Functional clustering of varved lake sediment to reconstruct past seasonal climate

Annually laminated (varved) lake sediments constitutes excellent environmental archives, and have the potential to play an important role for understanding past seasonal climate with their inherent annual time resolution and within-year seasonal patterns. We propose to use functional data analysis methods to extract the relevant information with respect to climate reconstruction from the rich but complex information in the varves, including the shapes of the seasonal patterns, the varying varve thickness, and the non-linear sediment accumulation rates. In particular we analyze varved sediment from lake Kassjön in northern Sweden, covering the past 6400 years. The properties of each varve reflect to a large extent weather conditions and internal biological processes in the lake the year that the varve was deposited. Functional clustering is used to group the seasonal patterns into different types, that can be associated with different weather conditions. The seasonal patterns were described by penalized splines and clustered by the k-means algorithm, after alignment. The observed (within-year) variability in the data was used to determine the degree of smoothing for the penalized spline approximations. The resulting clusters and their time dynamics show great potential for seasonal climate interpretation, in particular for winter climate changes.     

Avian Diversity and Functional Insectivory on North-Central Florida Farmlands

Abstract:  We studied the potential for native birds to control insect pests on farms. We assessed habitat factors correlated with diversity, distribution, and insect-foraging activity of native birds on farms in north-central Florida and then characterized common bird species that consumed insect biomass in crops as "functional insectivores" (birds most likely to contribute to pest control). Analyses of point-count survey data and foraging observations collected over 2 years on paired organic and conventional farm sites indicated that (1) farms supported most (82–96%) land birds known to breed in the region; (2) bird species richness and abundance varied significantly with matrix habitat and field border type (but not with year or farm management type); (3) the highest bird abundances were associated with mixed crop plantings, field borders, and adjacent matrix composed of forest and hedge; and (4) abundances of 10 species identified as functional insectivores were primarily influenced by crop type (mixed crops attracted significantly more insect foragers into fields than monocrops). We documented birds eating pest insects in crops and did not observe substantive crop damage by birds during growing-season observations. We advocate use of the term functional insectivore to emphasize the potential positive role of avian insectivory on farms during the growing season.     

Models for the sterile insect release method with the concurrent release of pesticides

Four different models of pest populations under control by the release of sterile individuals are examined to determine whether or not the release of pesticides in conjunction with steriles would further reduce the pest population equilibrium. It is found that single species without interactions with other species would generally have their equilibria reduced more with the release of both sterile individuals and pesticides than with the release of only steriles. As biotic interactions become more important, however, the feasibility of releasing pesticides in a sterile release programme becomes less sure and more dependent on the nature of the population regulation of the species involved. In particular, when predation on the pest species is heavy, the sterile release programme is likely to be hindered by the release of pesticides as well.     

A framework for allocating conservation resources among multiple threats and actions

Land managers decide how to allocate resources among multiple threats that can be addressed through multiple possible actions. Additionally, these actions vary in feasibility, effectiveness, and cost. We sought to provide a way to optimize resource allocation to address multiple threats when multiple management options are available, including mutually exclusive options. Formulating the decision as a combinatorial optimization problem, our framework takes as inputs the expected impact and cost of each threat for each action (including do nothing) and for each overall budget identifies the optimal action to take for each threat. We compared the optimal solution to an easy to calculate greedy algorithm approximation and a variety of plausible ranking schemes. We applied the framework to management of multiple introduced plant species in Australian alpine areas. We developed a model of invasion to predict the expected impact in 50 years for each species-action combination that accounted for each species’ current invasion state (absent, localized, widespread); arrival probability; spread rate; impact, if present, of each species; and management effectiveness of each species-action combination. We found that the recommended action for a threat changed with budget; there was no single optimal management action for each species; and considering more than one candidate action can substantially increase the management plan's overall efficiency. The approximate solution (solution ranked by marginal cost-effectiveness) performed well when the budget matched the cost of the prioritized actions, indicating that this approach would be effective if the budget was set as part of the prioritization process. The ranking schemes varied in performance, and achieving a close to optimal solution was not guaranteed. Global sensitivity analysis revealed a threat's expected impact and, to a lesser extent, management effectiveness were the most influential parameters, emphasizing the need to focus research and monitoring efforts on their quantification.     

