| 61. |
- Khalil, Hussein
(författare)
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Using Rhodamine B to assess the movement of small mammals in an urban slum
- 2021
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12, s. 2234-2242
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Tidskriftsartikel (refereegranskat)abstract
- The small mammals, especially rats are pest species that are present in cities world-wide. The rat moves around and into residences and other anthropogenic structures. It is especially ubiquitous in urban slums and a threat to infrastructure and public health due to the pathogens it carries and transmits. Effective control of rat populations in most urban areas has been unsuccessful, despite several rodent control efforts. Limited information about rat movement distance has hindered identification of control units and effective scales at which to enact control during interventions. We evaluated the suitability of Rhodamine B, a non-toxic biomarker, for assessing the distance travelled by rats in urban slums. We tracked rats over two campaigns between 2019 and 2020. Overall, 27.9% of trapped rats showed signs of Rhodamine B in their whiskers under fluorescence microscope. This shows that our method provides a viable alternative for investigating the movement of small mammals in this area. We found that rats move up to 90 m distance in urban slums, with smaller rats travelling more actively than bigger rats. Information obtained from this study should be useful in guiding efficient rodent control initiatives to reduce the risk of household rodent infestation and rodent-borne disease in urban slums.
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| 62. |
- Klinger, Yves P., et al.
(författare)
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iPhenology : Using open-access citizen science photos to track phenology at continental scale
- 2023
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Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 14:6, s. 1424-1431
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Tidskriftsartikel (refereegranskat)abstract
- Photo observations are a highly valuable but rarely used source of citizen science (CS) data. Recently, the number of publicly available photo observations has increased strongly, for example, due to the use of smartphone applications for species identification. This has enabled the raising of ecological insights in poorly studied subjects. One of the fields with the highest potential to benefit from the use of photo observations is phenology. We propose a workflow for iPhenology, the use of publicly available photo observations to track phenological events at large scales. The workflow comprises data acquisition, cleaning of observations, phenological classification and modelling spatiotemporal patterns of phenology. We explore the suitability of iPhenology to observe key phenological stages in the plant reproductive cycle of a model species and discuss limitations and future prospects of the approach using the example of an invasive species in Europe. We show that iPhenology is suitable to track key phenological events of widespread species. However, the number and quality of available observations may differ among species and phenological stages. Overall, publicly available CS photo observations are suitable to track key phenological events and can thus significantly advance the knowledge on the timing and drivers of plant phenology. In future, integrating the workflow with automated image processing and analysis may enable real-time tracking of plant phenology.
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| 63. |
- Knape, Jonas
(författare)
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Estimates from non-replicated population surveys rely on critical assumptions
- 2015
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 6, s. 298-306
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Tidskriftsartikel (refereegranskat)abstract
- N-mixture and occupancy models are often used to account for non-detections in population surveys. The consensus has been that the methods require data that are replicated in space, as well as within a short period of time while the population at each site remains closed, in order for parameters such as detection probabilities and expected abundances to be identifiable. The requirement of replication prohibits the use of N-mixture and occupancy models for many surveys in practice. Recently, some studies have argued that N-mixture and occupancy models for surveys with only one visit at each site are identifiable when covariates for both detection probabilities and expected abundances, with at least one distinct covariate for each, are available (Journal of Plant Ecology, 5, 2012, 22; Environmetrics, 23, 2012, 197). We investigate the reasons for why detection probabilities have traditionally been considered unestimable from non-replicated counts and how the new methods sidestep these issues. We further use simulations to investigate properties of the new estimators. We show that detection probabilities of the single-visit models with covariates are non-identifiable and that absolute abundances cannot be estimated when particular link functions are employed (log links for both expected abundance and detection probability). Further, assumptions about the range within which detection probabilities vary are necessary to render estimability. The possibility of estimating abundance from single-visit surveys therefore implicitly hinges on knowledge about the link functions. Simulations show that estimates of abundance can be highly variable and sensitive to the choice of link function. We further show how a reduced parameterization of an N-mixture model for surveys repeated over time, without replication under closure but where detection probabilities are constant over time, corresponds to a Poisson model. Non-robust estimation can result in misleading conclusions about population abundance. When estimating abundance from count data that are not replicated, it is therefore important to be aware of how imprecise estimators may be and how sensitive they are to model assumptions.
