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

Predicting habitat suitability and niche dynamics of Dactylorhiza hatagirea and Rheum webbianum in the Himalaya under projected climate change

In the era of anthropocene, global warming tends to alter the distribution range of the plant species. Highly fragile to such changes are the species that are endemic, inhabit higher elevations and show narrow distribution ranges. Predicting and plotting the appropriate suitable habitats and keeping knowledge of how climate change will affect future distribution become imperative for designing effective conservation strategies. In the current study we have used BIOMOD ensemble forecasting to study the current and predict the future potential distribution of Dactylorhiza hatagirea and Rheum webbianum and describe their niche dynamics in Himalayan biodiversity hotspots under climate change scenarios using ecospat R package. Results reveal sufficient internal evaluation metrics with area under curve (AUC) and true skill statistic (TSS) values greater than 0.8 i.e. 0.93 and 0.98 and 0.82 and 0.90 for D. hatageria and R. webbianum respectively, which signifies robustness of the model. Among different bioclimatic variables, bio_1, bio_3, bio_8, bio_14 and bio_15 were the most influential, showing greater impact on the potential distribution of these plant species. Range change analysis showed that both the studied species will show significant contraction of their suitable habitats under future climatic scenarios. Representative Concentration Pathway (RCP) 8.5 for the year 2070, indicate that the suitable habitats could be reduced by about 51.41% and 70.57% for D. hatagirea and R. webbianum respectively. The results of the niche comparisons between the current and future climatic scenarios showed moderate level of niche overlap for all the pairs with D. hatageria showing 61% overlap for current vs. RCP4.5 2050 and R. webbianum reflects 68% overlap for current vs. RCP4.5 2050. Furthermore, the PCA analysis revealed that climatic conditions for both the species vary significantly between current and future scenarios. The similarity and equivalence test showed that the niche between present and future climate change scenarios is comparable but not identical. From the current study we concluded that the influence of climate change on the habitat distribution of these plant species in the Himalayan biodiversity hotspots can be considered very severe. Drastic reduction in overall habitat suitability poses a high risk of species extinction and thereby threatens to alter the functions and services of these fragile ecosystems. Present results can be used by conservationists for mitigating the biodiversity decline and exploring undocumented populations on one hand and by policymakers in implementing the policy of conservation of species by launching species recovery programmes in future on the other. The outcomes of this study can contribute substantially to understand the consequences of climate change in the Himalayan biodiversity hotspots.

Modeling of Valeriana wallichii Habitat Suitability and Niche Dynamics in the Himalayan Region under Anticipated Climate Change

An increase in atmospheric greenhouse gases necessitates the use of species distribution models (SDMs) in modeling suitable habitats and projecting the impact of climate change on the future range shifts of the species. The present study is based on the BIOMOD ensemble approach to map the currently suitable habitats and predict the impact of climate change on the niche shift of Valeriana wallichii. We also studied its niche dynamics using the ecospat package in R software. Values of the area under curve (AUC) and true skill statistics (TSS) were highly significant (>0.9), which shows that the model has run better. From 19 different bioclimatic variables, only 8 were retained after correlation, among which bio_17 (precipitation of driest quarter), bio_1 (annual mean temperature), and bio_12 (annual mean precipitation) received the highest gain. Under future climate change, the suitable habitats will be significantly contracted by −94% (under representative concentration pathway RCP 8.5 for 2070) and −80.22% (under RCP 8.5 for 2050). There is a slight increase in habitat suitability by +16.69% (RCP 4.5 for 2050) and +8.9% (RCP 8.5 for 2050) under future climate change scenarios. The equivalency and similarity tests of niche dynamics show that the habitat suitability for current and future climatic scenarios is comparable but not identical. Principal Component Analysis (PCA) analysis shows that climatic conditions will be severely affected between current and future scenarios. From this study, we conclude that the habitats of Valeriana wallichii are highly vulnerable to climate shifts. This study can be used to alleviate the threat to this plant by documenting the unexplored populations, restoring the degraded habitats through rewilding, and launching species recovery plans in the natural habitats.

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.

Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies

Aims

Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses.

Location

Sub-Saharan Africa.

Methods

Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). We finally measure the rice production and GPD loss per country through the spatial index named “Pest Aggression Index”, based on the inferred connectivity magnitude.

Results

The most considerable losses in rice production are observed for Liberia, Sierra Leone and Madagascar in all future scenarios (2030, 2050, 2070). The future economic cost, calculated as USD lost from rice losses/country’s GDP results are high for Central African Republic (−0.6% in SSP_2.45 and −3.0% in SSP_3.70) and Guinea–Bissau (−0.4% in SSP_2.45 and −0.68% in SSP_3.70), with relevant losses also obtained for other countries.

