Comparing pseudo-absences generation techniques in Boosted Regression Trees models for conservation purposes: A case study on amphibians in a protected area

Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule

Background

Suitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution.

Methodology

We integrated climate-based ecological niche models with information about topography and rivers' network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85).

Results

Current weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a 'belt' connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe.

Conclusions

The outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats.

Quantification of Foraging Areas for the Northern Bald Ibis (Geronticus eremita) in the Northern Alpine Foothills: A Random Forest Model Fitted with Optical and Actively Sensed Earth Observation Data

The Northern Bald Ibis (Geronticus eremita, NBI) is an endangered migratory species, which went extinct in Europe in the 17th century. Currently, a translocation project in the frame of the European LIFE program is carried out, to reintroduce a migratory population with breeding colonies in the northern and southern Alpine foothills and a common wintering area in southern Tuscany. The population meanwhile consists of about 200 individuals, with about 90% of them carrying a GPS device on their back. We used biologging data from 2021 to model the habitat suitability for the species in the northern Alpine foothills. To set up a species distribution model, indices describing environmental conditions were calculated from satellite images of Landsat-8, and in addition to the well-proven use of optical remote sensing data, we also included Sentinel-1 actively sensed observation data, as well as climate and urbanization data. A random forest model was fitted on NBI GPS positions, which we used to identify regions with high predicted foraging suitability within the northern Alpine foothills. The model resulted in 84.5% overall accuracy. Elevation and slope had the highest predictive power, followed by grass cover and VV intensity of Sentinel-1 radar data. The map resulting from the model predicts the highest foraging suitability for valley floors, especially of Inn, Rhine, and Salzach-Valley as well as flatlands, like the Swiss Plateau and the agricultural areas surrounding Lake Constance. Areas with a high suitability index largely overlap with known historic breeding sites. This is particularly noteworthy because the model only refers to foraging habitats without considering the availability of suitable breeding cliffs. Detailed analyses identify the transition zone from extensive grassland management to intensive arable farming as the northern range limit. The modeling outcome allows for defining suitable areas for further translocation and management measures in the frame of the European NBI reintroduction program. Although required in the international IUCN translocation guidelines, the use of models in the context of translocation projects is still not common and in the case of the Northern Bald Ibis not considered in the present Single Species Action Plan of the African-Eurasian Migratory Water bird Agreement. Our species distribution model represents a contemporary snapshot, but sustainability is essential for conservation planning, especially in times of climate change. In this regard, a further model could be optimized by investigating sustainable land use, temporal dynamics, and climate change scenarios.

Worldclim 2.1 versus Worldclim 1.4: Climatic niche and grid resolution affect between‐version mismatches in Habitat Suitability Models predictions across Europe

The influence of climate on the distribution of taxa has been extensively investigated in the last two decades through Habitat Suitability Models (HSMs). In this context, the Worldclim database represents an invaluable data source as it provides worldwide climate surfaces for both historical and future time horizons. Thousands of HSMs‐based papers have been published taking advantage of Worldclim 1.4, the first online version of this repository. In 2017, Worldclim 2.1 was released. Here, we evaluated spatially explicit prediction mismatch at continental scale, focusing on Europe, between HSMs fitted using climate surfaces from the two Worldclim versions (between‐version differences). To this aim, we simulated occurrence probability and presence‐absence across Europe of four virtual species (VS) with differing climate‐occurrence relationships. For each VS, we fitted HSMs upon uncorrelated bioclimatic variables derived from each Worldclim version at three grid resolutions. For each factor combination, HSMs attaining sufficient discrimination performance on spatially independent test data were projected across Europe under current conditions and various future scenarios, and importance scores of the single variables were computed. HSMs failed in accurately retrieving the simulated climate‐occurrence relationships for the climate‐tolerant VS and the one occurring under a narrow combination of climatic conditions. Under current climate, noticeable between‐version prediction mismatch emerged across most of Europe for these two VSs, whose simulated suitability mainly depended upon diurnal or yearly variability in temperature; differently, between‐version differences were more clustered toward areas showing extreme values, like mountainous massifs or southern regions, for VSs responding to average temperature and precipitation trends. Under future climate, the chosen emission scenarios and Global Climate Models did not evidently influence between‐version prediction discrepancies, while grid resolution synergistically interacted with VSs' niche characteristics in determining extent of such differences. Our findings could help in re‐evaluating previous biodiversity‐related works relying on geographical predictions from Worldclim‐based HSMs.

