Resource availability and disturbance frequency shape evolution of plant life forms in Neotropical habitats

Organisms use diverse strategies to thrive in varying habitats. While life history theory partly explains these relationships, the combined impact of resource availability and disturbance frequency on life form strategy evolution has received limited attention. We use Chamaecrista species, a legume plant lineage with a high diversity of plant life forms in the Neotropics, and employ ecological niche modeling and comparative phylogenetic methods to examine the correlated evolution of plant life forms and environmental niches. Chamaephytes and phanerophytes have optima in environments characterized by moderate water and nutrient availability coupled with infrequent fire disturbances. By contrast, annual plants thrive in environments with scarce water and nutrients, alongside frequent fire disturbances. Similarly, geophyte species also show increased resistance to frequent fire disturbances, although they thrive in resource-rich environments. Our findings shed light on the evolution of plant strategies along environmental gradients, highlighting that annuals and geophytes respond differently to high incidences of fire disturbances, with one enduring it as seeds in a resource-limited habitat and the other relying on reserves and root resprouting systems in resource-abundant habitats. Furthermore, it deepens our understanding of how organisms evolve associated with their habitats, emphasizing a constraint posed by low-resource and high-disturbance environments.

Predicting the potential distribution of 12 threatened medicinal plants on the Qinghai-Tibet Plateau, with a maximum entropy model

Climate change is a vital driver of biodiversity patterns and species distributions, understanding how organisms respond to climate change will shed light on the conservation of endangered species. In this study, the MaxEnt model was used to predict the potential suitable area of 12 threatened medicinal plants in the QTP (Qinghai-Tibet Plateau) under the current and future (2050s, 2070s) three climate scenarios (RCP2.6, RCP4.5, RCP8.5). The results showed that the climatically suitable habitats for the threatened medicinal plants were primarily found in the eastern, southeast, southern, and some parts of the central regions on the QTP. Moreover, 25% of the threatened medicinal plants would have reduced suitable habitat areas within the next 30-50 years in the different future global warming scenarios. Among these medicinal plants, RT (Rheum tanguticum) would miss the most habitat (98.97%), while the RAN (Rhododendron anthopogonoides) would miss the least habitat (10.15%). Nevertheless, 33.3% of the threatened medicinal plants showed an increase in their future habitat area because of their physiological characteristics which are more adaptable to a wide range of climates. The climatic suitable habitat for 50% of the threatened medicinal plants would migrate to higher altitudes or higher latitudes regions. This study provides a data foundation for the conservation of biodiversity and wild medicinal plants on the QTP.

Climate change and anthropogenic activities shrink the range and dispersal of an endangered primate in Sichuan Province, China

The golden snub-nosed monkey (Rhinopithecus roxellana) is a rare and endemic species in China. The population of golden snub-nosed monkeys in Sichuan Province has an isolated genetic status, large population size, and low genetic diversity, making it highly vulnerable to environmental changes. Our study aimed to evaluate the potential impact of climate and land-use changes on the distribution and dispersal paths of the species in Sichuan Province. We used three general circulation models (GCMs), three greenhouse gas emission scenarios, and three land-use change scenarios suitable for China to predict the potential distributions of the golden snub-nosed monkey in the current and 2070s using the MaxEnt model. The dispersal paths were identified by the circuit theory. Our results suggested that the habitats of the golden snub-nosed monkey were reduced under all three GCM scenarios. The suitable habitats for the golden snub-nosed monkey would be reduced by 82.67%, 82.47%, and 75.17% under the RCP2.6, RCP4.5, and RCP8.5 scenarios, respectively, compared to the currently suitable habitat area. Additionally, we found that the density of future dispersal paths of golden snub-nosed monkeys would decrease, and the dispersal resistance would increase. Therefore, relevant wildlife protection agencies should prioritize the climatically suitable distributions and key dispersal paths of golden snub-nosed monkeys to improve their conservation. We identified key areas for habitat preservation and increased habitat connectivity under climate change, which could serve as a reference for future adaptation strategies.

Space-for-time substitutions in climate change ecology and evolution

In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

BACKGROUND AND AIMS

New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae.

METHODS

We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally.

KEY RESULTS

Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap.

CONCLUSIONS

We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.

Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500 km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from the early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.

