Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.
2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species‐specific estimates by leveraging detection information among species. Here, we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.
3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N‐mixture models. Our approach substantially increases precision in estimates of abundance compared with models that do not share detection information among species. We then expand this model and apply it to repeated detection/non‐detection data collected on six species of tits (Paridae) breeding at 119 1 km² sampling sites across a P. montanus hybrid zone in northern Switzerland (2004–2020). We find strong impacts of forest cover and elevation on population persistence and colonization in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonization probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.
4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.

     

Traits explain invasion of alien plants into tropical rainforests

• 1. The establishment of new botanic gardens in tropical regions highlights a need for weed risk assessment tools suitable for tropical ecosystems. The relevance of plant traits for invasion into tropical rainforests has not been well studied.
• 2. Working in and around four botanic gardens in Indonesia where 590 alien species have been planted, we estimated the effect of four plant traits, plus time since species introduction, on: (a) the naturalization probability and (b) abundance (density) of naturalized species in adjacent native tropical rainforests; and (c) the distance that naturalized alien plants have spread from the botanic gardens.
• 3. We found that specific leaf area (SLA) strongly differentiated 23 naturalized from 78 non‐naturalized alien species (randomly selected from 577 non‐naturalized species) in our study. These trends may indicate that aliens with high SLA, which had a higher probability of naturalization, benefit from at least two factors when establishing in tropical forests: high growth rates and occupation of forest gaps. Naturalized aliens had high SLA and tended to be short. However, plant height was not significantly related to species'' naturalization probability when considered alongside other traits.
• 4. Alien species that were present in the gardens for over 30 years and those with small seeds also had higher probabilities of becoming naturalized, indicating that garden plants can invade the understorey of closed canopy tropical rainforests, especially when invading species are shade tolerant and have sufficient time to establish.
• 5. On average, alien species that were not animal dispersed spread 78 m further into the forests and were more likely to naturalize than animal‐dispersed species. We did not detect relationships between the measured traits and estimated density of naturalized aliens in the adjacent forests.
• 6. Synthesis: Traits were able to differentiate alien species from botanic gardens that naturalized in native forest from those that did not; this is promising for developing trait‐based risk assessment in the tropics. To limit the risk of invasion and spread into adjacent native forests, we suggest tropical botanic gardens avoid planting alien species with fast carbon capture strategies and those that are shade tolerant.

     

The use of trail cameras to monitor species inhabiting artificial nest boxes

1. Artificial boxes are commonly used in studies of cavity‐dwelling animals of various taxa. One advantage of nest boxes is that cameras can be used to monitor animals inside the cavity, however, most cameras used today have to be built de novo or modified or are expensive.
2. Here, we describe a method for monitoring nest boxes using off‐the‐shelf models of trail cameras that can record photographs and videos in daylight and darkness (TCM; Trail Camera Method). The cameras can record sequentially within a given time lapse or an infra‐red motion sensor can be triggered by activity in the nest box.
3. Using TCM in a Great Tit (Parus major) nest box population, we studied the hourly pattern of the first egg laying and the first egg hatching. We found that Great Tits laid eggs within 2 h of the sunrise while the timing of hatching spanned the 24‐h day. Moreover, we found that the hour of hatching affects the nestlings’ mass on the 2nd day of life, but not on the 12th day of life.
4. Comparing to traditional nest box checks, TMC requires about 75% less time to obtain data on the timing of egg laying and hatching. Moreover, the hour estimation error was several orders of magnitude greater with the traditional method.
5. Our data demonstrate that commercially available trail cameras are an affordable and convenient method of monitoring artificial cavities. Trail cameras are small, standalone, weather‐proof devices with integrated powering, memory storage, lighting, and recording systems. They could be easily swapped between boxes or removed. After small modifications of the box, they could be used to monitor a wide variety of behaviors of many animal taxa.