Habitat models and assessment of habitat partitioning for Kemp’s ridley and loggerhead marine turtles foraging in Chesapeake Bay (USA)

Understanding the spatial distribution of a species is required to enact effective conservation. Complications to effective conservation can arise when the distributions of multiple target species are non-overlapping. Conservation efforts meant to protect one species may shift threats into the distribution of another species. Two species of marine turtle, loggerhead Caretta caretta and Kemp’s ridley Lepidochelys kempii, are common seasonally in Chesapeake Bay, a large estuary on the US east coast. Both species are protected under the US Endangered Species Act and face spatially complex threats in the region. We created habitat suitability models for these 2 species to inform conservation efforts in the region and explore the extent of overlap between their distributions. Argos satellite tags were deployed on 24 Kemp’s ridley and 10 loggerhead turtles to record animal locations within the Bay. Boosted regression tree models were created for each species using presence-only animal locations, predicting suitable habitat within the Bay. Habitat for Kemp’s ridley turtles was predicted in shallow, coastal areas of the southern Bay as well as in brackish areas of rivers. Loggerhead turtle habitat was predicted to extend farther north than Kemp’s ridley habitat and was generally found in deeper areas of the middle Bay. There is some evidence that these 2 species are partitioning habitat. Any conservation measures adopted to conserve marine turtles in the Chesapeake Bay should consider the habitat of both species holistically to avoid shifting impacts from one species to another.

Autumn larval cold tolerance does not predict the northern range limit of a widespread butterfly species

Climate change is driving range shifts, and a lack of cold tolerance is hypothesized to constrain insect range expansion at poleward latitudes. However, few, if any, studies have tested this hypothesis during autumn when organisms are subjected to sporadic low-temperature exposure but may not have become cold-tolerant yet. In this study, we integrated organismal thermal tolerance measures into species distribution models for larvae of the Giant Swallowtail butterfly, Papilio cresphontes (Lepidoptera: Papilionidae), living at the northern edge of its actively expanding range. Cold hardiness of field-collected larvae was determined using three common metrics of cold-induced physiological thresholds: the supercooling point, critical thermal minimum, and survival following cold exposure. P. cresphontes larvae were determined to be tolerant of chilling but generally die at temperatures below their SCP, suggesting they are chill-tolerant or modestly freeze-avoidant. Using this information, we examined the importance of low temperatures at a broad scale, by comparing species distribution models of P. cresphontes based only on environmental data derived from other sources to models that also included the cold tolerance parameters generated experimentally. Our modeling revealed that growing degree-days and precipitation best predicted the distribution of P. cresphontes, while the cold tolerance variables did not explain much variation in habitat suitability. As such, the modeling results were consistent with our experimental results: Low temperatures in autumn are unlikely to limit the distribution of P. cresphontes. Understanding the factors that limit species distributions is key to predicting how climate change will drive species range shifts.

Determinants of habitat suitability models transferability across geographically disjunct populations: Insights from Vipera ursinii urs inii

Transferability of habitat suitability models (HSMs), essential to accurately predict outside calibration conditions, has been seldom investigated at intraspecific level. We targeted Vipera ursinii ursinii, a meadow viper from southeastern France and central Italy, to assess determinants of transferability among geographically disjunct populations. We fitted HSMs upon occurrences of the Italian and French populations separately, as well as on the combined occurrence dataset. Internal transferability of HSMs, on spatially independent test data drawn from the calibration region, and their external transferability on the geographically disjunct populations were evaluated according to (a) use of full or spatially rarefied presence datasets; (b) ecology-driven or statistics-driven filtering of predictors; (c) modeling algorithm, testing generalized additive models and gradient boosting models; and (d) multivariate environmental novelty within test data. Niche overlap between French and Italian populations was also tested. Niche overlap was low, but niche divergence between the two populations' clusters was not corroborated. Nonetheless, wider niche breadth and heterogeneity of background environmental conditions characterizing the French populations led to low intercluster transferability. Although models fitted on the combined datasets did not attain consistently higher internal transferability than those separately fitted for the French and Italian populations, ensemble projection from the HSMs fitted on the joint occurrences produced more consistent suitability predictions across the full range of V. u. ursinii. Spatial thinning of occurrences ameliorated internal transferability but did not affect external transferability. The two approaches to predictors filtering did not differ in transferability of the respective HSMs but led to discrepant estimated environment-occurrence relationships and spatial predictions, while the two algorithms attained different relative rankings depending on the considered prediction task. Multivariate novelty of projection sites was negatively correlated to both internal transferability and external transferability. Our findings clarify issues researchers should keep in mind when using HSMs to get predictions across geographically disjunct populations.

