React or wait: which optimal culling strategy to control infectious diseases in wildlife

We applied optimal control theory to an SI epidemic model to identify optimal culling strategies for diseases management in wildlife. We focused on different forms of the objective function, including linear control, quadratic control, and control with limited amount of resources. Moreover, we identified optimal solutions under different assumptions on disease-free host dynamics, namely: self-regulating logistic growth, Malthusian growth, and the case of negligible demography. We showed that the correct characterization of the disease-free host growth is crucial for defining optimal disease control strategies. By analytical investigations of the model with negligible demography, we demonstrated that the optimal strategy for the linear control can be either to cull at the maximum rate at the very beginning of the epidemic (reactive culling) when the culling cost is low, or never to cull, when culling cost is high. On the other hand, in the cases of quadratic control or limited resources, we demonstrated that the optimal strategy is always reactive. Numerical analyses for hosts with logistic growth showed that, in the case of linear control, the optimal strategy is always reactive when culling cost is low. In contrast, if the culling cost is high, the optimal strategy is to delay control, i.e. not to cull at the onset of the epidemic. Finally, we showed that for diseases with the same basic reproduction number delayed control can be optimal for acute infections, i.e. characterized by high disease-induced mortality and fast dynamics, while reactive control can be optimal for chronic ones.     

Evaluation of Endophytic Bacteria as Potential Biological-Control Agents for Oak Wilt

Endophytic bacteria were isolated from surviving live oaks (Quercus fusiformis) in Texas, where oak wilt is epidemic, and evaluated as potential biological control agents for the disease. Of the 889 bacterial isolates tested, 183 showed in vitro inhibition of the pathogen, Ceratocystis fagacearum. Six isolates were further evaluated for colonization of containerized Spanish oaks (Quercus texana) and live oaks. In general, when injected into the stems, Bacillus species colonized Spanish oaks more extensively than Pseudomonas species; whereas, the opposite was true for live oaks. In containerized live oaks inoculated with the oak wilt pathogen, preinoculation with Pseudomonas denitrificans 1-15 reduced the number of diseased trees by 50% and in the same trial decreased the percentage of crown loss by 17%. In a second trial, no reduction in numbers of diseased trees was observed; however, preinoculation with either strain 1-15 or Pseudomonas putida 5-48 significantly reduced crown loss. These studies indicate that a potential exists for the utilization of selected bacteria to control oak wilt.     

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).     

The effect of fodder plant genotype on the variation of larval fitness traits in genotype classes of green oak leafroller moth

The effect of genetic variation of oak (Quercus pubescens L. and Q. petraea L.) on the genotype fitness components in green oak leafroller moth larvae (Tortrix viridana L.) at esterase (Est-4) and protease (Pts-4) loci was studied. The samples of larvae were collected from nine oak trees, whose genetic variation was assayed by RAPD-PCR using primer OPA14. The contributions of the factors of Yoak species/genotype and green oak leafroller moth genotype and their interaction to the variation of important size-related traits of the larvae were evaluated by two-way ANOVA. It was shown that the same larval genotype can display maximum fitness on the trees of one species or genotype and minimal, on the trees of other species or genotype. The interactions between the oak genotype and green oak leafroller moth genotype factors lead to the relationships that appear in statistically significant associations between genotype classes of green oak leafroller moth and oak. These results are discussed from the standpoint of a recently developed new field, community or ecosystem genetics.     

Native plant diversity increases herbivory to non-natives

There is often an inverse relationship between the diversity of a plant community and the invasibility of that community by non-native plants. Native herbivores that colonize novel plants may contribute to diversity–invasibility relationships by limiting the relative success of non-native plants. Here, we show that, in large collections of non-native oak trees at sites across the USA, non-native oaks introduced to regions with greater oak species richness accumulated greater leaf damage than in regions with low oak richness. Underlying this trend was the ability of herbivores to exploit non-native plants that were close relatives to their native host. In diverse oak communities, non-native trees were on average more closely related to native trees and received greater leaf damage than those in depauperate oak communities. Because insect herbivores colonize non-native plants that are similar to their native hosts, in communities with greater native plant diversity, non-natives experience greater herbivory.     

An SEI model for sarcoptic mange among chamois

We consider a simple model to study the dynamics of sarcoptic mange in a population of chamois. The epidemiological patterns observed during an epidemic in Italy are reconstructed and key parameters of the model are estimated from field data. In particular, we calculate the basic reproductive ratio R (0), a threshold value for chamois density for the occurrence of an epidemic and the speed of propagation of the epidemic wave. The model is then used to obtain indications on the effect of culling as a possible control measure in a closed population and extended to analyse the spatial diffusion of the epidemic. Our results are in agreement with mange epidemiology and observations, and suggest that intervention could be efficacious in reducing the impact of an epidemic.     

