| 21. |
- 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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| 22. |
- Adem Esmail, Blal, 1982-, et al.
(författare)
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Multi-criteria decision analysis for nature conservation : A review of 20 years of applications
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 42-53
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Tidskriftsartikel (refereegranskat)abstract
- 1. Multi-criteria decision analysis (MCDA) is a method to support decision-making, by exploring the balance between the pros and cons of different alternatives to ac- complish a specific goal. It assists in framing decision problems, illustrating the per- formance of alternatives across criteria, exploring trade-offs, formulating a decision and testing its robustness. This paper provides a structured review of empirical applications of MCDA to nature conservation published in the scientific literature over the last 20 years. The paper aims at taking stock of past experiences, and comparing them with best practices and common pitfalls identified in the literature, to provide recommendations for better MCDA application to conservation.2. The review follows the structure of a generalized MCDA process consisting of three key stages: (1) decision context and problem structuring, (2) analysis and (3) decision.3. The search identified 86 papers that describe MCDA applications to a range of top- ics, including conservation prioritization and planning; protected areas management and zoning; forest management and restoration; and mapping of biodiversity, naturalness and wilder. The results show that, concerning problem structuring, a small percentage of the reviewed MCDA engaged stakeholders other than the authors in identifying alternatives and formulating criteria (15% and 35% respectively). Concerning the analysis, criteria assessment was adequately justified by the authors (47%), at times also by involving other stakeholders (22%). Weighting was per- formed in almost all applications, whereas criteria aggregation was mostly based on the weighted linear combination (63%). Sensitivity analysis was largely overlooked (57%). Concerning decision, 45% of the articles provided only an overall ranking or suitability of alternatives, while 22% included additional rankings according to spe- cific criterion, and 8% further analyses and clustering of stakeholders’ preferences.4. The paper concludes by suggesting key elements of successful MCDA applications, including clear construction of the decision context; collaborative identification of alternatives and criteria that reflect the values at stake; adequate justification and communication of the methods for criteria assessment and weighting; reasoned choice of the criteria aggregation method, and comprehensive sensitivity analysis.
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| 23. |
- Arnoldi, Jean-Francois, et al.
(författare)
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Invasions of ecological communities : Hints of impacts in the invaders growth rate
- 2022
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 13:1, s. 167-182
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Tidskriftsartikel (refereegranskat)abstract
- 1. Theory in ecology and evolution often relies on the analysis of invasion processes, and general approaches exist to understand the early stages of an invasion. However, predicting the long-term transformations of communities following an invasion remains a challenging endeavour. 2. We propose a general analytical method that uses both resident community and invader dynamical features to predict whether an invasion causes large long-term impacts on the invaded community. 3. This approach reveals a direction in which classic invasion analysis, based on initial invasion growth rate, can be extended. Indeed, we explain how the density dependence of invasion growth, if properly defined, synthetically encodes the long-term biotic transformations caused by an invasion, and therefore predicts its ultimate outcome. This approach further clarifies how the density dependence of the invasion growth rate is as much a property of the invading population as it is one of the invaded community. 4. Our theory applies to any stable community model, and directs us towards new questions that may enrich the toolset of invasion analysis, and suggests that indirect interactions and dynamical stability are key determinants of invasion outcomes.
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| 24. |
- Auffret, Alistair G., et al.
(författare)
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HistMapR : Rapid digitization of historical land-use maps in R
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:11, s. 1453-1457
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Tidskriftsartikel (refereegranskat)abstract
- Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision. Comparing land use between maps from different time periods allows estimation of the magnitude of habitat change in an area. However, digitizing historical maps manually is time-consuming and analyses of change are usually carried out at small spatial extents or at low resolutions. HistMapR contains a number of functions that can be used to semi-automatically digitize historical land use according to a map's colours, as defined by the RGB bands of the raster image. We test the method on different historical land-use map series and compare results to manual digitizations. Digitization is fast, and agreement with manually digitized maps of around 80-90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.
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| 25. |
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| 26. |
- Bartoszek, Krzysztof, et al.
(författare)
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Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies
- 2024
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Ingår i: Methods in Ecology and Evolution. - : WILEY. - 2041-210X.
