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| 2. |
- Jonsson, Mattias, et al.
(författare)
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Ecological production functions for biological control services in agricultural landscapes
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:3, s. 243-252
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Tidskriftsartikel (refereegranskat)abstract
- Research relating to ecosystem services has increased, partly because of drastic declines in biodiversity in agricultural landscapes. However, the mechanistic linkages between land use, biodiversity and service provision are poorly understood and synthesized. This is particularly true for many ecosystem services provided by mobile organisms such as natural enemies to crop pests. These species are not only influenced by local land use but also by landscape composition at larger spatial scales. We present a conceptual ecological production function framework for predicting land-use impact on biological control of pests by natural enemies. We develop a novel, mechanistic landscape model for biological control of cereal aphids, explicitly accounting for the influence of landscape composition on natural enemies varying in mobility, feeding rates and other life history traits. Finally, we use the model to map biological control services across cereal fields in a Swedish agricultural region with varying landscape complexity. The model predicted that biological control would reduce crop damage by 45-70% and that the biological control effect would be higher in complex landscapes. In a validation with independent data, the model performed well and predicted a significant proportion of biological control variation in cereal fields. However, much variability remains to be explained, and we propose that the model could be improved by refining the mechanistic understanding of predator dynamics and accounting for variation in aphid colonization. We encourage scientists working with biological control to adopt the conceptual framework presented here and to develop production functions for other crop-pest systems. If this kind of ecological production function is combined with production functions for other services, the joint model will be a powerful tool for managing ecosystem services and planning for sustainable agriculture at the landscape scale.
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| 3. |
- Moller, Anders Pape, et al.
(författare)
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Clutch-size variation in Western Palaearctic secondary hole-nesting passerine birds in relation to nest box design
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:4, s. 353-362
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Tidskriftsartikel (refereegranskat)abstract
- Secondary hole-nesting birds that do not construct nest holes themselves and hence regularly breed in nest boxes constitute important model systems for field studies in many biological disciplines with hundreds of scientists and amateurs involved. Those research groups are spread over wide geographic areas that experience considerable variation in environmental conditions, and researchers provide nest boxes of varying designs that may inadvertently introduce spatial and temporal variation in reproductive parameters. We quantified the relationship between mean clutch size and nest box size and material after controlling for a range of environmental variables in four of the most widely used model species in the Western Palaearctic: great tit Parus major, blue tit Cyanistes caeruleus, pied flycatcher Ficedula hypoleuca and collared flycatcher F.albicollis from 365 populations and 79610 clutches. Nest floor area and nest box material varied non-randomly across latitudes and longitudes, showing that scientists did not adopt a random box design. Clutch size increased with nest floor area in great tits, but not in blue tits and flycatchers. Clutch size of blue tits was larger in wooden than in concrete nest boxes. These findings demonstrate that the size of nest boxes and material used to construct nest boxes can differentially affect clutch size in different species. The findings also suggest that the nest box design may affect not only focal species, but also indirectly other species through the effects of nest box design on productivity and therefore potentially population density and hence interspecific competition.
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| 4. |
- Silvestro, Daniele, et al.
(författare)
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PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data
- 2014
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 5:10, s. 1126-1131
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Tidskriftsartikel (refereegranskat)abstract
- Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth-death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at .
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| 5. |
- Bowlin, Melissa, et al.
(författare)
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The effects of geolocator drag and weight on the flight ranges of small migrants
- 2010
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 1:4, s. 398-402
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Tidskriftsartikel (refereegranskat)abstract
- 1. Researchers are currently placing hundreds of geolocators on migratory animals. Return rates for some small birds carrying these devices have been lower than expected, potentially because geo- locators increase drag during flight. 2. We measured the drag of three different geolocators (1 2g BAS-MK10, 1 0 g SOI-GL10 09 and 0 5 g SOI-GL05 10) in backpack-style harnesses on two preserved bird bodies in a wind tunnel.We then used these measurements to estimate the effects of this drag on the flight ranges of several small migratory birds. 3. Both theBAS-MK10 and SOI-GL05 10 significantly increased drag; the drag was also consider- ably higher when a geolocator was attached between the wings (wing harness) than on the rump (leg-loop harness). 4. The effects of the increased drag of these devices on the predicted flight ranges of birds were simi- lar to the effects of their weight and may thus explain the results of previous studies that showed decreased return rateswhen using geolocators and other tracking devices. 5. We recommend that researchers and manufacturers work to minimize the drag of geolocators and other externally attached tracking or data collection devices on flying and swimming animals. This can be accomplished with geolocators by attaching devices above birds rumps instead of between their wings and flattening the devices to reduce their height.
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| 6. |
- Lisovski, Simeon, et al.