Studies on the ectomycorrhizal community in a declining Quercus suber L. stand

This survey was carried out in a Quercus suber L. stand with many trees affected by the disease “oak decline”. Its aim was to obtain information about both the belowground ectomycorrhizal fungal community in a declining Q. suber stand as a whole, and the ectomycorrhizal fungal community of individual tree (EFT) detected in healthy and diseased plants. To this end, we first categorized the trees into four different decline classes (one for healthy plants and three for diseased plants) and then, by using morphological and molecular tools, we identified the ectomycorrhizas isolated from samples collected near the trees with different declining classes. The ectomycorrhizal community as a whole was seen to be composed of numerous ectomycorrhizal fungal species, only some of which appeared to be dominant (Cenococcum geophilum, Lactarius chrysorrheus, and some species of Tomentella genus), while most occurred sporadically. Results show that all root tips observed are mycorrhized and that decline class does not influence the number of ectomycorrhizal root tips found in the EFTs, thus oak decline does not impact the investment in ectomycorrhizal symbiosis. However, some statistical differences can be observed in the values of evenness and taxonomic distinctness in the EFT associated with trees with different states of health. Finally, both the analysis of similarity test and the ordination technique highlight a compositional difference between the EFT associated with trees in different health conditions, but also suggest that other factors may play a role in causing these differences.     

Contrasting ectomycorrhizal fungal communities on the roots of co-occurring oaks (Quercus spp.) in a California woodland

Plant host species is considered an important factor influencing ectomycorrhizal (EM) communities. To gain insights into the role of host species in structuring EM communities, EM communities on sympatric oak (Quercus) species were compared in the Sierra Nevada foothills of California. Using molecular methods (polymerase chain reaction, cloning, restriction fragment length polymorphism and DNA sequencing), EM fungi on roots of deciduous Quercus douglasii and evergreen Quercus wislizeni trees were identified from 64 soil cores. The total EM species richness was 140, of which 40 taxa were detected on both oak hosts. Greater diversity and frequency of EM fungi with epigeous fruiting habit were found on Q. wislizeni, while taxa in the Ascomycota were more frequent and diverse on Q. douglasii. Using ordination, it was determined that both soil extractable phosphorus and oak host species explained a significant proportion of the variation in EM species distribution. These results indicate that plant host species can be an important factor influencing EM fungal community composition, even within congeneric trees.     

Where Is the Extended Phenotype in the Wild? The Community Composition of Arthropods on Mature Oak Trees Does Not Depend on the Oak Genotype

Through a series of common garden experiments, it has been shown that heritable phenotypic differences between individual trees can affect arthropod communities. However, field studies under heterogeneous environmental conditions remain rare. In the present study, we investigated the genetic constitution of 121 mature oak host trees at different trophic levels from 10 sites across Bavaria, southern Germany and their associated insect communities. A total of 23,576 individuals representing 395 species of beetles and true bugs were evaluated. In particular, we determined whether the composition of arthropod communities is related to the oak genotype and whether the strength of the relationships decreases from lower to higher trophic levels, such as for phytophagous, xylophagous, zoophagous, and mycetophagous species. The genetic differentiation of oaks was assessed using eight microsatellite markers. We found no significant influence of the oak genotype on neither the full beetle and true bug community nor on any of the analyzed trophic guilds. In contrast, the community composition of the insects was highly related to the space and climate, such that the community similarity decreased with increases in spatial distance and climatic differences. The relationship with space and climate was much stronger in beetles than in true bugs, particularly in mycetophagous species. Our results suggest that spatial processes override the genetic effects of the host plant in structuring arthropod communities on oak trees. Because we used neutral markers, we cannot exclude the possibility that trait-specific markers may reveal a genetic imprint of the foundation tree species on the composition of the arthropod community. However, based on the strength of the spatial patterns in our data set, we assume that genetic differences among oaks are less important in the structuring of arthropod communities. Future whole-genome studies are required to draw a final conclusion.     

Genetic diversity increases insect herbivory on oak saplings

A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur) half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect) rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect). Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.     