Ecological response of an umbrella species to changing climate and land use: Habitat conservation for Asiatic black bear in the Sichuan-Chongqing Region, Southwestern China

Climate and land use changes are increasingly recognized as major threats to global biodiversity, with significant impacts on wildlife populations and ecosystems worldwide. The study of how climate and land use changes impact wildlife is of paramount importance for advancing our understanding of ecological processes in the face of global environmental change, informing conservation planning and management, and identifying the mechanisms and thresholds that underlie species' responses to shifting climatic conditions. The Asiatic black bear (Ursus thibetanus) is a prominent umbrella species in a biodiversity hotspot in Southwestern China, and its conservation is vital for safeguarding sympatric species. However, the extent to which this species' habitat may respond to global climate and land use changes is poorly understood, underscoring the need for further investigation. Our goal was to anticipate the potential impacts of upcoming climate and land use changes on the distribution and dispersal patterns of the Asiatic black bear in the Sichuan-Chongqing Region. We used MaxEnt modeling to evaluate habitat vulnerability using three General Circulation Models (GCMs) and three scenarios of climate and land use changes. Subsequently, we used Circuit Theory to identify prospective dispersal paths. Our results revealed that the current area of suitable habitat for the Asiatic black bear was 225,609.59 km² (comprising 39.69% of the total study area), but was expected to decrease by -53.1%, -49.48%, and -28.55% under RCP2.6, RCP4.5, and RCP8.5 projection scenarios, respectively. Across all three GCMs, the distribution areas and dispersal paths of the Asiatic black bear were projected to shift to higher altitudes and constrict by the 2070s. Furthermore, the results indicated that the density of dispersal paths would decrease, while the resistance to dispersal would increase across the study area. In order to protect the Asiatic black bear, it is essential to prioritize the protection of climate refugia and dispersal paths. Our findings provide a sound scientific foundation for the allocation of such protected areas in the Sichuan-Chongqing Region that are both effective and adaptive in the face of ongoing global climate and land use changes.

Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

Integral projection models (IPMs) can estimate the population dynamics of species for which both discrete life stages and continuous variables influence demographic rates. Stochastic IPMs for imperiled species, in turn, can facilitate population viability analyses (PVAs) to guide conservation decision-making. Biphasic amphibians are globally distributed, often highly imperiled, and ecologically well suited to the IPM approach. Herein, we present a stochastic size- and stage-structured IPM for a biphasic amphibian, the U.S. federally threatened California tiger salamander (CTS) (Ambystoma californiense). This Bayesian model reveals that CTS population dynamics show greatest elasticity to changes in juvenile and metamorph growth and that populations are likely to experience rapid growth at low density. We integrated this IPM with climatic drivers of CTS demography to develop a PVA and examined CTS extinction risk under the primary threats of habitat loss and climate change. The PVA indicated that long-term viability is possible with surprisingly high (20%-50%) terrestrial mortality but simultaneously identified likely minimum terrestrial buffer requirements of 600-1000 m while accounting for numerous parameter uncertainties through the Bayesian framework. These analyses underscore the value of stochastic and Bayesian IPMs for understanding both climate-dependent taxa and those with cryptic life histories (e.g., biphasic amphibians) in service of ecological discovery and biodiversity conservation. In addition to providing guidance for CTS recovery, the contributed IPM and PVA supply a framework for applying these tools to investigations of ecologically similar species.

Snake life history traits and their association with urban habitat use in a tropical city

Urbanisation changes landscapes, often simplifying and homogenising natural ecosystems while introducing novel environments. Although this transformation often adversely impacts native wildlife, generalist species that exhibit broad dietary and habitat requirements can persist and take advantage of urban environments. To understand which life history traits most influence the occurrence of a diverse snake assemblage in an urban environment, we leveraged a dataset of 5102 detection records for 12 snake species in the tropical city of Darwin, Australia. By building ecological niche models, calculating urban niche hypervolume, and compiling life history data, we analysed the diversity of environments occupied by each species and determined which landscape components were most associated with occurrence data. In keeping with our hypothesis that generalist species would be more successful, we found that species with broader habitat and dietary preferences, as well as a penchant for arboreality, were associated with larger urban niche hypervolumes and more frequent human–snake interactions. Additionally, we found that colubrid snakes had significantly larger urban niche hypervolumes than elapid species. These findings contribute to understanding how life history traits aid wildlife persistence in, and adaptation to, urban ecosystems, and have implications for landscape design and conservation management.

Temperature-habitat interactions constrain seasonal activity in a continental array of pitfall traps

Activity density (AD), the rate at which animals collectively move through their environment, emerges as the product of a taxon's local abundance and its velocity. We analyze drivers of seasonal AD using 47 localities from the National Ecological Observatory Network (NEON) both to better understand variation in ecosystem rates like pollination and seed dispersal as well as the constraints of using AD to monitor invertebrate populations. AD was measured as volume from biweekly pitfall trap arrays (ml trap^-1 14 days^-1 ). Pooled samples from 2017 to 2018 revealed AD extrema at most temperatures but with a strongly positive overall slope. However, habitat types varied widely in AD's seasonal temperature sensitivity, from negative in wetlands to positive in mixed forest, grassland, and shrub habitats. The temperature of maximum AD varied threefold across the 47 localities; it tracked the threefold geographic variation in maximum growing season temperature with a consistent gap of ca. 3°C across habitats, a novel macroecological result. AD holds potential as an effective proxy for investigating ecosystem rates driven by activity. However, our results suggest that its use for monitoring insect abundance is complicated by the many ways that both abundance and velocity are constrained by a locality's temperature and plant physiognomy.