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| 64. |
- Knape, Jonas
(författare)
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On assumptions behind estimates of abundance from counts at multiple sites
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7, s. 206-209
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Tidskriftsartikel (refereegranskat)abstract
- Count data of animals observed from multiple sites are commonly used to study variation in abundance across space and time. Because some individuals typically go undetected in such surveys, count data alone have traditionally been thought to not contain information about absolute abundance. In a recent paper, we showed that estimates of absolute abundance using single-visit methods with covariates (Solymos, et al. Environmetrics, 2012, 23, 197 ) can be biased arbitrarily low if the link function used for detection probability is mis-specified. Solymos & Lele (Methods in Ecology and Evolution, 2015, in press) argue that this is not a relevant issue in practice. We discuss the implications of the assumptions necessary for estimating abundance from the single-visit model and clarify and extend results in Knape & Korner-Nievergelt (Methods in Ecology and Evolution, 2015, 6, 298). We also discuss assumptions of the Dail-Madsen model. We show that for the single-visit model a partially scaled link function which covers the full range from 0 to 1 leads to the same scaling issue as the scaled link function used in Knape & Korner-Nievergelt (2015) which only covers a restricted range. We argue that there is essentially no information about absolute abundance contained in single-visit count data. Additional more direct data on detection probabilities is required to robustly estimate absolute abundances.
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| 65. |
- Knape, Jonas, et al.
(författare)
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Sensitivity of binomial N-mixture models to overdispersion: The importance of assessing model fit
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 2102-2114
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Tidskriftsartikel (refereegranskat)abstract
- 1. Binomial N-mixture models are commonly applied to analyse population survey data. By estimating detection probabilities, N-mixture models aim at extracting information about abundances in terms of absolute and not just relative numbers. This separation of detection probability and abundance relies on parametric assumptions about the distribution of individuals among sites and of detections of individuals among repeat visits to sites. Current methods for checking assumptions are limited, and their computational complexity has hindered evaluations of their performance.2. We use simulations and a case study to assess the sensitivity of binomial N-mixture models to overdispersion in abundance and in detection, develop computationally efficient graphical goodness of fit checks to detect it, and evaluate the ability of the checks to identify overdispersion.3. The simulations show that if the parametric assumptions are not exact the bias in estimated abundances can be severe: underestimation if there is overdispersion in abundance relative to the fitted model and overestimation if there is overdispersion in detection. Our goodness-of-fit checks performed well in detecting lack of fit when the abundance distribution was overdispersed, but struggled to detect lack of fit when detections were overdispersed. We show that the inability to detect lack of fit due to overdispersed detection is caused by a fundamental similarity between N-mixture models with beta-binomial detections and N-mixture models with negative binomial abundances.4. The strong biases that can occur in the binomial N-mixture model when the distribution of individuals among sites, or the detection model, is mis-specified implies that checking goodness of fit is essential for sound inference about abundance. To check the assumptions we provide computationally efficient goodness of fit checks that are available in an R-package nmixgof. However, even when a binomial N-mixture model appears to fit the data well, estimates are not robust in the presence of overdispersion. We show that problems can occur even when estimated detection probabilities are high, and that previously reported problems with negative binomial models cannot always be diagnosed by checking the sensitivity of abundance estimates to numerical cutoff values used in likelihood computations.
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| 66. |
- Krab, Eveline J, et al.