     

A modified niche model for generating food webs with stage‐structured consumers: The stabilizing effects of life‐history stages on complex food webs

1. Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life‐history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life‐history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies.
2. We extended the niche model developed by Williams and Martinez (Nature, 2000, 404, 180–183) to generate food webs that included trophic species with a life‐history stage structure. Our method aggregated trophic species based on niche overlap to form a life‐history structured population; therefore, it largely preserved the topological structure of food webs generated by the niche model. We applied the theory of allometric predator–prey body mass ratio and parameterized an allometric bioenergetic model augmented with biomass flow between stages via growth and reproduction to study the effects of a stage structure on the stability of food webs.
3. When life‐history stages were linked via growth and reproduction, more food webs persisted, and persisting food webs tended to retain more trophic species. Topological differences between persisting linked and unlinked food webs were small to modest. The slopes of biomass spectra were lower, and weak interaction links were more prevalent in the linked food webs than the unlinked ones, suggesting that a life‐history stage structure promotes characteristics that can enhance stability of complex food webs.
4. Our results suggest a positive relationship between the complexity and stability of complex food webs. A life‐history stage structure in food webs may play important roles in dynamics of and diversity in food webs.

     

Plant functional types broadly describe water use strategies in the Caatinga,a seasonally dry tropical forest in northeast Brazil

1. In seasonally dry tropical forests, plant functional type can be classified as deciduous low wood density, deciduous high wood density, or evergreen high wood density species. While deciduousness is often associated with drought‐avoidance and low wood density is often associated with tissue water storage, the degree to which these functional types may correspond to diverging and unique water use strategies has not been extensively tested.
2. We examined (a) tolerance to water stress, measured by predawn and mid‐day leaf water potential; (b) water use efficiency, measured via foliar δ¹³C; and (c) access to soil water, measured via stem water δ¹⁸O.
3. We found that deciduous low wood density species maintain high leaf water potential and low water use efficiency. Deciduous high wood density species have lower leaf water potential and variable water use efficiency. Both groups rely on shallow soil water. Evergreen high wood density species have low leaf water potential, higher water use efficiency, and access alternative water sources. These findings indicate that deciduous low wood density species are drought avoiders, with a specialized strategy for storing root and stem water. Deciduous high wood density species are moderately drought tolerant, and evergreen high wood density species are the most drought tolerant group.
4. Synthesis. Our results broadly support the plant functional type framework as a way to understand water use strategies, but also highlight species‐level differences.

     

Great tits do not compensate over time for a radio‐tag‐induced reduction in escape‐flight performance

The use of biologging and tracking devices is widespread in avian behavioral and ecological studies. Carrying these devices rarely has major behavioral or fitness effects in the wild, yet it may still impact animals in more subtle ways, such as during high power demanding escape maneuvers. Here, we tested whether or not great tits (Parus major) carrying a backpack radio‐tag changed their body mass or flight behavior over time to compensate for the detrimental effect of carrying a tag. We tested 18 great tits, randomly assigned to a control (untagged) or one of two different types of a radio‐tag as used in previous studies in the wild (0.9 g or 1.2 g; ~5% or ~6–7% of body mass, respectively), and determined their upward escape‐flight performance 1, 7, 14, and 28 days after tagging. In between experiments, birds were housed in large free‐flight aviaries. For each escape‐flight, we used high‐speed 3D videography to determine flight paths, escape‐flight speed, wingbeat frequency, and actuator disk loading (ratio between the bird weight and aerodynamic thrust production capacity). Tagged birds flew upward with lower escape‐flight speeds, caused by an increased actuator disk loading. During the 28‐day period, all groups slightly increased their body mass and their in‐flight wingbeat frequency. In addition, during this period, all groups of birds increased their escape‐flight speed, but tagged birds did so at a lower rate than untagged birds. This suggests that birds may increase their escape‐flight performance through skill learning; however, tagged birds still remained slower than controls. Our findings suggest that tagging a songbird can have a prolonged effect on the performance of rapid flight maneuvers. Given the absence of tag effects on reproduction and survival in most songbird radio‐tagging studies, tagged birds in the wild might adjust their risk‐taking behavior to avoid performing rapid flight maneuvers.     