Analysis of niche shift and potential suitable distributions of Dendrobium under the impact of global climate change

Dendrobium is a valuable traditional Chinese herb that contains active ingredients such as polysaccharides and alkaloids that have anti-aging, antioxidant, and immunomodulating effects. The appropriate distribution range of Dendrobium should be predicted from the perspective of ecological niche theory in order to preserve and utilize medicinal plant resources. In this study, Dendrobium nobile, Dendrobium officinale, and Dendrobium moniliforme were selected to predict the potential suitable distributions and ecological niche shifts. A comparison of 19 environmental variables of the three Dendrobium species revealed three climatic factors that differed significantly when the species were compared two at a time. The principal component analysis was carried out in order to screen seven climatic factors for ecological niche shift analysis. All three Dendrobium species were found to have a very similar ecological niche, but with a relatively small range of variability regarding certain climatic factors. Finally, the current and future suitable areas for these three Dendrobium species in China were predicted using the MaxEnt model and ArcGIS using the two representative concentration pathways (RCP 2.6 and 8.5). Overall, the analysis of the climatic factors' comparisons, niche shift, and current and future suitable areas of these three Dendrobium species provides a basis for medicinal plant resource conservation and utilization, and our methods could be applied to the study of other similar valuable medicinal plants.

Extensive range contraction predicted under climate warming for two endangered mountaintop frogs from the rainforests of subtropical Australia

Montane ecosystems cover approximately 20% of the Earth's terrestrial surface and are centres of endemism. Globally, anthropogenic climate change is driving population declines and local extinctions across multiple montane taxa, including amphibians. We applied the maximum entropy approach to predict the impacts of climate change on the distribution of two poorly known amphibian species (Philoria kundagungan and Philoria richmondensis) endemic to the subtropical uplands of the Gondwana Rainforests of Australia, World Heritage Area (GRAWHA). Firstly, under current climate conditions and also future (2055) low and high warming scenarios. We validated current distribution models against models developed using presence-absence field data. Our models were highly concordant with known distributions and predicted the current distribution of P. kundagungan to contract by 64% under the low warming scenario and by 91% under the high warming scenario and that P. richmondensis would contract by 50% and 85%, respectively. With large areas of habitat already impacted by wildfires, conservation efforts for both these species need to be initiated urgently. We propose several options, including establishing ex-situ insurance populations increasing the long-term viability of both species in the wild through conservation translocations.

Linking ecological niche models and common garden experiments to predict phenotypic differentiation in stressful environments: Assessing the adaptive value of marginal populations in an alpine plant

Environmental variation within a species' range can create contrasting selective pressures, leading to divergent selection and novel adaptations. The conservation value of populations inhabiting environmentally marginal areas remains in debate and is closely related to the adaptive potential in changing environments. Strong selection caused by stressful conditions may generate novel adaptations, conferring these populations distinct evolutionary potential and high conservation value under climate change. On the other hand, environmentally marginal populations may be genetically depauperate, with little potential for new adaptations to emerge. Here, we explored the use of ecological niche models (ENMs) linked with common garden experiments to predict and test for genetically determined phenotypic differentiation related to contrasting environmental conditions. To do so, we built an ENM for the alpine plant Silene ciliata in central Spain and conducted common garden experiments, assessing flowering phenology changes and differences in leaf cell resistance to extreme temperatures. The suitability patterns and response curves of the ENM led to the predictions that: (1) the environmentally marginal populations experiencing less snowpack and higher minimum temperatures would have delayed flowering to avoid risks of late-spring frosts and (2) those with higher minimum temperatures and greater potential evapotranspiration would show enhanced cell resistance to high temperatures to deal with physiological stress related to desiccation and heat. The common garden experiments revealed the expected genetically based phenotypic differentiation in flowering phenology. In contrast, they did not show the expected differentiation for cell resistance, but these latter experiments had high variance and hence lower statistical power. The results highlight ENMs as useful tools to identify contrasting putative selective pressures across species ranges. Linking ENMs with common garden experiments provides a theoretically justified and practical way to study adaptive processes, including insights regarding the conservation value of populations inhabiting environmentally marginal areas under ongoing climate change.

The effect of thermally robust ballistic mechanisms on climatic niche in salamanders

Many organismal functions are temperature-dependent due to the contractile properties of muscle. Spring-based mechanisms offer a thermally robust alternative to temperature-sensitive muscular movements and may correspondingly expand a species’ climatic niche by partially decoupling the relationship between temperature and performance. Using the ballistic tongues of salamanders as a case study, we explore whether the thermal robustness of elastic feeding mechanisms increases climatic niche breadth, expands geographic range size, and alters the dynamics of niche evolution. Combining phylogenetic comparative methods with global climate data, we find that the feeding mechanism imparts no discernable signal on either climatic niche properties or the evolutionary dynamics of most climatic niche parameters. Although biomechanical innovation in feeding influences many features of whole-organism performance, it does not appear to drive macro-climatic niche evolution in salamanders. We recommend that future work incorporate micro-scale environmental data to better capture the conditions that salamanders experience, and we discuss a few outstanding questions in this regard. Overall, this study lays the groundwork for an investigation into the evolutionary relationships between climatic niche and biomechanical traits in ectotherms.