Importance of Assessing Population Genetic Structure before Eradication of Invasive Species: Examples from Insular Norway Rat Populations

Abstract:  Determining the inter-island migration abilities of pest species and delimiting eradication units enable more viable long-term eradication campaigns because recurrent colonization from neighboring islands is avoided. We examined the genetic structure of the invasive Norway rat ( Rattus norvegicus ) to identify gene flow between islands and delimit population units at different geographical scales. We investigated variation in eight microsatellite loci in rat populations from 18 islands, representing five archipelagos off the Brittany coast (France). Although most of the islands are isolated from each other, short genetic distances, weak F_ST values between close islands, and a high level of cross-assignment showed that individuals collected on different islands could represent a single population unit. A Bayesian clustering method also supported the existence of high levels of gene flow between some neighboring islands. Thus, the statement "one island equals one population" can be false when inter-island distances are less than a few hundred meters. Genetic studies enable the definition of island clusters among which migration may occur that should be considered eradication units. To avoid reinvasion and to minimize ecological and economic costs, rats on all islands in an eradication unit should be eradicated simultaneously. We suggest that the genetic monitoring we performed here can be applied for management of any pest.     

Application of machine learning methods to palaeoecological data

A palaeoecological study was conducted to investigate past environmental conditions and vegetation dynamics around the southwestern Ljubljana Moor. In order to find potential regularities and/or dependencies among co-existent plant species through time, different machine learning methods were applied to pollen records from the cores taken at Bistra and Ho?evarica. The data comprised relative pollen frequencies of the most common plant genera/families at particular core depths that correspond to particular ages in the Early and Mid Holocene periods. The applied methods include equation discovery and hierarchical clustering. Both methods have found plausible and explainable relationships among identified plant genera/families.     

Effects of Elevated Atmospheric Carbon Dioxide on Insect-Plant Interactions

Abstract: In the enriched carbon dioxide atmosphere expected in the next century, many species of herbivorous insects will confront less nutritious host plants that will induce both lengthened larval developmental times and greater mortality. The limited data currently available suggest that the effect of increased atmospheric CO₂ on herbivory will be not only highly species-specific but also specific to each insect-plant system. Several scenarios can be predicted, however: (1) local extinctions will occur; (2) the endangered species status as well as the pest status of some insect species will change; (3) geographic distributions for some insect species will shift with host-plant ranges; and (4) changes in the population dynamics of affected insect species will influence their interactions with other insects and plants. For insect conservation purposes, it is critical to begin long-term studies on the effects of enhanced CO₂ levels on insect populations. An analysis of the available literature indicates that many orders containing insect species important for ecosystem conservation, and even those important as agricultural or medical pests, have not been examined. Without a major increase in research on this topic, we will be unprepared for the species changes that will occur, we will lose the opportunity to document just how some insects adapt to elevated CO₂ levels, and we will lack the information necessary for effective conservation efforts.     

文本聚类算法的分析与比较

聚类是一种重要的文本信息处理方法,文章介绍了常用的文本聚类算法,从这些算法的适用范围、初始参数的影响、终止条件以及对噪声的敏感性等方面对它们进行了分析与比较.对文本聚类算法的应用有一定的指导意义.     