The important role of scattered trees on the herbaceous diversity of a grazed Mediterranean dehesa

Scattered trees are considered keystone structures and play an important role in Mediterranean sylvopastoral systems. Such systems are associated with high biodiversity and provide important natural resources and ecosystem services. In this study, we measured the contribution of scattered trees and different grazing management (cattle, sheep and wildlife only) to the diversity of the grassland sward in a dehesa (open holm oak woodland) located in Central Spain. We analyzed alpha and beta diversity through measurement of species richness, Shannon-Wiener, and Whittaker indices, respectively; and the floristic composition of the herb layer using subplots within two adjacent plots (trees present vs. trees absent) under three different grazing management regimes, including wildlife only, during a year. We found a 20–30% increment in the alpha diversity of wooded plots, compared to those without trees, regardless of grazing management. All beta indices calculated showed more than 60% species turnover. Wooded plots were occupied by different herbaceous species in different heterogeneous microsites (under the canopy, in the ecotone or on open land) created by the trees. Livestock grazing modified species composition (e.g. more nitrophilous species) compared to wildlife only plots. In addition to all their other benefits, trees are important to maintaining grassland diversity in Mediterranean dehesas.     

The impact of local heterogeneity on alternative control strategies for foot-and-mouth disease

The 2001 epidemic of foot-and-mouth disease (FMD) in the UK resulted in the death of nearly 10 million livestock at a cost that was estimated to be up to 8 billion pounds. Owing to the controversy surrounding the epidemic, the question of whether or not alternative policies would have resulted in significantly better control of the epidemic remains of great interest. A hexagonal lattice simulation of FMD in Cumbria is used to address the central question of whether or not better use could have been made of expert knowledge of FMD transmission to target pre-emptive culling, by assuming that the premises at greatest risk of becoming infected can be targeted for culling. The 2000 UK census and the epidemiological database collected during the epidemic are used to describe key characteristics of disease transmission, and the model is fit to the epidemic time-series. Under the assumptions of the model, the parameters that best fit the epidemic in Cumbria indicate that a policy based on expert knowledge would have exacerbated the epidemic compared with the policy as implemented. However, targeting more distant, high-risk farms could be more valuable under different epidemic conditions, notably, if risk factors of sufficient magnitude could be identified to aid in prioritizing vaccination or culling of farms at high risk of becoming infected.     

外生菌根菌与森林树木的相互关系

生态系统的每个过程都伴随着各种微生物的活动,其中最重要的功能群之一是菌根真菌(菌根菌)。一般认为,菌根菌是自然界多数植物生存最基本的组成部分,陆地上约90％以上的高等植物都具有菌根菌。这些菌类的菌丝体与植物根系结合形成菌根,使植物生长成为可能,使不同种类植物的根系联在一起。根据菌根菌入侵植物根系的方式及菌根的形态特征,菌根可分为外生菌根、内生菌根和内外生菌根3组共7种类型。外生菌根主要出现在松科、桦木科、壳斗科等树种的森林生态系统中,在根系表面形成菌丝鞘,部分菌丝进入根系皮层细胞间隙形成哈氏网表面。菌根菌剂在森林经营中得到广泛地应用。外生菌根菌对森林树木的作用可归纳为：1)促进造林或育苗成活与生长;2)提高森林生态系统中植物的多样性、稳定性和生产力;3)对森林生态系统的综合效应,主要表现在增加植物一土壤联结,改善土壤结构,促进土壤微生物,增强植物器官的功能;4)抗拮植物根部病害病原菌等。树木与菌根菌相互关系研究主要包括：1)菌根共生的机理;2)菌根菌在退化森林生态系统恢复与改造中的作用;3)菌根菌的分布格局与森林生态系统服务功能的关系;4)菌根菌对森林生态系统的综合效应,如菌根菌与森林植物群落结构、物种多样性以及森林系统稳定性和生产力的研究。     

<Emphasis Type="Italic">Sporothrix inflata</Emphasis>, a root-inhabiting fungus of <Emphasis Type="Italic">Quercus robur</Emphasis> and <Emphasis Type="Italic">Q. petraea</Emphasis>

The anamorphic fungus Sporothrix inflata, known as a soil-borne fungus with worldwide distribution, was isolated for the first time from the cortex and central cylinder of living and dead roots of healthy and diseased oak trees (Quercus robur and Q. petraea). Isolation frequencies of S. inflata from oak roots varied according to the health status of trees, oak species, study sites, soil depth and root diameter. Colony morphology and growth rate of isolates are influenced by colony age and type of culture medium.     