Is climate change threatening or beneficial to the habitat distribution of global pangolin species? Evidence from species distribution modeling

Global climate change caused by fossil energy consumption is strongly threatening the species diversity of mammals. In particular, changes in temperature and precipitation have affected the habitat of pangolins. Thus, we employed the MaxEnt modeling approach to simulate the potential habitat distribution of pangolins under the current climate and future climate change scenarios during 2081-2100. The habitats of the two Phataginus pangolins were mainly affected by temperature and precipitation. Conversely, geomorphological factors mainly affected the habitat of pangolins in the genus Smutsia. Under the SSP5-8.5 scenario, the habitat of Smutsia gigantea increased by 460.8 Mha, while that of Smutsia temminckii decreased by 89.4 Mha. Temperature and altitude affected the habitat of Manis crassicaudata, while vegetation coverage affected the habitat of Manis javanica. Moreover, human activities threatened the habitat of pangolins in Africa and India. However, labor transfer in southern China weakened the negative effects of human activities on the survival of pangolins in rural regions. Due to the lack of uniform intergovernmental schemes regarding global pangolin protection, the illegal pangolin trade threatens pangolin species worldwide, especially in Africa. From current to future scenarios, climate change increased the habitats of Manis crassicaudata, Manis javanica, Smutsia gigantea and Phataginus tetradactyla, while the habitats of Manis pentadactyla and Smutsia temminckii were threatened. Moreover, the total habitat area of the pantropical distribution zone in the Southern Hemisphere (26°S-33°S) decreased, mainly due to the extensive reduction in Smutsia temminckii habitat. The habitat of the pantropical zone in the Northern Hemisphere (19°N-28°N) basically remained unchanged. Increases in the habitat of the tropical distribution zone (11°S-17°N) were dominated by habitat gains for Smutsia gigantea. These findings provide scientific evidence to support global pangolin protection.

Predicting the Potential Suitable Climate for Coconut (Cocos nucifera L.) Cultivation in India under Climate Change Scenarios Using the MaxEnt Model

Climate change and climate variability are projected to alter the geographic suitability of lands for crop cultivation. Early awareness of the future climate of the current cultivation areas for a perennial tree crop like coconut is needed for its adaptation and sustainable cultivation in vulnerable areas. We analyzed coconut's vulnerability to climate change in India, based on climate projections for the 2050s and the 2070s under two Representative Concentration Pathways (RCPs): 4.5 and 8.5. Based on the current cultivation regions and climate change predictions from seven ensembles of Global Circulation Models, we predict changes in relative climatic suitability for coconut cultivation using the MaxEnt model. Bioclimatic variables Bio 4 (temperature seasonality, 34.4%) and Bio 7 (temperature annual range, 28.7%) together contribute 63.1%, which along with Bio 15 (precipitation seasonality, 8.6%) determined 71.7% of the climate suitability for coconuts in India. The model projected that some current coconut cultivation producing areas will become unsuitable (plains of South interior Karnataka and Tamil Nadu) requiring crop change, while other areas will require adaptations in genotypic or agronomic management (east coast and the south interior plains), and yet in others, the climatic suitability for growing coconut will increase (west coast). The findings suggest the need for adaptation strategies so as to ensure sustainable cultivation of coconut at least in presently cultivated areas.

Developing fine-grained nationwide predictions of valuable forests using biodiversity indicator bird species

The use of indicator species in forest conservation and management planning can facilitate enhanced preservation of biodiversity from the negative effects of forestry and other uses of land. However, this requires detailed and spatially comprehensive knowledge of the habitat preferences and distributions of selected focal indicator species. Unfortunately, due to limited resources for field surveys, only a small proportion of the occurrences of focal species is usually known. This shortcoming can be circumvented by using modeling techniques to predict the spatial distribution of suitable sites for the target species. Airborne laser scanning (ALS) and other remote sensing (RS) techniques have the potential to provide useful environmental data covering systematically large areas for these purposes. Here, we focused on six bird of prey and woodpecker species known to be good indicators of boreal forest biodiversity values. We used known nest sites of the six indicator species based on nestling ringing records. Thus, the most suitable nesting sites of these species provide important information for biodiversity-friendly forest management and conservation planning. We developed fine-grained, that is, 96 × 96 m grid cell resolution, predictive maps across the whole of Finland of the suitable nesting habitats based on ALS and other RS data and spatial information on the distribution of important forest stands for the six studied biodiversity indicator bird species based on nesting-habitat suitability modeling, that is, the MaxEnt model. Habitat preferences of the study species, as determined by MaxEnt, were in line with the previous knowledge of species-habitat relations. The proportion of suitable habitats of these species in protected areas (PAs) was considerable, but our analysis also revealed many potentially high-quality forest stands outside PAs. However, many of these sites are increasingly threatened by logging because of increased pressures for using forests for bioeconomy and forest industry based on National Forest Strategy. Predicting habitat suitability based on information on the nest sites of indicator species provides a new tool for systematic conservation planning over large areas in boreal forests in Europe, and a corresponding approach would also be feasible and recommendable elsewhere where similar data are available.

