Different facets of the same niche: Integrating citizen science and scientific survey data to predict biological invasion risk under multiple global change drivers.

Citizen science initiatives have been increasingly used by researchers as a source of occurrence data to model the distribution of alien species. Since citizen science presence-only data suffer from some fundamental issues, efforts have been made to combine these data with those provided by scientifically structured surveys. Surprisingly, only a few studies proposing data integration evaluated the contribution of this process to the effective sampling of species' environmental niches and, consequently, its effect on model predictions on new time intervals. We relied on niche overlap analyses, machine learning classification algorithms and ecological niche models to compare the ability of data from citizen science and scientific surveys, along with their integration, in capturing the realized niche of 13 invasive alien species in Italy. Moreover, we assessed differences in current and future invasion risk predicted by each data set under multiple global change scenarios. We showed that data from citizen science and scientific surveys captured similar species niches though highlighting exclusive portions associated with clearly identifiable environmental conditions. In terrestrial species, citizen science data granted the highest gain in environmental space to the pooled niches, determining an increased future biological invasion risk. A few aquatic species modelled at the regional scale reported a net loss in the pooled niches compared to their scientific survey niches, suggesting that citizen science data may also lead to contraction in pooled niches. For these species, models predicted a lower future biological invasion risk. These findings indicate that citizen science data may represent a valuable contribution to predicting future spread of invasive alien species, especially within national-scale programmes. At the same time, citizen science data collected on species poorly known to citizen scientists, or in strictly local contexts, may strongly affect the niche quantification of these taxa and the prediction of their future biological invasion risk.

Climate shifts orchestrated hominin interbreeding events across Eurasia.

When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins' habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.

Plant invasion risk inside and outside protected areas: Propagule pressure, abiotic and biotic factors definitively matter.

Invasive alien species are among the main global drivers of biodiversity loss posing major challenges to nature conservation and to managers of protected areas. The present study applied a methodological framework that combined invasive Species Distribution Models, based on propagule pressure, abiotic and biotic factors for 14 invasive alien plants of Union concern in Italy, with the local interpretable model-agnostic explanation analysis aiming to map, evaluate and analyse the risk of plant invasions across the country, inside and outside the network of protected areas. Using a hierarchical invasive Species Distribution Model, we explored the combined effect of propagule pressure, abiotic and biotic factors on shaping invasive alien plant occurrence across three biogeographic regions (Alpine, Continental, and Mediterranean) and realms (terrestrial and aquatic) in Italy. We disentangled the role of propagule pressure, abiotic and biotic factors on invasive alien plant distribution and projected invasion risk maps. We compared the risk posed by invasive alien plants inside and outside protected areas. Invasive alien plant distribution varied across biogeographic regions and realms and unevenly threatens protected areas. As an alien's occurrence and risk on a national scale are linked with abiotic factors followed by propagule pressure, their local distribution in protected areas is shaped by propagule pressure and biotic filters. The proposed modelling framework for the assessment of the risk posed by invasive alien plants across spatial scales and under different protection regimes represents an attempt to fill the gap between theory and practice in conservation planning helping to identify scale, site, and species-specific priorities of management, monitoring and control actions. Based on solid theory and on free geographic information, it has great potential for application to wider networks of protected areas in the world and to any invasive alien plant, aiding improved management strategies claimed by the environmental legislation and national and global strategies.

The Different Fate of the Pyrenean Desman (Galemys pyrenaicus) and the Eurasian Otter (Lutra lutra) under Climate and Land Use Changes.

Climate and land use change can affect biodiversity in different ways, e.g., determining habitat loss, altering reproduction periods or disrupting biotic interactions. Here, we investigate the effects of climate and land use change on the spatial distribution of two semi-aquatic mammals, the Pyrenean desman (Galemys pyrenaicus) and the Eurasian otter (Lutra lutra). We first modeled the current potential distribution of the desman and the otter in the Iberian Peninsula, considering topographic, climatic and land use variables. Second, we predicted their potential distribution in 2050 under climate and land use change scenarios. We calculated the percentage of range gain/loss and shift predicted for the two species under such scenarios and quantified the present and future spatial overlap between the two species distribution. Irrespective of the scenario, desman models show loss of suitable habitat, whereas the otter will undergo an opposite trend. Aside from a preponderant habitat loss, the desman is predicted to increase its spatial overlap with otter range under the optimistic scenarios, potentially meaning it will face an exacerbated predation by otters. The potential increase of both habitat loss and otters' predation might represent a major threat for the desman, which may affect the long-term persistence of this endemic species in the Iberian Peninsula.