Ecological and Economic Services Provided by Birds on Jamaican Blue Mountain Coffee Farms

Abstract: Coffee farms can support significant biodiversity, yet intensification of farming practices is degrading agricultural habitats and compromising ecosystem services such as biological pest control. The coffee berry borer (Hypothenemus hampei) is the world's primary coffee pest. Researchers have demonstrated that birds reduce insect abundance on coffee farms but have not documented avian control of the berry borer or quantified avian benefits to crop yield or farm income. We conducted a bird‐exclosure experiment on coffee farms in the Blue Mountains, Jamaica, to measure avian pest control of berry borers, identify potential predator species, associate predator abundance and borer reductions with vegetation complexity, and quantify resulting increases in coffee yield. Coffee plants excluded from foraging birds had significantly higher borer infestation, more borer broods, and greater berry damage than control plants. We identified 17 potential predator species (73% were wintering Neotropical migrants), and 3 primary species composed 67% of migrant detections. Average relative bird abundance and diversity and relative resident predator abundance increased with greater shade‐tree cover. Although migrant predators overall did not respond to vegetation complexity variables, the 3 primary species increased with proximity to noncoffee habitat patches. Lower infestation on control plants was correlated with higher total bird abundance, but not with predator abundance or vegetation complexity. Infestation of fruit was 1–14% lower on control plants, resulting in a greater quantity of saleable fruits that had a market value of US$44–$105/ha in 2005/2006. Landscape heterogeneity in this region may allow mobile predators to provide pest control broadly, despite localized farming intensities. These results provide the first evidence that birds control coffee berry borers and thus increase coffee yield and farm income, a potentially important conservation incentive for producers.     

Brazilian free-tailed bats as insect pest regulators in transgenic and conventional cotton crops.

During the past 12000 years agricultural systems have transitioned from natural habitats to conventional agricultural regions and recently to large areas of genetically engineered (GE) croplands. This GE revolution occurred for cotton in a span of slightly more than a decade during which a switch occurred in major cotton production areas from growing 100% conventional cotton to an environment in which 95% transgenics are grown. Ecological interactions between GE targeted insects and other insectivorous insects have been investigated. However, the relationships between ecological functions (such as herbivory and ecosystem transport) and agronomic benefits of avian or mammalian insectivores in the transgenic environment generally remain unclear, although the importance of some agricultural pest management services provided by insectivorous species such as the Brazilian free-tailed bat, Tadarida brasiliensis, have been recognized. We developed a dynamic model to predict regional-scale ecological functions in agricultural food webs by using the indicators of insect pest herbivory measured by cotton boll damage and insect emigration from cotton. In the south-central Texas Winter Garden agricultural region we find that the process of insectivory by bats has a considerable impact on both the ecology and valuation of harvest in Bacillus thuringiensis (Bt) transgenic and nontransgenic cotton crops. Predation on agricultural pests by insectivorous bats may enhance the economic value of agricultural systems by reducing the frequency of required spraying and delaying the ultimate need for new pesticides. In the Winter Garden region, the presence of large numbers of insectivorous bats yields a regional summer dispersion of adult pest insects from Bt cotton that is considerably reduced from the moth emigration when bats are absent in either transgenic or non-transgenic crops. This regional decrease of pest numbers impacts insect herbivory on a transcontinental scale. With a few exceptions, we find that the agronomics of both Bt and conventional cotton production is more profitable when large numbers of insectivorous bats are present.     

Risk assessment in the face of a changing environment: gypsy moth and climate change in Utah.

The importance of efficaciously assessing the risk for introduction and establishment of pest species is an increasingly important ecological and economic issue. Evaluation of climate is fundamental to determining the potential success of an introduced or invasive insect pest. However, evaluating climatic suitability poses substantial difficulties; climate can be measured and assessed in a bewildering array of ways. Some physiological filter, in essence a lens that focuses climate through the requirements and constraints of a potential pest introduction, is required. Difficulties in assessing climate suitability are further exacerbated by the effects of climate change. Gypsy moth (Lymantria dispar L.) is an exotic, tree-defoliating insect that is frequently introduced into the western United States. In spite of an abundance of potential host species, these introductions have yet to result in established populations. The success of eradication efforts and the unsuccessful establishment of many detected and undetected introductions may be related to an inhospitable climate. Climatic suitability for gypsy moth in the western United States, however, is potentially improving, perhaps rapidly, due to a general warming trend that began in the mid 1970s and continues today. In this work, we describe the application of a physiologically based climate suitability model for evaluating risk of gypsy moth establishment on a landscape level. Development of this risk assessment system first required amassing databases that integrated the gypsy moth climatic assessment model, with host species distributions, and climate (historical, present, and future). This integrated system was then used to evaluate climate change scenarios for native host species in Utah, with the result that risk of establishment will dramatically increase during the remainder of the 21st century under reasonable climate change scenarios. We then applied the risk assessment system to several case histories of detected gypsy moth introductions in Utah. These applications demonstrated the general utility of the system for predicting risk of establishment and for designing improved risk detection strategies.     