Analysis of Conservation Gaps and Landscape Connectivity for Snow Leopard in Qilian Mountains of China

Human modification and habitat fragmentation have a substantial influence on large carnivores, which need extensive, contiguous habitats to survive in a landscape. The establishment of protected areas is an effective way to offer protection for carnivore populations by buffering them from anthropogenic impacts. In this study, we used MaxEnt to model habitat suitability and to identify conservation gaps for snow leopard (Panthera uncia) in the Qilian Mountains of China, and then assessed the impact of highways/railways and their corridors on habitat connectivity using a graph-based landscape connectivity model. Our results indicated that the study area had 51,137 km2 of potentially suitable habitat for snow leopards and that there were four protection gaps outside of Qilian Mountain National Park. The findings revealed that the investigated highway and railway resulted in a decrease in connectivity at a regional scale, and that corridor development might enhance regional connectivity, which strengthens the capacity of central habitat patches to act as stepping stones and improve connections between western and eastern habitat patches. This study emphasized the need for assessing the impact of highways and railways, as well as their role in corridor development, on species’ connectivity. Based on our results, we provide some detailed recommendations for designing protection action plans for effectively protecting snow leopard habitat and increasing habitat connectivity.

Maxent Modeling for Identifying the Nature Reserve of Cistanche deserticola Ma under Effects of the Host (Haloxylon Bunge) Forest and Climate Changes in Xinjiang, China

Cistanche deserticola Ma is a traditional Chinese medicinal plant exclusively parasitizing on the roots of Haloxylon ammodendron (C. A. Mey.) Bunge and H. Persicum Bunge ex Boiss and the primary cultivated crop of the desert economy. Its wild resources became scarce due to over-exploitation and poaching for economic benefits. To protect the biological diversity of the desert Haloxylon–Cistanche community forest, the optimal combination of desert ecology and economy industry, and their future survival, this paper examines the conservation areas of wild C. deserticola from the perspective of hosts’ effects and climate changes. To identify conservation areas, the potential distributions generated by MaxEnt in two strategies (AH: abiotic and hosts factors; HO: hosts factors only) compare the model’s performance, the niche range overlap, and the changing trend in climate changes. The results show the following: (1) The HO strategy is more suitable for prediction and identifying the core conservation areas in hosts and climate changes (indirectly affected by host distributions) for C. deserticola. (2) The low-suitable habitat and the medium-suitable habitat are both sensitive to the climate changes; the reduction reaches 48.2% (SSP585, 2081–2100) and 26.6%(SSP370, 2081–2100), respectively. The highly suitable habitat is always in growth, with growth reaching 27.3% (SSP585, 2081–2100). (3) Core conservation areas and agriculture and education areas are 317,315.118 km2 and 319,489.874 km2, respectively. This study developed a predictive model for Maxent under climate change scenarios by limiting host and abiotic factors and inverted the natural habitat of C. deserticola to provide scientific zoning for biodiversity conservation in desert Haloxylon–Cistanche community forests systems, providing an effective reference for decision makers.

Automatic variable selection in ecological niche modeling: A case study using Cassin’s Sparrow (Peucaea cassinii)

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max’s Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin’s Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim’s Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species’ bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA’s Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.

The overlap of suitable tea plant habitat with Asian elephant (Elephus maximus) distribution in southwestern China and its potential impact on species conservation and local economy

The expansion of land being used for cash crop cultivation has threatened wildlife in recent decades. Tea has become the dominant cash crop in southwestern China. Unfortunately, tea plantations may threaten Asian elephant (Elephus maximus) populations via habitat loss and fragmentation. Identifying areas of suitable habitat for tea plant cultivation, and where this habitat overlaps with Asian elephant distribution, is vital for planning land use, managing nature reserves, shaping policy, and maintaining local economies. Here, we assess the potential impact of tea plantations on Asian elephants in southwestern Yunnan province, China. We used MaxEnt modeling with bioclimatic and environmental variables to identify suitable habitat for tea plant cultivation under the current climate scenario, and then overlapped this habitat with 9 known Asian elephant distribution areas (G1-G9) to determine "threatened areas." Our results showed that (1) annual precipitation (48.1% contribution), temperature constancy (29 % contribution), and slope (8.7 % contribution) were key in determining suitable habitat for tea plants; (2) the cumulative area of suitable habitat for tea plants was 13,784.88 km², mainly distributed in Menghai (3934.53 km²), Lancang (3198.67 km²), and Jinghong (2657.74 km²); (3) the distribution area of elephants was 943.75 km², and these areas overlapped with suitable tea plant habitat primarily located in G4 (379.40 km²), G3 (251.18), and G7 (168.03 km²); and (4) threatened areas in G1 and G7 were predominately located along the periphery of current nature reserves. Win-win solutions that work for elephant conservation and economic development include rescoping nature reserve boundaries, strengthening management on the periphery of nature reserves, establishing ecological corridors and new nature reserves within regions where elephants are currently distributed, planting alternative cash crops, and financial subsidies to farmers. This study improves understanding of human-elephant coexistence, and will assist in guiding land use policy for the future conservation outcomes seeking to promote responsible and profitable cash crop farming and elephant conservation.

