial and temporal patterns of P. stenoptera can provide reference for the development of forest management and protection strategies.     

Compliance to Brazil's Forest Code will not protect biodiversity and ecosystem services

In striking contrast to heartening events in the adjacent Amazon, Brazil's Cerrado biome has seen continued deforestation over the past decade. Though approved in 2012, no study evaluated the impacts of new Brazilian Forest Code (FC) revision on biodiversity and ecosystem services. Here, we report the first assessment of the likely loss and gain in biodiversity and ecosystem services expected if the FC is properly enforced across 200 million hectares of the Cerrado. We also discuss the challenges associated to compliance with the law and present opportunities for conservation. Establishing restoration programmes in private properties with currently less native vegetation than required by the FC could create habitat for 25% more threatened species than now found in these places and could also increase water security and carbon stock in 56.6 MtC. More important, trading environmental reserve quotas coupled with the strategic expansion of protected areas on private and public land could definitely rescue the Cerrado from the brink.     

Habitat area and climate stability determine geographical variation in plant species range sizes

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ~ 85 000 plant species across the New World. We assess prominent hypothesised range‐size controls, finding that plant range sizes are codetermined by habitat area and long‐ and short‐term climate stability. Strong short‐ and long‐term climate instability in large parts of North America, including past glaciations, are associated with broad‐ranged species. In contrast, small habitat areas and a stable climate characterise areas with high concentrations of small‐ranged species in the Andes, Central America and the Brazilian Atlantic Rainforest region. The joint roles of area and climate stability strengthen concerns over the potential effects of future climate change and habitat loss on biodiversity.