The semiochemically mediated interactions between bacteria and insects

In natural environment, semiochemicals are involved in many interactions between the different trophic levels involving insects, plants and hosts for parasitoids or prey for predators. These volatile compounds act as messengers within or between insect species, inducing particular behaviours, such as the localisation of a source of food, the orientation to an adequate oviposition site, the selection of a suitable breeding site and the localisation of hosts or prey. In this sense, bacteria have been shown to play an important role in the production of volatile compounds which ones act as semiochemicals. This review, focusing on the semiochemically mediated interactions between bacteria and insects, highlights that bacterial semiochemicals act as important messengers for insects. Indeed, in most of the studies reported here, insects respond to specific volatiles emitted by specific bacteria hosted by the insect itself (gut, mouthparts, etc.) or present in the natural environment where the insect evolves. Particularly, bacteria from the families Enterobacteriaceae, Pseudomonaceae and Bacillaceae are involved in many interactions with insects. Because semiochemicals naturally produced by bacteria could be a very interesting option for pest management, advances in this field are discussed in the context of biological control against insect pests.     

Conservation Strategies for Endemic Fish Species Threatened by the Three Gorges Dam

Abstract:   The largest damming project to date, the Three Gorges Dam has been built along the Yangtze River (China), the most species-rich river in the Palearctic region. Among 162 species of fish inhabiting the main channel of the upper Yangtze, 44 are endemic and are therefore under serious threat of global extinction from the dam. Accordingly, it is urgently necessary to develop strategies to minimize the impacts of the drastic environmental changes associated with the dam. We sought to identify potential reserves for the endemic species among the 17 tributaries in the upper Yangtze, based on presence/absence data for the 44 endemic species. Potential reserves for the endemic species were identified by characterizing the distribution patterns of endemic species with an adaptive learning algorithm called a "self-organizing map" (SOM). Using this method, we also predicted occurrence probabilities of species in potential reserves based on the distribution patterns of communities. Considering both SOM model results and actual knowledge of the biology of the considered species, our results suggested that 24 species may survive in the tributaries, 14 have an uncertain future, and 6 have a high probability of becoming extinct after dam filling.     

Instream and offstream environmental conditions and stream biotic integrity: Importance of scale and site similarities for learning and prediction

Two different methods to predict biotic integrity were tested and compared in the present paper. The first one tries to predict the fish indices of biotic integrity (IBI) at the state or regional scale based on the most similar observations to a specific target site of interest using the simple to implement k-nearest neighbors (or kNN) method. Two different distance functions were considered to find the k-nearest neighbors: the Euclidean and the Mahalanobis. The second method was applied on the same datasets and consisted of a step-wise multiple regression. The two modeling approaches yielded similar results but kNN proved to be more time-efficient and very fast computationally for the given dataset sizes, which allowed applying a leave-one-out cross validation.In an attempt to reveal the importance of scale in the prediction of IBI, regression models were constructed at the state (or regional) scale and at the more refined cluster of sampling sites scale. Clusters of sites were extracted using Kohonen's self-organizing maps (SOM) followed by k-means clustering of the SOM neurons. Cluster-level regression models, constructed after site patterning, performed better in IBI prediction than global regression models constructed without any previous site patterning. The importance of identifying groups of sites with similar environmental characteristics affecting the IBI was revealed. The combined use of site patterning and regression modeling for IBI prediction also helped identifying important variables acting at the local scale which remain latent at the global scale.     