Estimation of breeding probability can make monitoring data more revealing: a case study of amphibians

Monitoring programs serve to detect trends in the distribution and abundance of species. To do so, monitoring programs often use static state variables. Dynamic state variables that describe population dynamics might be more valuable because they allow for a mechanistic understanding of the processes that lead to population trends. We fit multistate occupancy models to data from a country-wide multispecies amphibian occupancy monitoring program and estimated occupancy and breeding probabilities. If breeding probabilities are determinants of occupancy dynamics, then they may serve in monitoring programs as state variables that describe dynamic processes. The results showed that breeding probabilities were low and that a large proportion of the populations had to be considered to be non-breeding populations (i.e., populations where adults are present but no breeding occurs). For some species, the majority of populations were non-breeding populations. We found that non-breeding populations have lower persistence probabilities than populations where breeding occurs. Breeding probabilities may thus explain trends in occupancy but they might also explain other ecological phenomena, such as the success of invasive species, which had high breeding probabilities. Signs of breeding, i.e., the presence of eggs and larvae, were often hard to detect. Importantly, non-breeding populations also had low detection probabilities, perhaps because they had lower abundances. We suggest that monitoring programs should invest more in the detection of life history stages indicative of breeding, and also into the detection of non-breeding populations. We conclude that breeding probability should be used as a state variable in monitoring programs because it can lead to deeper insights into the processes driving occupancy dynamics.

Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis)

BACKGROUND

Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies' niche to inform strategic conservation actions.

METHODS

We modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996-2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context.

RESULTS

Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evidence that Humboldt martens were associated with old-growth structural indices. This case study provides an example of how limited information on rare or lesser-known species can lead to differing interpretations, emphasizing the need for study-level replication in ecology. Humboldt marten conservation would benefit from continued survey effort to clarify range extent, population sizes, and fine-scale habitat use.

Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.

Ecological niche models display nonlinear relationships with abundance and demographic performance across the latitudinal distribution of Astragalus utahensis (Fabaceae)

The potential for ecological niche models (ENMs) to accurately predict species' abundance and demographic performance throughout their geographic distributions remains a topic of substantial debate in ecology and biogeography. Few studies simultaneously examine the relationship between ENM predictions of environmental suitability and both a species' abundance and its demographic performance, particularly across its entire geographic distribution. Yet, studies of this type are essential for understanding the extent to which ENMs are a viable tool for identifying areas that may promote high abundance or performance of a species or how species might respond to future climate conditions. In this study, we used an ensemble ecological niche model to predict climatic suitability for the perennial forb Astragalus utahensis across its geographic distribution. We then examined relationships between projected climatic suitability and field-based measures of abundance, demographic performance, and forecasted stochastic population growth (λs). Predicted climatic suitability showed a J-shaped relationship with A. utahensis abundance, where low-abundance populations were associated with low-to-intermediate suitability scores and abundance increased sharply in areas of high predicted climatic suitability. A similar relationship existed between climatic suitability and λs from the center to the northern edge of the latitudinal distribution. Patterns such as these, where density or demographic performance only increases appreciably beyond some threshold of climatic suitability, support the contention that ENM-predicted climatic suitability does not necessarily represent a reliable predictor of abundance or performance across large geographic regions.

Niche divergence corresponds to genetic differentiation within the parrot-beaked tortoise Homopus areolatus (Reptilia: Testudinidae), endemic to South Africa

We assessed genetic differentiation and habitat suitability for Homopus areolatus during current and Last Glacial Maximum (LGM) conditions. The ND4 locus retrieved two monophyletic mtDNA clades with lower diversity in clade 1, in the west, than in clade 2, in the south-east. Clade 1 showed a north–south and clade 2 a west-to-east genetic divergence, and the clades co-occur in the syntaxis zone of the Cape Fold Mountains. The clades occupy distinct niches with limited overlap. Rainfall seasonality contributed most to habitat suitability, with clade 1 being restricted to winter rainfall and clade 2 to all-year rainfall regions. Precipitation variables contributed 90% and 60%, respectively, to habitat suitability of clades 1 and 2, with temperature, particularly mean temperature of the driest quarter, being of greater importance for clade 2 than clade 1. Suitable habitat shrank from the LGM to current conditions, probably due to reduced rainfall in the west and higher temperatures in most regions. We conclude that patterns of genetic divergence are strongly associated with ecological niche divergence of H. areolatus clades. More studies are needed to assess the taxonomic status of clade 1, particularly in view of its shrinking habitat due to climate change and anthropogenic factors.