Effective distance of volatile cues for plant–plant communication in beech

In response to volatiles emitted from a plant infested by herbivorous arthropods, neighboring undamaged conspecific plants become better defended against herbivores; this is referred to as plant‒plant communication. Although plant‒plant communication occurs in a wide range of plant species, most studies have focused on herbaceous plants. Here, we investigated plant‒plant communication in beech trees in two experimental plantations in 2018 and one plantation in 2019. Approximately 20% of the leaves of a beech tree were clipped in half in the spring seasons of 2018 and 2019 (clipped tree). The damage levels to leaves in the surrounding undamaged beech trees were evaluated 90 days after the clipping (assay trees). In both years, the damage levels decreased with a reduction in the distance from the clipped tree. In 2019, we also recorded the damage levels of trees that were not exposed to volatiles (nonexposed trees) as control trees and found that those that were located <5 m away from clipped trees had significantly less leaf damage than nonexposed trees. By using a gas chromatograph–mass spectrometer, ten and eight volatile compounds were detected in the headspaces of clipped and unclipped leaves, respectively. Among them, the amount of (Z)‐3‐hexenyl acetate in clipped leaves was significantly higher than that in nonclipped leaves. Our result suggests that green leaf volatiles such as (Z)‐3‐hexenol and (Z)‐3‐hexenyl acetate and other volatile organic compounds emitted from clipped trees induced defenses in the neighboring trees within the 5 m radius. The effective distances of plant‒plant communication in trees were discussed from the viewpoint of the arthropod community structure in forest ecosystems.     

Plotting receiver operating characteristic and precision–recall curves from presence and background data

1. The receiver operating characteristic (ROC) and precision–recall (PR) plots have been widely used to evaluate the performance of species distribution models. Plotting the ROC/PR curves requires a traditional test set with both presence and absence data (namely PA approach), but species absence data are usually not available in reality. Plotting the ROC/PR curves from presence‐only data while treating background data as pseudo absence data (namely PO approach) may provide misleading results.
2. In this study, we propose a new approach to calibrate the ROC/PR curves from presence and background data with user‐provided information on a constant c, namely PB approach. Here, c defines the probability that species occurrence is detected (labeled), and an estimate of c can also be derived from the PB‐based ROC/PR plots given that a model with good ability of discrimination is available. We used five virtual species and a real aerial photography to test the effectiveness of the proposed PB‐based ROC/PR plots. Different models (or classifiers) were trained from presence and background data with various sample sizes. The ROC/PR curves plotted by PA approach were used to benchmark the curves plotted by PO and PB approaches.
3. Experimental results show that the curves and areas under curves by PB approach are more similar to that by PA approach as compared with PO approach. The PB‐based ROC/PR plots also provide highly accurate estimations of c in our experiment.
4. We conclude that the proposed PB‐based ROC/PR plots can provide valuable complements to the existing model assessment methods, and they also provide an additional way to estimate the constant c (or species prevalence) from presence and background data.

     

Great tits search for,capture, kill and eat hibernating bats

Ecological pressure paired with opportunism can lead to surprising innovations in animal behaviour. Here, we report predation of great tits (Parus major) on hibernating pipistrelle bats (Pipistrellus pipistrellus) at a Hungarian cave. Over two winters, we directly observed 18 predation events. The tits specifically and systematically searched for and killed bats for food. A substantial decrease in predation on bats after experimental provisioning of food to the tits further supports the hypothesis that bat-killing serves a foraging purpose in times of food scarcity. We finally conducted a playback experiment to test whether tits would eavesdrop on calls of awakening bats to find them in rock crevices. The tits could clearly hear the calls and were attracted to the loudspeaker. Records for tit predation on bats at this cave now span more than ten years and thus raise the question of whether cultural transmission plays a role for the spread of this foraging innovation.     