Main conclusions

Since our results are spatially explicit and focused on each country, we encourage careful land-use planning. Our findings could support best practices to avoid the future settlement of new cultivations in territories where rice would be attacked by pulla group and the virus, bringing economic and biodiversity losses.

Ecological assessment and environmental niche modelling of Himalayan rhubarb (Rheum webbianum Royle) in northwest Himalaya

In an era of anthropocene, threatened and endemic species with small population sizes and habitat specialists experience a greater global conservation concern in view of being at higher risk of extinction. Predicting and plotting appropriate potential habitats for such species is a rational method for monitoring and restoring their dwindling populations in expected territories. Ecological niche modelling (ENM) coalesces species existence sites with environmental raster layers to construct models that describe possible distributions of plant species. The present study is aimed to study the potential distribution and cultivation hotspots for reintroducing the high value, vulnerable medicinal herb (Rheum webbianum) in the Union territories of Jammu and Kashmir and Ladakh using population attributes and ecological niche modelling approach. Sixty-three populations inventoried from twenty-eight areas display a significant change in the phytosociological attributes on account of various anthropogenic threats. The current potential habitats coincide with actual distribution records and the mean value of Area Under Curve (AUC) was 0.98 and the line of predicted omission was almost adjacent to omission in training samples, thus validating a robustness of the model. The potential habitat suitability map based on the current climatic conditions predicted a total of 103760 km2 as suitable area for the growth of Rheum webbianum. Under the future climatic conditions, there is a significant reduction in the habitat suitability ranging from -78531.34 Km2 (RCP 4.5 for 2050) to -77325.81 (RCP 8.5 for 2070). Furthermore, there is a slight increase in the suitable habitats under future climatic conditions, ranging from +21.99 Km2 under RCP 8.5 (2050) to +3.14 Km2 under RCP 4.5 (2070). The Jackknife tests indicated Precipitation of Driest Month (BIO14) as the most contributing climatic variable in governing the distribution of R. webbianum. Therefore, scientifically sound management strategies are urgently needed to save whatever populations are left in-situ to protect this species from getting extinct. Present results can be used by conservationists for mitigating the biodiversity decline and exploring undocumented populations of R. webbianum on one hand and by policymakers in implementing the policy of conservation of species with specific habitat requirements by launching species recovery programmes in future on the other.

From Remote Sensing to Species Distribution Modelling: An Integrated Workflow to Monitor Spreading Species in Key Grassland Habitats

Remote sensing (RS) has been widely adopted as a tool to investigate several biotic and abiotic factors, directly and indirectly, related to biodiversity conservation. European grasslands are one of the most biodiverse habitats in Europe. Most of these habitats are subject to priority conservation measure, and several human-induced processes threaten them. The broad expansions of few dominant species are usually reported as drivers of biodiversity loss. In this context, using Sentinel-2 (S2) images, we investigate the distribution of one of the most spreading species in the Central Apennine: Brachypodium genuense. We performed a binary Random Forest (RF) classification of B. genuense using RS images and field-sampled presence/absence data. Then, we integrate the occurrences obtained from RS classification into species distribution models to identify the topographic drivers of B. genuense distribution in the study area. Lastly, the impact of B. genuense distribution in the Natura 2000 (N2k) habitats (Annex I of the European Habitat Directive) was assessed by overlay analysis. The RF classification process detected cover of B. genuense with an overall accuracy of 94.79%. The topographic species distribution model shows that the most relevant topographic variables that influence the distribution of B. genuense are slope, elevation, solar radiation, and topographic wet index (TWI) in order of importance. The overlay analysis shows that 74.04% of the B. genuense identified in the study area falls on the semi-natural dry grasslands. The study highlights the RS classification and the topographic species distribution model’s importance as an integrated workflow for mapping a broad-expansion species such as B. genuense. The coupled techniques presented in this work should apply to other plant communities with remotely recognizable characteristics for more effective management of N2k habitats.

Niches of nine mangrove species in a Sonneratia apetala-colonized area of Dongzhai Harbor, Hainan Island, China