Is scat marking a reliable tool for otter census and surveys at the landscape scale?

Biological significance of scat marking by otters has been a controversial subject among scientists. Using multiyear (2014-2017) data of otter spraint counts in South Korea, this study aimed to test whether the observed pattern of spraint presence/absence is driven by detection error and if/how scat counts can be a proxy for otter abundance at the landscape scale. To test the first hypothesis, spraint presence/absence was analyzed through occupancy models, which relied on environmental variables related to otter detectability and presence. Spraint count models were used to test the second hypothesis against resource-related covariates in combination with landscape, anthropogenic, and climate variables through machine learning algorithms (MLAs). The detection probability has specifically decreased in areas characterized by high rainfall and human population densities, whereas the probability has increased near food-rich sites, characterized by high marking frequencies. The temporal trends of spraint count predictions were in line with changes in the diversity of fish communities in 2014-2017 instead of fish biomass, suggesting that the availability of feeding resources is higher where fish communities are more diverse. Because diverse fish communities can attract otters, fish diversity conservation is critical for preserving this mammal's populations. This fine scale four-year monitoring has contributed to the disentanglement of the role of spraint presence/absence and spraint counts in detectability and population trends. This will assist in identifying key resource areas and planning strategies to promote otter conservation and dispersal dynamics.

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

[This corrects the article DOI: 10.1371/journal.pone.0226949.].

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 paleoclimatic 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.

A 450 million years long latitudinal gradient in age-dependent extinction.

Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age-dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age-dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern.

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.

Where will it cross next? Optimal management of road collision risk for otters in Italy.

Collisions with vehicles represent the main conflict between infrastructures and wildlife, causing damages to both humans and animals. As to the latter, road mortality is a growing phenomenon and the largest single cause of death for many vertebrates. When focusing on endangered species, the Eurasian otter (Lutra lutra) is among the most vulnerable to road-kills, which represent the predominant cause of deaths recorded in Europe. We propose a large scale spatially-explicit assessment of road-kill risk for the Eurasian otter in Italy as a tool to identify road stretches at high collision risk, thus optimizing the location of mitigation measures. The modelling approach was produced for South Central Italy, hosting the only remnant viable population of otters in Italy. We used a maximum entropy approach including 56 road collision events recorded between 2004 and 2016 through a citizen science initiative, along with seven environmental predictors measured on 1 km grid cells. Four predictors were selected to describe roads characteristics, i.e. density of highways, and of state, regional and local roads. The remaining three variables referred to the quality of otter habitat in the surrounding of the collision sites, i.e. elevation, density of freshwater bodies, and a measure of landscape heterogeneity calculated on land-cover categories. The model achieved a good predictive accuracy (AUC > 0.8; Boyce index > 0.8). The collision probability was mostly affected by elevation, density of state roads, and density of freshwater bodies. Specifically, collision risk was higher in areas at low elevation and medium density of state roads located near rivers and wetlands. In addition, model predictions evidenced that implementing mitigation measures along 10% of road network in the study area could have potentially hampered ca. 50% of otter casualties recorded during the study period.

OpenMICE: an open spatial and temporal data set of small mammals in south-central Italy based on owl pellet data.

The use of database technologies as a tool for implementing data for quantitative ecological studies and biodiversity conservation planning has recently attracted the attention of the biological community. Despite the fact that the number of biodiversity data sets is quickly rising, online databases of small mammals are still scarce, especially for Mediterranean ecosystems. We implemented the first standardized and accessible georeferenced European database of small mammal occurrences, abundances, and functional traits. Data derived from owl pellets was obtained from different sources, including original field surveys, publications, gray literature, existing databases, and museum collections. The OpenMICE database covers the years 1972 to 2017 and includes nearly 50,000 individuals from 23 species (13 Rodentia and 10 Eulipotyphla) at 190 sites in south-central Italy. Our specific goals in compiling this data set were as follows: (1) to make data that is usually accessible to a restricted audience widely available; (2) to identify the gaps in knowledge about small mammal communities and guide future sampling and conservation efforts; and (3) to gain a first insight into small mammal diversity and abundance in the study area. The potential applications of our spatial relational database are many, from individual-based to community-based models as potential indicators of environmental changes at different geographical scales. Given the long-term support for data storage, the OpenMICE database could be further expanded to include other geographical contexts and implemented with new information and traits. We would appreciate that researchers cite this paper if using all or part of the data set. We also request that researchers and teachers inform us of how they are using the data. We intend to keep it up to date as novel studies become available (see Data Availability).