花椒农林复合生态系统的简化对某些相关因子的影响

对单一种植和复合种植两种模式的花椒林地(即有草模式和无草模式)进行了相关生态因子的对比调查,以评价现存花椒林单一模式的合理性．结果表明,在单一种植模式下,花椒林的高度、地径和冠幅虽显著优于复合模式,但是病虫害严重;两种模式中土壤含水率均是随土层厚度的增加而增大,但是变幅有较大差异：复合模式的变幅较稳定,为7．59%～23．79％;而单一模式的变化较剧烈,为4．73％～49．72％,复合模式的土壤含水率显著高于单一模式．复合模式的昆虫种类、多样性、丰富度和均匀度也明显高于单一模式,其中单一模式中的肉食性和寄生性昆虫种类低于复合模式,而植食性蚜虫数量则高于复合模式,暗示单一模式中天敌的栖境和资源以及特定的食草昆虫与有益菌缺少．讨论认为,杂草在花椒林生态系统中起着重要的生态作用,现存的单一种植模式虽然对花椒的生长和产量有利,但却是以牺牲农林系统的可持续发展以及生物多样性为代价的．表3参9。     

A Risk-Assessment System for Screening Out Invasive Pest Plants from Hawaii and Other Pacific Islands

Abstract:  Ecosystems of Hawaii and other Pacific Islands have been greatly affected by invasive pest plants, and ongoing, deliberate plant introductions make it likely that additional pest plants will become established. We tested the ability of a modified version of the Australian and New Zealand weed risk-assessment system to identify pest plants in Hawaii and other Pacific Islands. We used information taken from outside Hawaii to predict the behavior—"pest" or "not a pest"—of almost 200 plant species introduced to Hawaii and other Pacific Islands. The screening system initially recommended further evaluation of 24% of these species, but an additional secondary screening was applied to this group, thereby reducing the rate of indecision to only 8%. To independently test the accuracy of the screening system, we compared its decisions—pest or not a pest—to opinions of 25 expert botanists and weed scientists who had substantial field experience in Hawaii or other Pacific Islands. We asked the experts to rate each species as "major pest,""minor pest," or "not a pest" in native or managed ecosystems. The screening system correctly identified 95% of major pests and 85% of nonpests. Among minor pests identified by the experts, 33% were classified as nonpests by the screening system. Use of the screening system to assess proposed plant introductions to Hawaii or other Pacific Islands and to identify high-risk species used in horticulture and forestry would greatly reduce future pest-plant problems and allow entry of most nonpests. The screening process is objective, rapid, and cost-efficient. With minor modifications, it is likely to be useful in many parts of the world.     

Generalist cuckoo bees (Hymenoptera: Apoidea: Sphecodes) are species-specialist at the individual level

Intensive and incessant arms races between a parasite and its host are generally expected to lead to parasite specialization. Nevertheless, some parasitic species still successfully attack wide spectra of hosts. One of the solutions to the evolutionary enigma of the long-term existence of generalist parasites is their specialization at an individual level, a phenomenon well known, e.g., in European common cuckoo. Over its range, it parasitizes a number of bird species; however, individual females are mostly specialists possessing adaptations to a particular host species. In this study, we test the possibility of individual specialization in generalist cuckoo bees, the insect counterparts of avian cuckoos. Females of cuckoo bees lay each egg into a single brood cell in the nests of other bee species. The host’s offspring is destroyed by the parasitic female or later by her larvae, which feed on pollen supplies accumulated by the host. Both studied cleptoparasitic bees (Sphecodes ephippius and Sphecodes monilicornis) are widely distributed in Europe, where they have been reported to use broad host spectra. We recorded several host species (including some previously unknown) for both cuckoo bee species, and confirmed that these parasites are indeed generalist even at a small local scale. However, we demonstrate that exactly as in the avian cuckoos, each female in both species of generalist bee parasites tends to attack just one host species.     