Projecting the potential distribution of ticks in China under climate and land use change

Ticks are known as vectors of several pathogens causing various human and animal diseases including Lyme borreliosis, tick-borne encephalitis, and Crimean-Congo hemorrhagic fever. While China is known to have more than 100 tick species well distributed over the country, our knowledge on the likely distribution of ticks in the future remains very limited, which hinders the prevention and control of the risk of tick-borne diseases. In this study, we selected four representative tick species which have different regional distribution foci in mainland China. i.e., Dermacentor marginatus, Dermacentor silvarum, Haemaphysalis longicornis and Ixodes granulatus. We used the MaxEnt model to identify the key environmental factors of tick occurrence and map their potential distributions in 2050 under four combined climate and socioeconomic scenarios (i.e., SSP1-RCP2.6, SSP2-RCP4.5, SSP3-RCP7.0 and SSP5-RCP8.5). We found that the extent of the urban fabric, cropland and forest, temperature annual range and precipitation of the driest month were the main determinants of the potential distributions of the four tick species. Under the combined scenarios, with climate warming, the potential distributions of ticks shifted to further north in China. Due to a decrease in the extent of forest, the distribution probability of ticks declined in central and southern China. In contrast with previous findings on an estimated amplification of tick distribution probability under the extreme emission scenario (RCP8.5), our studies projected an overall reduction in the distribution probability under RCP8.5, owing to an expected effect of land use. Our results could provide new data to help identify the emerging risk areas, with amplifying suitability for tick occurrence, for the prevention and control of tick-borne zoonoses in mainland China. Future directions are suggested towards improved quantity and quality of the tick occurrence database, comprehensiveness of factors and integration of different modelling approaches, and capability to model pathogen spillover at the human-tick interface.

Golden carbon of Sargassum forests revealed as an opportunity for climate change mitigation

Marine climate change mitigation initiatives have recently attracted a great deal of interest in the role of natural carbon sinks, particularly on coastal systems. Brown seaweeds of the genus Sargassum are the largest canopy-forming algae in tropical and subtropical environments, with a wide global distribution on rocky reefs and as floating stands. Because these algae present high amounts of biomass, we suggest their contribution is relevant for global carbon stocks and consequently for mitigating climate change as CO2 remover. We modelled global distributions and quantified carbon stocks as above-ground biomass (AGB) with machine learning algorithms and climate data. Sargassum AGB totaled 13.1 Pg C at the global scale, which is a significant amount of carbon, comparable to other key marine ecosystems, such as mangrove forests, salt marshes and seagrass meadows. However, specific techniques related to bloom production and management, or the utilization of biomass for biomaterials, should be fostered.

Niche space of corals along the Florida reef tract

Over the last three decades corals have declined precipitously in the Florida Keys. Their population decline has prompted restoration effort. Yet, little effort has been invested in understanding the contemporary niche spaces of coral species, which could assist in prioritizing conservation habitats. We sought to predict the probability of occurrence of 23 coral species, including the critically endangered Acropora cervicornis, using observations at 985 sites from 2011–2015. We ran boosted regression trees to evaluate the relationship between the presence of these corals and eight potential environmental predictors: (i) bathymetry (m), (ii) mean of daily sea surface temperature (SST) (°C), (iii) variance of SST (°C), (iv) range of SST (°C), (v) chlorophyll-a concentration (mg m³), (vi) turbidity (m^-1), (vii) wave energy (kJ m^-2), and (viii) distance from coast (km). The Marquesas and the lower and upper Florida Keys were predicted to support the most suitable habitats for the 23 coral species examined. A. cervicornis had one of the smallest areas of suitable habitat, which was limited to the lower and upper Florida Keys, the Dry Tortugas, and nearshore Broward-Miami reefs. The best environmental predictors of site occupancy of A. cervicornis were SST range (4–5°C) and turbidity (K₄₉₀ between 0.15–0.25 m^-1). Historically A. cervicornis was reported in clear oligotrophic waters, although the present results find the coral species surviving in nearshore turbid conditions. Nearshore, turbid reefs may shade corals during high-temperature events, and therefore nearshore reefs in south Florida may become important refuges for corals as the ocean temperatures continue to increase.