Reactions of the fauna on the bark of trees to the frequency of fires in a North American savanna

Summary The arthropod communities living on the bark of the oak species Quercus macrocarpa and Q. ellipsoidalis were investigated in a North American oak savanna. Differences were found in the community structure of the arthropods living on the bark of these two tree species, although they have the same fissured bark type. In the North American oak savanna ecosystem the most important disturbance factor is fire, which maintains species richness. Highest numbers of species and specimens were found at moderately disturbed sites. Three main ecological groups of arthropods living on the bark of trees can be distinguished in relation to the degree of disturbance: (1) Inhabitants of bark of trees restricted to undisturbed sites: they do not occur in fire-disturbed areas; (2) Inhabitants of bark of trees adapted to a moderate degree of disturbance: many species occur in high numbers only in moderately disturbed areas; and (3) Specialist inhabitants of bark of trees in heavily disturbed areas. The number of specimens of these species increases per trunk with the frequency of disturbance.     

An SEI model for sarcoptic mange among chamois

We consider a simple model to study the dynamics of sarcoptic mange in a population of chamois. The epidemiological patterns observed during an epidemic in Italy are reconstructed and key parameters of the model are estimated from field data. In particular, we calculate the basic reproductive ratio R ₀, a threshold value for chamois density for the occurrence of an epidemic and the speed of propagation of the epidemic wave. The model is then used to obtain indications on the effect of culling as a possible control measure in a closed population and extended to analyse the spatial diffusion of the epidemic. Our results are in agreement with mange epidemiology and observations, and suggest that intervention could be efficacious in reducing the impact of an epidemic.     

Local genetic structure in a North American epiphytic lichen, Ramalina menziesii (Ramalinaceae)

Epiphytic lichens possess unique life history traits that can have conflicting effects on genetic structure: symbiotic mutualism between a fungus with its algal or cyanobacterial photobiont, association with a host plant, and ability to reproduce sexually and asexually. Our study species, Ramalina menziesii, has small ascospores that can facilitate long-distance gene movement, and it is capable of clonal reproduction. The goals of this study are to test whether different haplotypes were differentially distributed across host plant species, to look for evidence of asexual vs. sexual reproduction, and to assess the local genetic structure of the population. We sampled individuals from multiple trees of three oak species in four lichen subpopulations within a savanna ecosystem. Using DNA sequence data from four fungal nuclear loci, we found no tendency for host specialization. Alleles were randomly distributed across subpopulations. The frequency of multilocus genotypes was consistent with a randomly mating population. Sexual reproduction involving relichenization appeared to be the predominant mode of reproduction of R. menziesii at this study site. We found no significant local genetic structure suggesting widespread gene flow at the local scale. The genetic structure of this lichen is comparable to that of widely distributed epiphytic plants.     

Phytophagy on phylogenetically isolated trees: why hosts should escape their relatives

Hosts belonging to the same species suffer dramatically different impacts from their natural enemies. This has been explained by host neighbourhood, that is, by surrounding host-species diversity or spatial separation between hosts. However, even spatially neighbouring hosts may be separated by many million years of evolutionary history, potentially reducing the establishment of natural enemies and their impact. We tested whether phylogenetic isolation of oak hosts from neighbouring trees within a forest canopy reduces phytophagy. We found that an increase in phylogenetic isolation by 100 million years corresponded to a 10-fold decline in phytophagy. This was not due to poorer living conditions for phytophages on phylogenetically isolated oaks. Neither species diversity of neighbouring trees nor spatial distance to the closest oak affected phytophagy. We suggest that reduced pressure by natural enemies is a major advantage for individuals within a host species that leave their ancestral niche and grow among distantly related species.     

Fast R-CNN深度学习和无人机遥感相结合在松材线虫病监测中的初步应用研究

松材线虫病因其破坏性强、传播速度快和防治难度大等特点,严重威胁着我国的松林资源.及时发现、定位和清理病死松树是控制松材线虫病蔓延的有效手段.本研究利用小型无人机获得松材线虫病疫点的可见光和多光谱的航摄影像.根据松树针叶颜色变化,将松材线虫Bursaphelenchus xylophilus侵染的松树分为病树和枯死树两种类型.将无人机遥感正摄影像图切割成瓦片图,根据不同植被指数的特征差异,筛选出含病树和枯死树的瓦片图.训练Fast R-CNN深度学习框架形成最终模型,通过模型运算获得病枯死松树的分布地图及坐标点位置.研究结果显示Fast R-CNN深度学习和无人机遥感相结合能有效识别出病树和枯死树,正确率分别达到90％和82％,漏检率分别为23％和34％,可为大面积监测松材线虫病的发生现状和流行动态、评估防控效果和灾害损失提供技术支撑.