Insect fauna associated with sugarcane plantations in Sri Lanka

A survey conducted over 13 years (1986-1999) in sugarcane plantations in Sri Lanka to identify insects associated with sugarcane recorded a total of 103 insect species comprising Coleoptera (31 spp.), Dictyoptera (2 spp.), Diptera (5 spp.), 12 Heteroptera (12 spp.), Homoptera (18 spp.), Hymenoptera (7 spp.), Isoptera (3 spp.), Lepidoptera (13 spp.), Orthoptera (9 spp.), and one species each of Thysanoptera, Nuroptera and Trichoptera. Among them were forty-six species of sugarcane pests. In addition, 27 species of natural enemies of sugarcane pests belonging to the orders Coleoptera, Diptera and Hymenoptera were identified Epiricania melanoleuca (Fletcher) introduced into Sri Lanka from Pakistan in 1991 for the control of the sugarcane planthopper was also recorded. Five new pest species previously not recorded from sugarcane in Sri Lanka have been identified.     

Fish assemblages composition in a natural, then regulated, stream: A quantitative long-term study

This paper tests the hypothesis how effectively fish assemblage composition was shaped by local climate changes and by engineering impact in 1989. This was possible due to the monitoring protocols of the present study, which allowed estimation of the magnitude of anthropogenic changes from changes naturally occurring in nature. Fish were sampled at the end of every growing season (October) for 23 years at five contiguous sites in a stream, before (1979-1988) and after (1989-2001) regulation. In each sample, six successive electrofishing passes were used to calculate the density and mean biomass for assemblage analysis using the Zippin model. During the study, the natural, meandering stream with pools, riffles, and a moderate canopy was modified into a straight stream of uniform width and depth, stripped of all vegetation. The output layer of a self-organizing map (SOM, the artificial neural network algorithm) applied in this study for site similarity analysis was partitioned into six subclusters placed in two main clusters. Subclusters in the upper part of the SOM were occupied chiefly by regulated stream samples and those in the lower part of the SOM by natural stream samples. Subclusters in the middle position, contained both natural (19) and regulated (20) samples in nearly equal proportion. In addition, the SOM contained one subcluster with sites only from the regulated period and another with only natural sites. Differences between subclusters were attributed to differences in climate, with some differences profound. Warming of the local weather, which became most evident in the 1990s, may have resulted in changes in fish assemblages. This is shown in the SOM, in which samples from the 1980s with cold years dominate the bottom of the SOM, whereas those from the 1990s and later are at the top. Subclusters dominated by regulated or natural sites were not always significantly different when the number of species and diversity indices were considered. Clear differences between the regulated and natural samples involved qualitative characteristics and mainly concerned assemblage composition. They were also confirmed by significant IndVal values (indicator species) and neither mixed subcluster contained important species in their assemblages.     

Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival

Host-specific mortality driven by natural enemies is a widely discussed mechanism for explaining plant diversity. In principle, populations of plant species can be regulated by distinct host-specific natural enemies that have weak or nonexistent effects on heterospecific competitors, preventing any single species from becoming dominant and thus promoting diversity. Two of the first steps in exploring the role of natural enemies in diversity regulation are to (1) identify potential enemies and (2) evaluate their levels of host specificity by determining if interactions between any one host and its enemy have equivalent survival impacts on co-occurring host species. We developed a bioinformatics framework to evaluate impacts of potential pathogens on seedling survival, for both single and multiple infections. Importantly, we consider scenarios not only if there are specialist pathogens for each plant, but also when generalist pathogens have differential effects on multiple host species, and when co-infection has species-specific effects. We then applied this analytical framework to a field experiment using molecular techniques to detect potential fungal pathogens on co-occurring tree seedling hosts. Combinatorial complexity created by 160 plant-fungus interactions was reduced to eight combinations that affect seedling survival. Potential fungal pathogens had broad host ranges, but seedling species were each regulated by different combinations of fungi or by generalist fungi that had differential effects on multiple plant species. Soil moisture can have the potential to shift the nature of the interactions in some plant-fungal combinations from neutral to detrimental. Reassessing the assumption of single-enemy-single-host interactions broadens the mechanisms through which natural enemies can influence plant diversity.