Domestication of tomato has reduced the attraction of herbivore natural enemies to pest‐damaged plants

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PhenoSpace: A Shiny application to visualize trait data in the phenotypic space of the global spectrum of plant form and function

1. A recent analysis of variation in six major traits conducted on a large worldwide sample of vascular plant species showed that three‐quarters of trait variation was captured by a two‐dimensional global spectrum of plant form and function (“global spectrum” hereafter). We developed the PhenoSpace application, whose aim is to visualize and export the position of any individual/population/species in the phenotypic space of the global spectrum.
2. PhenoSpace is a Shiny application that helps users to manipulate and visualize data pertaining to the global spectrum of plant form and function. It is freely accessible at the following URL: https://shiny.cefe.cnrs.fr/PhenoSpace/.
3. PhenoSpace has three main functionalities. First, it allows users to visualize the phenotypic space of the global spectrum using different combinations of traits and growth forms. Second, trait data from any new user‐defined dataset can be projected onto the phenotypic space of the global spectrum, provided that at least two of the six traits are available. Finally, figures produced and loadings of the imported data on the PCA axes can be downloaded, allowing users to conduct further analyses.
4. PhenoSpace fulfills the practical goal of positioning plants in the phenotypic space of the global spectrum, making it possible to compare trait variation at any level of organization against the worldwide background. This serves a major aim of comparative plant ecology, which is to put specific sets of individuals, populations or species into a broader context, facilitating comparison and synthesis of results across different continents and environments using relevant indicators of plant design and function.

     

Integrating demography and distribution modeling for the iconic Leontopodium alpinum Colm. in the Romanian Carpathians

1. Both climate change and human exploitation are major threats to plant life in mountain environments. One species that may be particularly sensitive to both of these stressors is the iconic alpine flower edelweiss (Leontopodium alpinum Colm.). Its populations have declined across Europe due to over‐collection for its highly prized flowers. Edelweiss is still subject to harvesting across the Romanian Carpathians, but no study has measured to what extent populations are vulnerable to anthropogenic change.
2. Here, we estimated the effects of climate and human disturbance on the fitness of edelweiss. We combined demographic measurements with predictions of future range distribution under climate change to assess the viability of populations across Romania.
3. We found that per capita and per‐area seed number and seed mass were similarly promoted by both favorable environmental conditions, represented by rugged landscapes with relatively cold winters and wet summers, and reduced exposure to harvesting, represented by the distance of plants from hiking trails. Modeling these responses under future climate scenarios suggested a slight increase in per‐area fitness. However, we found plant ranges contracted by between 14% and 35% by 2050, with plants pushed into high elevation sites.
4. Synthesis. Both total seed number and seed mass are expected to decline across Romania despite individual edelweiss fitness benefiting from a warmer and wetter climate. More generally, our approach of coupling species distribution models with demographic measurements may better inform conservation strategies of ways to protect alpine life in a changing world.

     

Early learning affects social dominance: interspecifically cross-fostered tits become subdominant

Social dominance influences the outcome of competitive interactionsover limited resources, and may hence be important for individualfitness. Theory thus predicts that its heritability will below and that non-genetic determinants of dominance should prevail.In this field experiment we reciprocally cross-fostered greattits (Parus major) to blue tits (Parus caeruleus) to investigatethe impact of early social experience on dominance status incompetition over food during winter. Controlling for potentialeffects of age, size, sex and site-related dominance, we showthat cross-fostered birds of both species were subdominant toconspecific immigrants, while controls originating from unmanipulatedbroods were dominant to conspecific immigrants. Furthermore,blue tits reared by blue tit parents but with at least one greattit broodmate had lower dominance status relative to conspecificimmigrants than did controls. Although great tits generallydominated blue tits, cross-fostered birds of both species initiatedmarginally more fights against the other species than did theirrespective controls, suggesting faulty species recognition.Since both social parents and broodmates strongly influencethe dominance behavior of offspring later in life, we concludethat social conditions experienced at an early age are crucialfor the determination of subsequent social dominance.     