(författare)
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A simple experimental set-up to disentangle the effects of altered temperature and moisture regimes on soil organisms
- 2015
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Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 6:10, s. 1159-1168
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Tidskriftsartikel (refereegranskat)abstract
- Climate manipulation experiments in the field and laboratory incubations are common methods to study the impact of climate change on soils and their biota. However, both types of methods have drawbacks either on their mechanistic interpretation or ecological relevance. We propose an experimental set-up that combines the best of both methods and can be easily obtained by modifying widely available Tullgren soil fauna extractors. This set-up creates or alters temperature and moisture gradients within intact field soil cores, after which soil biota, their activity and vertical movements can be studied. We assessed the performance and demonstrated the applicability of this set-up through a case study on Collembola response to changes in microclimatic gradients in peat bogs. Warming created a vertical temperature gradient of 14 degrees C in peat cores without varying soil moisture conditions, while at a given temperature regime, precipitation and drought treatments shifted natural soil moisture gradients to 'wetter' and 'drier', respectively. This allowed for disentangling interacting warming and moisture effects on soil fauna. In our case study, Collembola communities showed peat layer-specific responses to these climate treatments. Warming decreased Collembola density and altered community composition in the shallowest layer, whereas precipitation increase affected Collembola community composition in the deepest layer. We showed that climate change can have layer-specific effects on soil organisms that are 'hidden' by not taking microclimatic vertical gradients into account. This experimental set-up facilitates studying (multitrophic) organism responses to climate changes, with only a small adjustment of equipment that is often already present in soil ecology laboratories. Moreover, this set-up can be easily customized to study many more other research questions related to wide-ranging organisms and ecosystems.
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| 67. |
- Lennox, Robert J., et al.
(författare)
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Positioning aquatic animals with acoustic transmitters
- 2023
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:10, s. 2514-2530
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Forskningsöversikt (refereegranskat)abstract
- Geolocating aquatic animals with acoustic tags has been ongoing for decades, relying on the detection of acoustic signals at multiple receivers with known positions to calculate a 2D or 3D position, and ultimately recreate the path of an aquatic animal from detections at fixed stations.This method of underwater geolocation is evolving with new software and hardware options available to help investigators design studies and calculate positions using solvers based predominantly on time-difference-of-arrival and time-of-arrival.We provide an overview of the considerations necessary to implement positioning in aquatic acoustic telemetry studies, including how to design arrays of receivers, test performance, synchronize receiver clocks and calculate positions from the detection data. We additionally present some common positioning algorithms, including both the free open-source solvers and the ‘black-box’ methods provided by some manufacturers for calculating positions.This paper is the first to provide a comprehensive overview of methods and considerations for designing and implementing better positioning studies that will support users, and encourage further knowledge advances in aquatic systems.
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| 68. |
- Maciute, Adele, et al.
(författare)
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A microsensor-based method for measuring respiration of individual nematodes
- 2021
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12:10, s. 1841-1847
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Tidskriftsartikel (refereegranskat)abstract
- Meiofauna (invertebrates that pass through a 1-mm mesh sieve, but are retained on a 40-µm mesh) represent the most abundant and diverse animal group on Earth, but empirical evidence of their role in benthic respiration, production and carbon cycling across ecosystems is not well documented. Moreover, how meiofauna respond to changing oxygen conditions is poorly understood. We further developed an incubation system, in which oxygen and temperature conditions are easily controlled and single meiofaunal nematode respiration is resolved in glass capillary tubes, using Clark-type oxygen microsensor. We performed the respiration measurements after exposing nematodes to different ambient oxygen concentrations, which resulted in 3–60µM O2 during hypoxic and 80–210µM O2 during oxic incubations in close proximity to the respective nematodes. Individual nematode respiration rates ranged from 0.02 to 1.30nmol O2 ind.−1day−1 and were 27% lower during hypoxic than oxic incubations. Rates derived from established allometric relations were on average fourfold higher than our direct measurements. The presented method is suitable for single nematode respiration measurements and can be adapted to a wide range of experimental conditions. Therefore, it can be used to assess meiofauna contribution to ecosystem processes and investigate species-specific responses to changing environmental conditions, for example, oxygen stress, increasing water temperature.
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| 69. |
- May, Michael R., et al.
(författare)
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A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:8, s. 947-959
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Tidskriftsartikel (refereegranskat)abstract
- The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction approximate to 23Ma. This new approach - the CPP on Mass-Extinction Times (CoMET) model - provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
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| 70. |
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