Current and future suitable habitat areas for Nasuella olivacea (Gray, 1865) in Colombia and Ecuador and analysis of its distribution across different land uses

Nasuella olivacea is an endemic mammal from the Andes of Ecuador and Colombia. Due to its rarity, aspects about its natural history, ecology and distribution patterns are not well known, therefore, research is needed to generate knowledge about this carnivore and a first step is studying suitable habitat areas. We performed Ecological Niche Models and applied future climate change scenarios (2.6 and 8.5 RCP) to determine the potential distribution of this mammal in Colombia and Ecuador, with current and future climate change conditions; furthermore, we analysed its distribution along several land covers. We found that N. olivacea is likely to be found in areas where no records have been reported previously; likewise, climate change conditions would increase suitable distribution areas. Concerning land cover, 73.4% of N. olivacea potential distribution was located outside Protected Areas (PA), 46.1% in Forests and 40.3% in Agricultural Lands. These findings highlight the need to further research understudied species, furthering our understanding about distribution trends and responses to changing climatic conditions, as well as informig future PA designing. These are essential tools for supporting wildlife conservation plans, being applicable for rare species whose biology and ecology remain unknown.

Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow

When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide restriction site-associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.

Islands in the desert: environmental distribution modelling of endemic flora reveals the extent of Pleistocene tropical relict vegetation in southern Arabia

BACKGROUND AND AIMS

Southern Arabia is a global biodiversity hotspot with a high proportion of endemic desert-adapted plants. Here we examine evidence for a Pleistocene climate refugium in the southern Central Desert of Oman, and its role in driving biogeographical patterns of endemism.

METHODS

Distribution data for seven narrow-range endemic plants were collected systematically across 195 quadrats, together with incidental and historic records. Important environmental variables relevant to arid coastal areas, including night-time fog and cloud cover, were developed for the study area. Environmental niche models using presence/absence data were built and tuned for each species, and spatial overlap was examined.

KEY RESULTS

A region of the Jiddat Al Arkad reported independent high model suitability for all species. Examination of environmental data across southern Oman indicates that the Jiddat Al Arkad displays a regionally unique climate with higher intra-annual stability, due in part to the influence of the southern monsoon. Despite this, the relative importance of environmental variables was highly differentiated among species, suggesting that characteristic variables such as coastal fog are not major cross-species predictors at this scale.

CONCLUSIONS

The co-occurrence of a high number of endemic study species within a narrow monsoon-influenced region is indicative of a refugium with low climate change velocity. Combined with climate analysis, our findings provide strong evidence for a southern Arabian Pleistocene refugium in Oman's Central Desert. We suggest that this refugium has acted as an isolated temperate and mesic island in the desert, resulting in the evolution of these narrow-range endemic flora. Based on the composition of species, this system may represent the northernmost remnant of a continuous belt of mesic vegetation formerly ranging from Africa to Asia, with close links to the flora of East Africa. This has significant implications for future conservation of endemic plants in an arid biodiversity hotspot.

Potential impact of climate change on the geographical distribution of two wild vectors of Chagas disease in Chile: Mepraia spinolai and Mepraia gajardoi

Background

Mepraia gajardoi and Mepraia spinolai are endemic triatomine vector species of Trypanosoma cruzi, a parasite that causes Chagas disease. These vectors inhabit arid, semiarid and Mediterranean areas of Chile. Mepraia gajardoi occurs from 18° to 25°S, and M. spinolai from 26° to 34°S. Even though both species are involved in T. cruzi transmission in the Pacific side of the Southern Cone of South America, no study has modelled their distributions at a regional scale. Therefore, the aim of this study is to estimate the potential geographical distribution of M. spinolai and M. gajardoi under current and future climate scenarios.

Methods

We used the Maxent algorithm to model the ecological niche of M. spinolai and M. gajardoi, estimating their potential distributions from current climate information and projecting their distributions to future climatic conditions under representative concentration pathways (RCP) 2.6, 4.5, 6.0 and 8.5 scenarios. Future predictions of suitability were constructed considering both higher and lower public health risk situations.

Results

The current potential distributions of both species were broader than their known ranges. For both species, climate change projections for 2070 in RCP 2.6, 4.5, 6.0 and 8.5 scenarios showed different results depending on the methodology used. The higher risk situation showed new suitable areas, but the lower risk situation modelled a net reduction in the future potential distribution areas of M. spinolai and M. gajardoi.

Conclusions

The suitable areas for both species may be greater than currently known, generating new challenges in terms of vector control and prevention. Under future climate conditions, these species could modify their potential geographical range. Preventive measures to avoid accidental human vectorial transmission by wild vectors of T. cruzi become critical considering the uncertainty of future suitable areas projected in this study.

kuenm: an R package for detailed development of ecological niche models using Maxent

Background

Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way.