(författare)
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Geolocation by light: accuracy and precision affected by environmental factors
- 2012
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 3:3, s. 603-612
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Tidskriftsartikel (refereegranskat)abstract
- 1. Geolocation by light allows for tracking animal movements, based on measurements of light intensity over time by a data-logging device (geolocator). Recent developments of ultra-light devices (<2 g) broadened the range of target species and boosted the number of studies using geolocators. However, an inherent problem of geolocators is that any factor or process that changes the natural light intensity pattern also affects the positions calculated from these light patterns. Although the most important factors have been identified, estimation of their effect on the accuracy and precision of positions estimated has been lacking but is very important for the analyses and interpretation of geolocator data. 2. The threshold method is mainly used to derive positions by defining sunrise and sunset times from the light intensity pattern for each recorded day. This method requires calibration: a predefined sun elevation angle for estimating latitude by fitting the recorded day/night lengths to theoretical values across latitudes. Therewith, almost constant shading can be corrected for by finding the appropriate sun elevation angle. 3. Weather, topography and vegetation are the most important factors that influence light intensities. We demonstrated their effect on the measurement of day/night length, time of solar midnight/noon and the resulting position estimates using light measurements from stationary geolocators at known places and from geolocators mounted on birds. Furthermore, we investigated the influence of different calibration methods on the accuracy of the latitudinal positions. 4. All three environmental factors can influence the light intensity pattern significantly. Weather and an animals behaviour result in increased noise in positioning, whereas topography and vegetation result in systematic shading and biased positions. Calibration can significantly shift the estimated latitudes and potentially increase the accuracy, but detailed knowledge about the particular confounding factors and the behaviour of the studied animal is crucial for the choice of the most appropriate calibration method.
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| 7. |
- Sahlin, Ullrika, et al.
(författare)
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A benefit analysis of screening for invasive species - base-rate uncertainty and the value of information
- 2011
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 2:5, s. 500-508
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Tidskriftsartikel (refereegranskat)abstract
- 1.. Implementation of the full spectra of screening tools to prevent the introduction of invasive species results in a need to evaluate the cost-efficiency of gathering the information needed to screen for these species. 2. We show how the Bayesian value of information approach can be used to derive the benefit of a screening model based on species traits, which in combination with the base rate of invasiveness, i.e. the proportion of invasive species among those introduced and established, predicts species-specific invasiveness. 3. A pre-posterior Bayesian analysis demonstrated that the benefit of the screening model of invasiveness depends on both the accuracy in predictions and the uncertainty in the base rate of invasiveness. However, even though increasing model accuracy always generates higher model benefit, acknowledging or neglecting the uncertainty in the base rate of invasiveness does not. This means that uncertainty in the base rate is important to consider in the cost-benefit analysis of the screening model. 4. As an example, we derived the benefit of basing decisions on a screening model trained for a data set on species traits of invasive and non-invasive marine macroalgae introduced into Europe. The benefit ranged from 0.6% to 19% of the loss of introducing an invasive species, where the actual value can be estimated if we know the monetary values of impacts from introducing invasive and not introducing non-invasive species. 5. Cost-benefit analyses of screening models for invasive species is one means to reach efficient management of the risks of non-indigenous species. Value of information is a useful tool for benefit analysis of predictive models with respect to decision-making, which goes beyond the investigations of model accuracy. Here, we use value of information analysis to evaluate which sources of uncertainty that is most worth while to reduce and how to set the cost of gathering further species-specific information which will improve the accuracy of a screening.
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| 9. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 10. |
- Byrnes, J. E. K., et al.
(författare)
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Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:2, s. 111-124
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Extensive research shows that more species-rich assemblages are generally more productive and efficient in resource use than comparable assemblages with fewer species. But the question of how diversity simultaneously affects the wide variety of ecological functions that ecosystems perform remains relatively understudied. It presents several analytical and empirical challenges that remain unresolved. In particular, researchers have developed several disparate metrics to quantify multifunctionality, each characterizing different aspects of the concept and each with pros and cons. We compare four approaches to characterizing multifunctionality and its dependence on biodiversity, quantifying (i) magnitudes of multiple individual functions separately, (ii) the extent to which different species promote different functions, (iii) the average level of a suite of functions and (iv) the number of functions that simultaneously exceeds a critical threshold. We illustrate each approach using data from the pan-European BIODEPTH experiment and the R multifunc package developed for this purpose, evaluate the strengths and weaknesses of each approach and implement several methodological improvements. We conclude that an extension of the fourth approach that systematically explores all possible threshold values provides the most comprehensive description of multifunctionality to date. We outline this method and recommend its use in future research. © 2013 British Ecological Society.
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