Testing for effects of climate change on competitive relationships and coexistence between two bird species

Climate change is expected to have profound ecological effects, yet shifts in competitive abilities among species are rarely studied in this context. Blue tits (Cyanistes caeruleus) and great tits (Parus major) compete for food and roosting sites, yet coexist across much of their range. Climate change might thus change the competitive relationships and coexistence between these two species. Analysing four of the highest-quality, long-term datasets available on these species across Europe, we extend the textbook example of coexistence between competing species to include the dynamic effects of long-term climate variation. Using threshold time-series statistical modelling, we demonstrate that long-term climate variation affects species demography through different influences on density-dependent and density-independent processes. The competitive interaction between blue tits and great tits has shifted in one of the studied sites, creating conditions that alter the relative equilibrium densities between the two species, potentially disrupting long-term coexistence. Our analyses show that long-term climate change can, but does not always, generate local differences in the equilibrium conditions of spatially structured species assemblages. We demonstrate how long-term data can be used to better understand whether (and how), for instance, climate change might change the relationships between coexisting species. However, the studied populations are rather robust against competitive exclusion.     

Microhabitat selection for singing and other behaviour in great tits, Parus major: Some visual and acoustical considerations

Territorial male great tits (Parus major L.) usually forage on the ground, sing from perches with a mean height of 9.3 m, and perform most other activities between 2 and 4 m. Analyses of their habitat's visual and acoustical stratification indicate that great tits sing from high perches to make themselves hard to locate visually rather than to make their songs carry farther. The birds' selection of inconspicuous singing spots is further substantiated by their striking preference for hawthorn trees, which have an extremely dense crown and produce leaves very early in the year.     

Density dependent effects between three competitive bird species

Summary Density and breeding success of the great tit Parus major, blue tit Parus caeruleus and collared flycatcher Ficedula albicollis were studied in nest box colony in oak forest over a period of 19 years.Intraspecific density dependent clutch size reduction was found with blue tit and great tit. In interspecific relation the high density of blue tits reduced the clutch size of great tits.In the hatching period neither intraspecific nor interspecific density dependence were showed between the tits when the third competitive species, collared flycatcher was present. The collared flycatcher significantly reduced the hatching success of both tit species and the number of fledglings of great tit.The effects of the great tits and combined density of the great and blue tits on the hatching failure and number of fledglings of collared flycatcher were found when the density of the tits was high. There were not significant relationships to the single density of blue tits.The temporal variability of the competition of the three bird species is discussed.     

Temporal patterns of forest seedling emergence across different disturbance histories

1. Forest ecosystems experience a myriad of natural and anthropogenic disturbances that shape ecological communities. Seedling emergence is a critical, preliminary stage in the recovery of forests post​ disturbance and is triggered by a series of abiotic and biotic changes. However, the long‐term influence of different disturbance histories on patterns of seedling emergence is poorly understood.
2. Here, we address this research gap by using an 11‐year dataset gathered between 2009 and 2020 to quantify the influence of different histories of natural (wildfire) and anthropogenic (clearcut and postfire salvage logging) disturbances on emerging seedlings in early‐successional Mountain Ash forests in southeastern Australia. We also describe patterns of seedling emergence across older successional forests varying in stand age (stands that regenerated in <1900s, 1939, 1970–90, and 2007–11).
3. Seedling emergence was highest in the first three years post disturbance. Stand age and disturbance history significantly influenced the composition and abundance of plant seedlings. Specifically, in salvage‐logged forests, plant seedlings were the most different from similarly aged forests with other disturbance histories. For instance, relative to clearcut and unlogged, burnt forests of the same age, salvage logging had the lowest overall richness, the lowest counts of Acacia seedlings, and an absence of common species including Acacia obliquinervia, Acacia frigescens, Cassinia arcuealta, Olearia argophylla, Pimelea axiflora, Polyscias sambucifolia, and Prosanthera melissifolia over the survey period.
4. Synthesis: Our findings provide important new insights into the influence of different disturbance histories on regenerating forests and can help predict plant community responses to future disturbances, which may influence forest recovery under altered disturbance regimes.