Cold-blooded in the Ice Age: "refugia within refugia", inter-and intraspecific biogeographic diversification of European whipsnakes (Squamata, Colubridae, Hierophis).

In this work, we performed a biogeographic analysis with Bayesian binary MCMC (BBM) statistical dispersal-vicariance analysis (S-DIVA) and species distribution models (SDM) on three phylogenetically closely related Mediterranean whipsnakes (Hierophis gemonensis, H. carbonarius, H. viridiflavus), to investigate the pathways of their geographical diversification and locate putative refugial areas in the last glacial maximum (LGM). Our analysis suggests that the diversification processes between the studied species overall followed an east-west route, from eastern Greece to the Iberian Peninsula and continental France, highlighting a significant role of dispersal and vicariance processes at both inter- and intraspecific levels. In particular, the main lineage-splitting events between H. gemonensis, H. carbonarius and H. viridiflavus coincide with two events of vicariance, involving respectively eastern Greece and eastern Italy, and eastern Italy and western Italy, Iberian Peninsula and continental France. SDM analyses highlight the occurrence of multiple putative glacial refugia in the Balkans, Italy and southern France, which represent well the occurrence of distinct "refugia within refugia" in the main Mediterranean peninsulas. Furthermore, our results suggest how these refugia may have played an important role during the Quaternary climatic oscillations in shaping the current haplotype distribution of European whipsnakes.

Assessing habitat quality in relation to the spatial distribution of protected areas in Italy.

The conservation of species and habitats is increasingly threatened by anthropogenic impacts, particularly land use change, from local to global scales. Although many efforts have been carried out so far to halt or at least reduce the biodiversity loss (e.g., the establishment of protected areas' networks), there are still both knowledge and policy gaps slowing the conservation of species and habitats in complex environments, such as the Mediterranean region. In particular, the human-driven impacts and threats on biodiversity need more careful analysis. Accordingly, this paper aims to assess the habitat quality and degradation in Italy in relation with the spatial pattern of the current protected areas' network, mainly to identify priority areas of intervention, thus supporting large-scale conservation strategies. A survey of experts was conducted to identify the main threats for biodiversity from different land uses at the national scale. The InVEST software was then applied to assess and map habitat quality and degradation with a high spatial resolution (20 m). The relationship between habitat quality and degradation as well as their hotspots, and alternative PA categories were also explored. Results indicate that: (i) habitat quality and degradation depend on the location and intensity of the anthropogenic impacts and are sensitive to different protection levels; (ii) the combination of the survey of experts and the spatially-explicit assessment of habitat quality and degradation is useful to highlight variations of the current conditions of biodiversity and habitats; and (iii) the identification of hotspots allows one to identify priority areas for conservation. Accordingly, the proposed approach may be used to strengthen the conservation efforts in similar contexts, and thus support the implementation of the biodiversity-related policies over the long term.

A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin.

The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently-more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea daffodil especially during LGM because of strong variation in coastline caused by glaciations.

A systematic conservation planning approach to fire risk management in Natura 2000 sites.