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Tidskriftsartikel (refereegranskat)abstract
- <ol><li>The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models.</li><li>Taking advantage of it, we redesigned the R package mvSLOUCH.</li><li>Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein-Uhlenbeck processes.</li><li>The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.</li> </ol>
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| 27. |
- 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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| 28. |
- Bradter, Ute, et al.
(författare)
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Can opportunistically collected Citizen Science data fill a data gap for habitat suitability models of less common species?
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 1667-1678
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Tidskriftsartikel (refereegranskat)abstract
- 1. Opportunistically collected species observations contributed by volunteer reporters are increasingly available for species and regions for which systematically collected data are not available. However, it is unclear if they are suitable to produce reliable habitat suitability models (HSMs), and hence if the species-habitat relationships found and habitat suitability maps produced can be used with confidence to advice conservation management and address basic and applied research questions.2. We evaluated HSMs with opportunistically collected observations against HSMs with systematically collected observations. We enhanced the opportunistically collected presence-only data by adding inferred species absences. To obtain inferred absences, we asked individual reporters about their identification skills and if they reported certain species consistently and combined this information with their observations. We evaluated several HSM methods using a forest bird species, Siberian jay (Perisoreus infaustus), in Sweden: logistic regression with inferred absences, two versions of MaxEnt, a model combining presence-absence with presence-only observations and a Bayesian site-occupancy-detection model.3. All HSM methods produced nationwide habitat suitability maps of Siberian jay that agreed well with systematically collected observations (AUC: 086-0.88) and were very similar to a habitat suitability map produced from the HSM with systematically collected observations (Spearman rho: 0.94-0.98). At finer geographical scales there were differences among methods.4. At finer scale, the resulting habitat suitability maps from logistic regression with inferred absences agreed better with results from systematically collected observations than other methods. The species-habitat relationships found with logistic regression also agreed well with those found from systematically collected data and with prior expectations based on the species ecology.5. Synthesis and application. For many regions and species, systematically collected data are not available. By using inferred absences from high-quality, opportunistically collected contributions of few very active reporters in logistic regression we obtained HSMs that produced results similar to those from a systematic survey. Adding high-quality inferred absences to opportunistically collected data is likely possible for many less common species across various organism groups. Well-performing HSMs are important to facilitate applications such as spatial conservation planning and prioritization, monitoring of invasive species, understanding species habitat requirements or climate change studies.
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| 29. |
- 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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| 30. |
- Campione, Nicolas E., et al.
(författare)
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Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:9, s. 913-923
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Tidskriftsartikel (refereegranskat)abstract
- Body mass is strongly related to both physiological and ecological properties of living organisms. As a result, generating robust, broadly applicable models for estimating body mass in the fossil record provides the opportunity to reconstruct palaeobiology and investigate evolutionary ecology on a large temporal scale. A recent study provided strong evidence that the minimum circumference of stylopodial elements (humerus and femur) is conservatively associated with body mass in living quadrupeds. Unfortunately, this model is not directly applicable to extinct bipeds, such as non-avian dinosaurs. This study presents a new equation that mathematically corrects the quadruped equation for use in bipeds. It is derived from the systemic difference in the circumference-to-area scaling relationship of two circles (hypothetical quadruped) and one circle (hypothetical biped), which represent the cross-section of the main weight-bearing limb bones. When applied to a newly constructed data set of femoral circumferences and body masses in living birds, the new equation reveals errors that are significantly lower than other published equations, but significantly higher than the error inherent in the avian data set. Such errors, however, are expected given the unique overall femoral circumference-body mass scaling relationship found in birds. Body mass estimates for a sample of bipedal dinosaurs using the new model are consistent with recent estimates based on volumetric life reconstructions, but, in contrast, this equation is simpler to use, with the concomitant potential to provide a wider set of body mass estimates for extinct bipeds. Although it is evident that no one estimation model is flawless, the combined use of the corrected quadrupedal equations and the previously published quadrupedal equation offer a consistent approach with which to estimate body masses in both quadrupeds and bipeds. These models have implications for conducting large-scale macroevolutionary analyses of body size throughout the evolutionary history of terrestrial vertebrates, and, in particular, across major changes in body plan, such as the evolution of bipedality in archosaurs and quadrupedality in dinosaurs.
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