Painting maps with bats: Species distribution modelling in bat research and conservation

Species distribution models (SDMs) offer an effective tool for identifying species conservation requirements and forecasting how global environmental changes will affect species diversity and distribution. This approach is particularly relevant for bats because their nocturnal behaviour hinders detectability and identification in flight. Despite their important contribution to global biodiversity and wide geographical ranges, bats have been under-represented in early SDM studies, and only in the last few years has this approach become more widely used in bat research. We carried out a meta-analysis of the published literature to review the history of the use of SDMs in bat research and their application in conservation, climate change assessments and genetic studies. We focus on the geographical coverage, theme and modelling algorithm of published studies, and compare studies that are uniquely dedicated to bats to multi-taxa studies that include bats. We provide recommendations for good modelling practices through considering spatial scale and spatial biases, selecting ecologically relevant variables, following rigorous modelling protocols, and recognising the limitations of extrapolation across temporal scales. We suggest future developments that will further favour the use of SDMs to study bat ecology and biogeography, as well as inform conservation management. We conclude that despite an increase in bat SDM studies, their scope and application can be further enhanced through incorporating dispersal, landscape connectivity and biotic interactions between bats, their prey and their pathogens

Potential distribution of Xylella fastidiosa in Italy: a maximum entropy model

Species distribution models may provide realistic scenarios to explain the influence of bioclimatic variables in the context of emerging plant pathogens. Xylella fastidiosa is a xylem-limited Gram-negative bacterium causing severe diseases in many plant species. We developed a maximum entropy model for X. fastidiosa in Italy. Our objectives were to carry out a preliminary analysis of the species’ potential geographical distribution and determine which eco-geographical variables may favour its presence in other Italian regions besides Apulia. The analysis of single variable contribution showed that precipitation of the driest (40.3%) and wettest (30.4%) months were the main factors influencing model performance. Altitude, precipitation of warmest quarter, mean temperature of coldest quarter, and land cover provided a total contribution of 19.5%. Based on the model predictions, X. fastidiosa has a high probability (> 0.8) of colonizing areas characterized by: i) low altitude (0–150 m a.s.l.); ii) precipitations in the driest month < 10 mm, in the wettest month ranging between 80–110 mm and during the warmest quarter < 60 mm; iii) mean temperature of coldest quarter ≥ 8°C; iv) agricultural areas comprising intensive agriculture, complex cultivation patterns, olive groves, annual crops associated with permanent crops, orchards and vineyards; forest (essentially oak woodland); and Mediterranean shrubland. Species distribution models showed a high probability of X. fastidiosa occurrence in the regions of Apulia, Calabria, Basilicata, Sicily, Sardinia and coastal areas of Campania, Lazio and south Tuscany. Maxent models achieved excellent levels of predictive performance according to area under curve (AUC), true skill statistic (TSS) and minimum difference between training and testing AUC data (AUCdiff). Our study indicated that X. fastidiosa has the potential to overcome the current boundaries of distribution and affect areas of Italy outside Apulia

Testing for changes in rate of evolution and position of the climatic niche of clades

1. There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra- specific level (hence they ignore phylogeny) or rely on the Brownian motion model of evolution to estimate phylogenetic effects on climatic niche variation. The Brownian mo-tion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not in-dicate that the effect of shared ancestry was relevant to niche evolution.2. We introduce a new phylogenetic comparative method which describes sig-nificant changes in the width and position of the climatic niche at the inter-specific (clade) level, while making no a priori assumption about how niche evolution took place.3. We devised the R function phylo.niche.shift to estimate whether the climatic niches of individual clades in the tree are either wider or narrower than expected, and whether the niche occupies unexpected climates. We tested phylo.niche.shift on realistic virtual species’ distribution patterns applied to a phylogeny of 365 extant primate species.4. We demonstrate via simulations that the new method is fast and accurate under widely different climatic niche evolution scenarios. phylo.niche.shift showed that the capuchin monkeys and langurs occupy much wider, and prosimian much narrower, climatic niche space than expected by their phylogenetic positions.5. phylo.niche.shift may help to improve research on niche evolution by allow-ing researchers to test specific hypotheses on the factors affecting clades’ realised niche width and position, and the potential effects of climate change on species’ distribution

A new, fast method to search for morphological convergence with shape data

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4-6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence

From Smart Apes to Human Brain Boxes. A Uniquely Derived Brain Shape in Late Hominins Clade

Modern humans have larger and more globular brains when compared to other primates. Such anatomical features are further reflected in the possession of a moderately asymmetrical brain with the two hemispheres apparently rotated counterclockwise and slid anteroposteriorly on one another, in what is traditionally described as the Yakovlevian torque. Developmental disturbance in human brain asymmetry, or lack thereof, has been linked to several cognitive disorders including schizophrenia and depression. More importantly, the presence of the Yakovlevian torque is often advocated as the exterior manifestation of our unparalleled cognitive abilities. Consequently, studies of brain size and asymmetry in our own lineage indirectly address the question of what, and when, made us humans, trying to trace the emergence of brain asymmetry and expansion of cortical areas back in our Homo antecedents. Here, we tackle this same issue by studying the evolution of human brain size, shape, and asymmetry on a phylogenetic tree including 19 apes and Homo species, inclusive of our fellow ancestors. We found that a significant positive shift in the rate of brain shape evolution pertains to the clade including modern humans, Neanderthals, and Homo heidelbergensis. Although the Yakovlevian torque is well evident in these species and levels of brain asymmetry are correlated to changes in brain shape, further early Homo species possess the torque. Even though a strong allometric component is present in hominoid brain shape variability, this component seems unrelated to asymmetry and to the rate shift we recorded. These results suggest that changes in brain size and asymmetry were not the sole factors behind the fast evolution of brain shape in the most recent Homo species. The emergence of handedness and early manifestations of cultural modernity in the archeological record nicely coincide with the same three species sharing the largest and most rapidly evolving brains among all hominoids