The distribution of mangroves is influenced by the environment. We aimed to understand the ecological adaptability of various mangrove species within the range of the exotic species, Sonneratia apetala Buch.-Ham., in Dongzhai Harbor, Hainan Island, China. We used three niche breadth indexes (Simpson, Levins, and Shannon-Weiner) and two niche overlap indexes (Pianka and Levins) to quantitatively determine the niche characteristics of nine mangrove species. The results showed that the order of the niche breadth values of mangrove species was as follows: Aegiceras corniculatum (Linn.) Blanco > Kandelia obovata Sheue et al. > Bruguiera gymnorrhiza (L.) Poir. > Avicennia marina (Forsk.) Vierh. Hailanci > S. apetala > S. caseolaris (L.) Engl. > Rhizophora stylosa Griff > Ceriops tagal (Perr.) C. B. Rob. > B. sexangula (Lour.) Poir. Pearson correlation analysis revealed that the niche breadth of each population was significantly correlated with the importance value of the population in the whole sample (R1 = R2 = 0.771, R3 = 0.644, p < .05). The nine mangrove species were divided into three groups by Bray-Curtis cluster analysis; the groups were similar to the distribution of mangrove species in the natural state as determined by tide level. Niche similarity analysis showed that the niche similarity of most mangroves ranged between 0.5 and 0.8 and that the species pairs A. corniculatum-B. gymnorrhiza, A. corniculatum-Avicennia marina, and K. obovata-S. caseolaris were characterized by large niche similarity ratios. Although it had a moderate niche breadth, S. apetala had a relatively broad niche overlap with mangroves in the mid- and low-tide zones (S. caseolaris, A. corniculatum, K. obovata, and Avicennia marina), a moderate overlap with B. gymnorrhiza and R. stylosa, only a slight overlap with C. tagal, and no overlap with B. sexangular. There was no obvious linear relationship between niche width and niche overlap of mangroves. Due to its inefficiency in utilizing certain resources and relatively high degree of resource selection, it seems likely that S. apetala will not pose a threat to the survival of native plants, let alone completely replace native species.

Stand out from the Crowd: Small-Scale Genetic Structuring in the Endemic Sicilian Pond Turtle

The geographical pattern of genetic diversity was investigated in the endemic Sicilian pond turtle Emys trinacris across its entire distribution range, using 16 microsatellite loci. Overall, 245 specimens of E. trinacris were studied, showing high polymorphic microsatellite loci, with allele numbers ranging from 7 to 30. STRUCTURE and GENELAND analyses showed a noteworthy, geographically based structuring of the studied populations in five well-characterized clusters, supported by a moderate degree of genetic diversity (FST values between 0.075 and 0.160). Possible explanations for the genetic fragmentation observed are provided, where both natural and human-mediated habitat fragmentation of the Sicilian wetlands played a major role in this process. Finally, some conservation and management suggestions aimed at preventing the loss of genetic variability of the species are briefly reported, stressing the importance of considering the five detected clusters as independent Management Units.

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.

A Review of the Effects of Climate Change on Chelonians

Climate change is occurring at an unprecedented rate and has begun to modify the distribution and phenology of organisms worldwide. Chelonians are expected to be particularly vulnerable due to limited dispersal capabilities as well as widespread temperature-dependent sex determination. The number of papers published about the effects of climate change on turtles has increased exponentially over the last decade; here, I review the data from peer-reviewed publications to assess the likely impacts of climate change on individuals, populations, and communities. Based upon these studies future research should focus on: (1) Individual responses to climate change, particularly with respect to thermal biology, phenology, and microhabitat selection; (2) improving species distribution models by incorporating fine-scale environmental variables as well as physiological processes; (3) identifying the consequences of skewed sex ratios; and (4) assessments of community resilience and the development of methods to mitigate climate change impacts. Although detailed management recommendations are not possible at this point, careful consideration should be given regarding how to manage low vagility species as habitats shift poleward. In the worst-case scenario, proactive management may be required in order to ensure that widespread losses do not occur.

Phylogeography and species distribution modelling of Cryptocephalusbarii (Coleoptera: Chrysomelidae): is this alpine endemic species close to extinction?

The alternation of glacial and interglacial cycles of the Quaternary period contributed in shaping the current species distribution. Cold-adapted organisms experienced range expansion and contraction in response to the temperature decrease and increase, respectively. In this study, a fragment of the mitochondrial marker COI was used to investigate the phylogeography of Cryptocephalusbarii, a cold-adapted alpine leaf beetle species endemic of Orobie Alps, northern Italy. The relationships among populations, their divergence time, and the most probable migration model were estimated and are discussed in light of the Pleistocene climate oscillations. Through a species distribution modelling analysis, the current habitat suitability was assessed and the distribution in a future global warming scenario predicted. The main divergence events that led to the actual population structure took place from ~750,000 to ~150,000 years ago, almost following the pattern of the climate oscillations that led to the increase of the connections between the populations during cold periods and the isolation on massifs in warm periods. The most supported migration model suggests that the species survived to past adverse climatic conditions within refugia inside and at the limit of the actual range. The species distribution modelling analysis showed that C.barii is extremely sensitive to air temperature variations, thus the increase of temperature caused by global warming will reduce the suitable areas within the species range, leading to its possible extinction in the next 50 years. Cryptocephalusbarii is a representative case of how cold adapted and limited distributed species have been and could be affected by climate change, that highlights the implementation of conservation actions.

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.