Predicting poaching risk in marine protected areas for improved patrol efficiency

Marine Protected Areas (MPAs) are effective resource management and conservation measures, but their success is often hindered by non-compliant activities such as poaching. Understanding the risk factors and spatial patterns of poaching is therefore crucial for efficient law enforcement. Here, we conducted explanatory and predictive modelling of poaching from recreational fishers within no-take zones of Australia's Great Barrier Reef Marine Park (GBRMP) using Boosted Regression Trees (BRT). Combining patrol effort data, observed distribution of reported incidents, and spatially-explicit environmental and human risk factors, we modeled the occurrence probability of poaching incidents and mapped poaching risk at fine-scale. Our results: (i) show that fishing attractiveness, accessibility and fishing capacity play a major role in shaping the spatial patterns of poaching; (ii) revealed key interactions among these factors as well as tipping points beyond which poaching risk increased or decreased markedly; and (iii) highlight gaps in patrol effort that could be filled for improved resource allocation. The approach developed through this study provide a novel way to quantify the relative influence of multiple interacting factors in shaping poaching risk, and hold promises for replication across a broad range of marine or terrestrial settings.

Investigating the Current and Future Co-Occurrence of Ambrosia artemisiifolia and Ophraella communa in Europe through Ecological Modelling and Remote Sensing Data Analysis

The common ragweed Ambrosia artemisiifolia has spread throughout Europe since the 1800s, infesting croplands and causing severe allergic reactions. Recently, the ragweed leaf beetle Ophraella communa was found in Italy and Switzerland; considering that it feeds primarily on A. artemisiifolia in its invaded ranges, some projects started biological control of this invasive plant through the adventive beetle. In this context of a ‘double’ invasion, we assessed the influence of climate change on the spread of these alien species through ecological niche modelling. Considering that A. artemisiifolia mainly lives in agricultural and urbanized areas, we refined the models using satellite remote-sensing data; we also assessed the co-occurrence of the two species in these patches. A. artemisiifolia is predicted to expand more than O. communa in the future, with the medium and high classes of suitability of the former increasing more than the latter, resulting in lower efficacy for O. communa to potentially control A. artemisiifolia in agricultural and urbanized patches. Although a future assessment was performed through the 2018 land-cover data, the predictions we propose are intended to be a starting point for future assessments, considering that the possibility of a shrinkage of target patches is unlikely to occur.

Evidences for a shared history for spectacled salamanders, haplotypes and climate

The so-called glacial refugia, formed during the Pleistocene climatic oscillations, played a major role in shaping the distribution of European species, triggering migrations or isolating populations. Many of these events were recently investigated by genetic data, mainly for the European Last Glacial stage, in the Iberic, Italian and Greek-Balkan peninsulas. The amphibian genus Salamandrina, the most ancient living salamandrid lineage, was widespread in Europe until the climatic oscillations of Miocene probably forced it to shelter in the only suitable territory at that time, the Apennines. Nowadays this genus is endemic of peninsular Italy with two parapatric species, S. perspicillata and S. terdigitata, sharing an area of secondary contact formed after the Last Glacial Maximum. Climate is generally identified as the key factor for the interpretation of genetic data. In this research, we directly measure climate influences on the two Salamandrina known species through Ensemble Modelling techniques and post-modelling GIS analyses, integrating updated genetic data in this process. Our results confirm the hypotheses of southwards (and subsequent northwards) shifts, identify glacial refugia and corridors used for the post-glacial re-colonization. Finally, we map a contact zone deserving more sampling effort to disentangle the introgression and hybridization observed.