The masked invader strikes again: The conquest of Italy by the Northern raccoon

The Northern raccoon Procyon lotor is a species native to North and Central America, but alien populations have established in Europe, several Caribbean islands, Azerbaijan, Uzbekistan and Japan, being introduced for fur farming, hunting, or as pets/attraction in animal parks. In the introduced range, raccoons may impact on breeding birds and amphibians, exert crop damages and transmit pathologies to wild species and humans. The species has been introduced also in Italy, where the only known reproductive population is observed since 2004 in Lombardy, along the Adda river. We reconstructed the current distribution range of the Northern raccoon in Italy, collecting information from scientific papers, articles in newspapers and books, as well from experts and local reporters. A total of 53 occurrence points were collected from observation sites. Since 2008, records from Lombardy increased, and sporadic observations were reported from seven other regions. A complete lack of records from the Northernmost provinces of Lombardy (Varese, Como and Sondrio) suggests that the only Italian population does not derive from a range expansion from Switzerland, but it should be considered as an independent, new introduction. Accidental observations of single individuals possibly escaped from captivity are often ignored, and only few animals were removed from the wild. An analysis of the potential distribution of the species was performed in a species distribution modeling framework (MaxEnt). A global model was built up considering the occurrences of reproductive populations from the native range and introduced areas in Europe and Japan and then projected to Italy. The model suggested a good suitability for the plains in Central-Northern Italy and a very low suitability of the Alpine region, thus providing support to the hypothesis that the Italian population did not derive from dispersal from Switzerland. If escapes or releases of raccoons will continue, there is a risk that the species could colonize other areas, making its containment more difficult

Diversification Rates and the Evolution of Species Range Size Frequency Distribution

The geographic range sizes frequency distribution (RFD) within clades is typically right-skewed with untransformed data, and bell-shaped or slightly left-skewed under the log-transformation. This means that most species within clades occupy diminutive ranges, whereas just a few species are truly widespread. A number of ecological and evolutionary explanations have been proposed to account for this pattern. Among the latter, much attention has been given to the issue of how extinction and speciation probabilities influence RFD. Numerous accounts now convincingly demonstrate that extinction rate decreases with range size, both in living and extinct taxa. The relationship between range size and speciation rate, though, is much less obvious, with either small or large ranged species being proposed to originate more daughter taxa. Herein, we used a large fossil database including twenty-one animal clades and more than 80,000 fossil occurrences distributed over more than 400 million years of marine metazoans (exclusive of vertebrates) evolution, to test the relationship between extinction rate, speciation rate, and range size. As expected, we found that extinction rate almost linearly decreases with range size. In contrast, speciation rate peaks at the large (but not the largest) end of the range size spectrum. This is consistent with the peripheral isolation mode of allopatric speciation being the main mechanism of species origination. The huge variation in phylogeny, fossilization potential, time of fossilization, and the overarching effect of mass extinctions suggest caution must be posed at generalizing our results, as individual clades may deviate significantly from the general pattern

The role of habitat fragmentation in Pleistocene megafauna extinction in Eurasia

The idea that several small, rather than a single large, habitat areas should hold the highest total species richness (the so-called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long-term dimension of extinction risk. Here, we provide the first long-term evaluation of the role of habitat fragmentation in species extinction, focusing on 22 large mammal species that lived in Eurasia during the last 200 000 years. By combining species distribution models and landscape pattern analysis, we compared temporal dynamics of habitat spatial structure between extinct and extant species, estimating the size, number and degree of the geographical isolation of their suitable habitat patches. Our results evidenced that extinct mammals went through considerable habitat fragmentation during the last glacial period and started to fare worse than extant species from about 50 ka. In particular, our modelling effort constrains the fragmentation of habitats into a narrow time window, from 46 to 36 ka ago, surprisingly coinciding with known extinction dates of several megafauna species. Landscape spatial structure was the second most important driver affecting megafauna extinction risk (ca 38% importance), after body mass (ca 39%) and followed by dietary preferences (ca 20%). Our results indicate a major role played by landscape fragmentation on extinction. Such evidence provides insights on what might likely happen in the future, with climate change, habitat loss and fragmentation acting as the main forces exerting their negative effects on biodiversity

A major change in rate of climate niche envelope evolution during hominid history

Homo sapiens is the only species alive able to take advantage of its cognitive abilities to inhabit almost all environments on Earth. Humans are able to culturally construct, rather than biologically inherit, their occupied climatic niche to a degree unparalleled within the animal kingdom. Precisely when hominins acquired such an ability remains unknown, and scholars disagree on the extent to which our ancestors shared this same ability. Here, we settle this issue using fine-grained palaeoclimatic data, extensive archaeological data and phylogenetic comparative methods. Our results indicate that whereas early hominins were forced to live under physiologically suitable climatic conditions, with the emergence of H. heidelbergensis, the Homo climatic niche expanded beyond its natural limits, despite progressive harshening in global climates. This indicates that technological innovations providing effective exploitation of cold and seasonal habitats predated the emergence of Homo sapiens