Results

This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric.

Discussion

Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.

Identifying refugia and corridors under climate change conditions for the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Hubei Province, China

Using a case study of an isolated management unit of Sichuan snub-nosed monkey (Rhinopithecus roxellana), we assess the extent that climate change will impact the species' habitat distribution in the current period and projected into the 2050s. We identify refugia that could maintain the population under climate change and determine dispersal paths for movement of the population to future suitable habitats. Hubei Province, China. We identified climate refugia and potential movements by integrating bioclimatic models with circuit theory and least-cost model for the current period (1960-1990) and the 2050s (2041-2060). We coupled a maximum entropy algorithm to predict suitable habitat for the current and projected future periods. Suitable habitat areas that were identified during both time periods and that also satisfied home range and dispersal distance conditions were delineated as refugia. We mapped potential movements measured as current flow and linked current and future habitats using least-cost corridors. Our results indicate up to 1,119 km2 of currently suitable habitat within the study range. Based on our projections, a habitat loss of 67.2% due to climate change may occur by the 2050s, resulting in a reduced suitable habitat area of 406 km2 and very little new habitat. The refugia areas amounted to 286 km2 and were located in Shennongjia National Park and Badong Natural Reserve. Several connecting corridors between the current and future habitats, which are important for potential movements, were identified. Our assessment of the species predicted a trajectory of habitat loss following anticipated future climate change. We believe conservation efforts should focus on refugia and corridors when planning for future species management. This study will assist conservationists in determining high-priority regions for effective maintenance of the endangered population under climate change and will encourage increased habitat connectivity.

Climatic Niche Model for Overwintering Monarch Butterflies in a Topographically Complex Region of California

We use climatic conditions that are associated with known monarch butterfly overwintering groves in California to build a Maxent model, and focus on the fine scale probability of overwintering grove occurrence in a topographically complex region of the state (Santa Barbara County). Grove locations are known from recent and historical surveys and a long-term citizen science database. The climatic niche model performs well, predicting that overwintering habitat is most likely to occur along the coast and at low elevations, as shown by empirical data. We then use climatic variables in conjunction with climate change scenarios to model the future location of overwintering habitat, and find a substantial shift in the predicted distribution. Under a plausible scenario, the probability of occurrence of overwintering habitat directly reflects elevation, with coastal regions having a reduced probability relative to today, and higher elevation sites increasing in probability. Under a more extreme scenario, high probability sites are only located along ridgelines and in mountaintop regions of the county. This predicted shift in distribution is likely to have management implications, as sites that currently lack monarchs may become critical to conservation in the future. Our results suggest that estimating the size of the western overwintering population in the future will be problematic, unless annual counts compensate for a shift in the distribution and a potential change in the number and location of occupied sites.

Climate change-driven range losses among bumblebee species are poised to accelerate

Climate change has shaped bee distributions over the past century. Here, we conducted the first species-specific assessment of future climate change impacts on North American bumblebee distributions, using the most recent global change scenarios developed in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC). We assessed potential shifts in bumblebee species distributions with models generated using Maxent. We tested different assumptions about bumblebee species’ dispersal capacities, drawing on observed patterns of range shifts to date, dispersal rates observed for bumblebee queens, and, lastly, assuming unlimited dispersal. Models show significant contractions of current ranges even under scenarios in which dispersal rates were high. Results suggest that dispersal rates may not suffice for bumblebees to track climate change as rapidly as required under any IPCC scenario for future climate change. Areas where species losses are projected overlap for many species and climate scenarios, and are concentrated in eastern parts of the continent. Models also show overlap for range expansions across many species, suggesting the presence of “hotspots” where management activities could benefit many species, across all climate scenarios. Broad-scale strategies are likely to be necessary to improve bumblebee conservation prospects under climate change.

Differences between microhabitat and broad-scale patterns of niche evolution in terrestrial salamanders

The extent to which closely related species share similar niches remains highly debated. Ecological niches are increasingly analysed by combining distribution records with broad-scale climatic variables, but interactions between species and their environment often occur at fine scales. The idea that macroscale analyses correctly represent fine-scale processes relies on the assumption that average climatic variables are meaningful predictors of processes determining species persistence, but tests of this hypothesis are scarce. We compared broad- and fine-scale (microhabitat) approaches by analyzing the niches of European plethodontid salamanders. Both the microhabitat and the macroecological approaches identified niche differences among species, but the correspondence between micro- and macroecological niches was weak. When exploring niche evolution, the macroecological approach suggested a close relationship between niche and phylogenetic history, but this relationship did not emerge in fine-scale analyses. The apparent pattern of niche evolution emerging in broad-scale analyses likely was the by-product of related species having closely adjacent ranges. The environment actually experienced by most of animals is more heterogeneous than what is apparent from macro-scale predictors, and a better combination between macroecological and fine-grained data may be a key to obtain robust ecological generalizations.