A primary challenge in conservation biology is to preserve the most representative biodiversity while simultaneously optimizing the efforts associated with conservation. In Europe, the implementation of the Natura 2000 network requires protocols to recognize and map threats to biodiversity and to identify specific mitigation actions. We propose a systematic conservation planning approach to optimize management actions against specific threats based on two fundamental parameters: biodiversity values and threat pressure. We used the conservation planning software Marxan to optimize a fire management plan in a Natura 2000 coastal network in southern Italy. We address three primary questions: i) Which areas are at high fire risk? ii) Which areas are the most valuable for threatened biodiversity? iii) Which areas should receive priority risk-mitigation actions for the optimal effect?, iv) which fire-prevention actions are feasible in the management areas?. The biodiversity values for the Natura 2000 spatial units were derived from the distribution maps of 18 habitats and 89 vertebrate species of concern in Europe (Habitat Directive 92/43/EEC). The threat pressure map, defined as fire probability, was obtained from digital layers of fire risk and of fire frequency. Marxan settings were defined as follows: a) planning units of 40 × 40 m, b) conservation features defined as all habitats and vertebrate species of European concern occurring in the study area, c) conservation targets defined according with fire sensitivity and extinction risk of conservation features, and d) costs determined as the complement of fire probabilities. We identified 23 management areas in which to concentrate efforts for the optimal reduction of fire-induced effects. Because traditional fire prevention is not feasible for most of policy habitats included in the management areas, alternative prevention practices were identified that allows the conservation of the vegetation structure. The proposed approach has potential applications for multiple landscapes, threats and spatial scales and could be extended to other valuable natural areas, including protected areas.

What story does geographic separation of insular bats tell? A case study on Sardinian rhinolophids.

Competition may lead to changes in a species' environmental niche in areas of sympatry and shifts in the niche of weaker competitors to occupy areas where stronger ones are rarer. Although mainland Mediterranean (Rhinolophus euryale) and Mehely's (R. mehelyi) horseshoe bats mitigate competition by habitat partitioning, this may not be true on resource-limited systems such as islands. We hypothesize that Sardinian R. euryale (SAR) have a distinct ecological niche suited to persist in the south of Sardinia where R. mehelyi is rarer. Assuming that SAR originated from other Italian populations (PES)--mostly allopatric with R. mehelyi--once on Sardinia the former may have undergone niche displacement driven by R. mehelyi. Alternatively, its niche could have been inherited from a Maghrebian source population. We: a) generated Maxent Species Distribution Models (SDM) for Sardinian populations; b) calibrated a model with PES occurrences and projected it to Sardinia to see whether PES niche would increase R. euryale's sympatry with R. mehelyi; and c) tested for niche similarity between R. mehelyi and PES, PES and SAR, and R. mehelyi and SAR. Finally we predicted R. euryale's range in Northern Africa both in the present and during the Last Glacial Maximum (LGM) by calibrating SDMs respectively with SAR and PES occurrences and projecting them to the Maghreb. R. mehelyi and PES showed niche similarity potentially leading to competition. According to PES' niche, R. euryale would show a larger sympatry with R. mehelyi on Sardinia than according to SAR niche. Such niches have null similarity. The current and LGM Maghrebian ranges of R. euryale were predicted to be wide according to SAR's niche, negligible according to PES' niche. SAR's niche allows R. euryale to persist where R. mehelyi is rarer and competition probably mild. Possible explanations may be competition-driven niche displacement or Maghrebian origin.

The use of climatic niches in screening procedures for introduced species to evaluate risk of spread: a case with the American Eastern grey squirrel.

Species introduction represents one of the most serious threats for biodiversity. The realized climatic niche of an invasive species can be used to predict its potential distribution in new areas, providing a basis for screening procedures in the compilation of black and white lists to prevent new introductions. We tested this assertion by modeling the realized climatic niche of the Eastern grey squirrel Sciurus carolinensis. Maxent was used to develop three models: one considering only records from the native range (NRM), a second including records from native and invasive range (NIRM), a third calibrated with invasive occurrences and projected in the native range (RCM). Niche conservatism was tested considering both a niche equivalency and a niche similarity test. NRM failed to predict suitable parts of the currently invaded range in Europe, while RCM underestimated the suitability in the native range. NIRM accurately predicted both the native and invasive range. The niche equivalency hypothesis was rejected due to a significant difference between the grey squirrel's niche in native and invasive ranges. The niche similarity test yielded no significant results. Our analyses support the hypothesis of a shift in the species' climatic niche in the area of introductions. Species Distribution Models (SDMs) appear to be a useful tool in the compilation of black lists, allowing identifying areas vulnerable to invasions. We advise caution in the use of SDMs based only on the native range of a species for the compilation of white lists for other geographic areas, due to the significant risk of underestimating its potential invasive range.