     

Restoration of species‐rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation—Findings of a practical restoration project in southeastern Germany

Restoration of species‐rich grasslands is a key issue of conservation. The transfer of seed‐containing local plant material is a proven technique to restore species‐rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species Knautia arvensis and Plantago lanceolata.For our study, we selected fifteen study sites in southeastern Germany. We analyzed species diversity and composition and used molecular markers to investigate genetic variation within and among populations of the study species from grasslands that served as source sites for restoration and grasslands, which were restored by transfer of green hay and threshed local plant material.The results revealed no significant differences in species diversity and composition between grasslands at source and restoration sites. Levels of genetic variation within populations of the study species Knautia arvensis and Plantago lanceolata were comparable at source and restoration sites and genetic variation among populations at source and their corresponding restoration sites were only marginal different.Our study suggests that the transfer of local plant material is a restoration approach highly suited to preserve the composition of species‐rich grasslands and the natural genetic pattern of typical grassland plant species.     

Context‐dependent outcomes in a reproductive mutualism between two freshwater fish species

1. The development of encompassing general models of ecology is precluded by underrepresentation of certain taxa and systems. Models predicting context‐dependent outcomes of biotic interactions have been tested using plants and bacteria, but their applicability to higher taxa is largely unknown.
2. We examined context dependency in a reproductive mutualism between two stream fish species: mound nest‐building bluehead chub Nocomis leptocephalus and mountain redbelly dace Chrosomus oreas, which often uses N. leptocephalus nests for spawning. We hypothesized that increased predator density and decreased substrate availability would increase the propensity of C. oreas to associate with N. leptocephalus and decrease reproductive success of both species.
3. In a large‐scale in situ experiment, we manipulated egg predator density and presence of both symbionts (biotic context), and replicated the experiment in habitats containing high‐ and low‐quality spawning substrate (abiotic context).
4. Contradictory to our first hypothesis, we observed that C. oreas did not spawn without its host. The interaction outcome switched from commensalistic to mutualistic with changing abiotic and biotic contexts, although the net outcome was mutualistic.
5. The results of this study yielded novel insight into how context dependency operates in vertebrate mutualisms. Although the dilution effect provided by C. oreas positively influenced reproductive success of N. leptocephalus, it was not enough to overcome both egg predation and poor spawning habitat quality. Outcomes of the interaction may be ultimately determined by associate density. Studies of context dependency in vertebrate systems require detailed knowledge of species life‐history traits.

     

Sclerotinia sclerotiorum Thioredoxin1 (SsTrx1) is required for pathogenicity and oxidative stress tolerance

Sclerotinia sclerotiorum infects host plant tissues by inducing necrosis to source nutrients needed for its establishment. Tissue necrosis results from an enhanced generation of reactive oxygen species (ROS) at the site of infection and apoptosis. Pathogens have evolved ROS scavenging mechanisms to withstand host‐induced oxidative damage. However, the genes associated with ROS scavenging pathways are yet to be fully investigated in S. sclerotiorum. We selected the S. sclerotiorum Thioredoxin1 gene (SsTrx1) for our investigations as its expression is significantly induced during S. sclerotiorum infection. RNA interference‐induced silencing of SsTrx1 in S. sclerotiorum affected the hyphal growth rate, mycelial morphology, and sclerotial development under in vitro conditions. These outcomes confirmed the involvement of SsTrx1 in promoting pathogenicity and oxidative stress tolerance of S. sclerotiorum. We next constructed an SsTrx1‐based host‐induced gene silencing (HIGS) vector and mobilized it into Arabidopsis thaliana (HIGS‐A) and Nicotiana benthamiana (HIGS‐N). The disease resistance analysis revealed significantly reduced pathogenicity and disease progression in the transformed genotypes as compared to the nontransformed and empty vector controls. The relative gene expression of SsTrx1 increased under oxidative stress. Taken together, our results show that normal expression of SsTrx1 is crucial for pathogenicity and oxidative stress tolerance of S. sclerotiorum.