Coupling GIS spatial analysis and Ensemble Niche Modelling to investigate climate change-related threats to the Sicilian pond turtle Emys trinacris, an endangered species from the Mediterranean

The pond turtle Emys trinacris is an endangered endemic species of Sicily showing a fragmented distribution throughout the main island. In this study, we applied "Ensemble Niche Modelling", combining more classical statistical techniques as Generalized Linear Models and Multivariate Adaptive Regression Splines with machine-learning approaches as Boosted Regression Trees and Maxent, to model the potential distribution of the species under current and future climatic conditions. Moreover, a "gap analysis" performed on both the species' presence sites and the predictions from the Ensemble Models is proposed to integrate outputs from these models, in order to assess the conservation status of this threatened species in the context of biodiversity management. For this aim, four "Representative Concentration Pathways", corresponding to different greenhouse gases emissions trajectories were considered to project the obtained models to both 2050 and 2070. Areas lost, gained or remaining stable for the target species in the projected models were calculated. E. trinacris' potential distribution resulted to be significantly dependent upon precipitation-linked variables, mainly precipitation of wettest and coldest quarter. Future negative effects for the conservation of this species, because of more unstable precipitation patterns and extreme meteorological events, emerged from our analyses. Further, the sites currently inhabited by E. trinacris are, for more than a half, out of the Protected Areas network, highlighting an inadequate management of the species by the authorities responsible for its protection. Our results, therefore, suggest that in the next future the Sicilian pond turtle will need the utmost attention by the scientific community to avoid the imminent risk of extinction. Finally, the gap analysis performed in GIS environment resulted to be a very informative post-modeling technique, potentially applicable to the management of species at risk and to Protected Areas' planning in many contexts.

Histological and ultrastructural alterations of the Italian newt (Lissotriton italicus) skin after exposure to ecologically relevant concentrations of nonylphenol ethoxylates

Nonylphenol ethoxylates (NPEs) are well known endocrine disruptors. Widespread environmental contamination from NPEs is an issue of great concern. Despite amphibians are often exposed to such contaminants, very little attention has been dedicated to this vertebrate group. No information is available on the effects of NPEs onto the amphibian skin and only few reports have been conducted on fish. Here, histological and ultrastructural modifications of the skin have been evaluated in the Italian newt Lissotriton italicus. After a short-term exposure to two ecologically relevant concentrations of NP, severe pathological alterations, both dose and time-dependent, have been observed. The main effects were an increased mucous secretion, the dilation of the endomembrane, the wrinkling of the epidermal surface, the appearance of tubercles, the increased cellular turnover, continuous shedding processes. Some of the described skin alterations can easily interfere with physiological functions, such as osmoregulation and body protection, with detrimental consequences for the amphibian populations.

Morphological and immunohistochemical reactions of the larval epidermis in the Italian newt (Lissotriton italicus) after exposure to low pH

Mounting evidence suggests that amphibians are globally and currently the most threatened group of vertebrates and different causes might be responsible for this phenomenon. Acidification of water bodies is a global environmental issue that has been proposed as a possible cause for amphibian populations decline. Indeed, it has been widely demonstrated that low pH may exert harmful effects on amphibians, either directly or by increasing the adverse effects of other stressors. Surprisingly only few studies documented the response of amphibian integument to acidic pH conditions and no data are available on the effects of a non-lethal level of pH onto the amphibian larval epidermis. The present study showed that acidic pH (4.5) condition has severe effects on the epidermis of the Italian newt (Lissotriton italicus, formerly Triturus italicus) inducing both morphological and functional alterations. The increase of mucus is the first evident effect of acid injury, followed by the flattening of the epithelium and the appearance of a keratinized shedding layer. The immunolabeling of cytokeratins substantially changes acquiring an adult-like pattern. Also aquaporin 3 and iNOS expression modify their distribution according to a change of the histological features of the epidermis. These results clearly indicate that a short-term exposure to a sub-lethal pH disrupts the epidermis morphology and function in L. italicus larvae. Since the skin exerts a prominent role in both respiration and osmoregulation, the described alterations may adversely affect the overall ionic balance, with a long chain of cascading effects significantly decreasing newts survival probabilities when environmental pH lowering occurs.