| 1. |
|
|
| 2. |
- Bukkuri, Anuraag, et al.
(författare)
-
Integrating eco-evolutionary dynamics into matrix population models for structured populations : Discrete and continuous frameworks
- 2023
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:6, s. 1475-1488
-
Tidskriftsartikel (refereegranskat)abstract
- State-structured populations are ubiquitous in biology, from the age-structure of animal societies to the life cycles of parasitic species. Understanding how this structure contributes to eco-evolutionary dynamics is critical not only for fundamental understanding but also for conservation and treatment purposes. Although some methods have been developed in the literature for modelling eco-evolutionary dynamics in structured population, such methods are wholly lacking in the (Formula presented.) function evolutionary game theoretic framework. In this paper, we integrate standard matrix population modelling into the (Formula presented.) function framework to create a theoretical framework to probe eco-evolutionary dynamics in structured populations. This framework encompasses age- and stage-structured matrix models with basic density- and frequency-dependent transition rates and probabilities. For both discrete and continuous time models, we define and characterize asymptotic properties of the system such as eco-evolutionary equilibria (including ESSs) and the convergence stability of these equilibria. For multistate structured populations, we introduce an ergodic flow preserving folding method for analysing such models. The methods developed in this paper for state-structured populations and their extensions to multistate-structured populations provide a simple way to create, analyse and simulate eco-evolutionary dynamics in structured populations. Furthermore, their generality allows these techniques to be applied to a variety of problems in ecology and evolution.
|
|
| 3. |
- Dunkley, Katie, et al.
(författare)
-
A low-cost, long-running, open-source stereo camera for tracking aquatic species and their behaviours
- 2023
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:10, s. 2549-2556
-
Tidskriftsartikel (refereegranskat)abstract
- Ecologists are now widely utilising video data to quantify the behaviours and interactions of animals in the wild. This process can be facilitated by collecting videos in stereo, which can provide information about animals' positions, movements and behaviours in three-dimensions (3D). However, there are no published designs that can collect underwater 3D stereo data at high spatial and temporal resolutions for extended periods (days). Here, we present complete hardware and software solutions for a long-running, open-source, underwater stereo camera rig, costing £1337. This stereo camera can continuously record aquatic species and their behaviours/interactions in high resolution (1080 p and 30 fps) and in 3D, over multiple days. We provide full design guides for the cameras and a travel-friendly rig, and include guidance and open-source code for calibrating the cameras in space and time. We also show how these cameras could be used to track animals' body parts and positions, and how their size, posture and behaviour can be inferred. This stereo camera will facilitate the collection of high-resolution ecological and behavioural data, such as affiliative, agonistic or trophic interactions between species, which can inform us about the health and structure of ecosystems. These data will assist ecologists and conservationists in monitoring and understanding the impacts of current environmental pressures on ecosystem functioning.
|
|
| 4. |
- Gardner, Emma, et al.
(författare)
-
Reliably predicting pollinator abundance : Challenges of calibrating process-based ecological models
- 2020
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 11:12, s. 1673-1689
-
Tidskriftsartikel (refereegranskat)abstract
- Pollination is a key ecosystem service for global agriculture but evidence of pollinator population declines is growing. Reliable spatial modelling of pollinator abundance is essential if we are to identify areas at risk of pollination service deficit and effectively target resources to support pollinator populations. Many models exist which predict pollinator abundance but few have been calibrated against observational data from multiple habitats to ensure their predictions are accurate. We selected the most advanced process-based pollinator abundance model available and calibrated it for bumblebees and solitary bees using survey data collected at 239 sites across Great Britain. We compared three versions of the model: one parameterised using estimates based on expert opinion, one where the parameters are calibrated using a purely data-driven approach and one where we allow the expert opinion estimates to inform the calibration process. All three model versions showed significant agreement with the survey data, demonstrating this model's potential to reliably map pollinator abundance. However, there were significant differences between the nesting/floral attractiveness scores obtained by the two calibration methods and from the original expert opinion scores. Our results highlight a key universal challenge of calibrating spatially explicit, process-based ecological models. Notably, the desire to reliably represent complex ecological processes in finely mapped landscapes necessarily generates a large number of parameters, which are challenging to calibrate with ecological and geographical data that are often noisy, biased, asynchronous and sometimes inaccurate. Purely data-driven calibration can therefore result in unrealistic parameter values, despite appearing to improve model-data agreement over initial expert opinion estimates. We therefore advocate a combined approach where data-driven calibration and expert opinion are integrated into an iterative Delphi-like process, which simultaneously combines model calibration and credibility assessment. This may provide the best opportunity to obtain realistic parameter estimates and reliable model predictions for ecological systems with expert knowledge gaps and patchy ecological data.
|
|
| 5. |
- Jonsson, Mattias, et al.
(författare)
-
Ecological production functions for biological control services in agricultural landscapes
- 2014
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:3, s. 243-252
-
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.
|
|
| 6. |
- Lürig, Moritz D.
(författare)
-
phenopype : A phenotyping pipeline for Python
- 2022
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 13:3, s. 569-576
-
Tidskriftsartikel (refereegranskat)abstract
- Digital images are an intuitive way to capture, store and analyse organismal phenotypes. Many biologists are taking images to collect high-dimensional phenotypic information from specimens to investigate complex ecological, evolutionary and developmental phenomena, such as relationships between trait diversity and ecosystem function, multivariate natural selection or developmental plasticity. As a consequence, images are being collected at ever-increasing rates, but extraction of the contained phenotypic information poses a veritable analytical bottleneck. phenopype is a high-throughput phenotyping pipeline for the programming language Python that aims at alleviating this bottleneck. The package facilitates immediate extraction of high-dimensional phenotypic data from digital images with low levels of background noise and complexity. At the core, phenopype provides functions for rapid signal processing-based image preprocessing and segmentation, data extraction, as well as visualization and data export. This functionality is provided by wrapping low-level computer vision libraries (such as OpenCV) into accessible functions to facilitate scientific image analysis. In addition, phenopype provides a project management ecosystem to streamline data collection and to increase reproducibility. phenopype offers two different workflows that support users during different stages of scientific image analysis. The low-throughput workflow uses regular Python syntax and has greater flexibility at the cost of reproducibility, which is suitable for prototyping during the initial stages of a research project. The high-throughput workflow allows users to specify and store image-specific settings for analysis in human-readable YAML format, and then execute all functions in one step by means of an interactive parser. This approach facilitates rapid program-user interactions during batch processing, and greatly increases scientific reproducibility. Overall, phenopype intends to make the features of powerful but technically involved low-level CV libraries available to biologists with little or no Python coding experience. Therefore, phenopype is aiming to augment, rather than replace the utility of existing Python CV libraries, allowing biologists to focus on rapid and reproducible data collection. Furthermore, image annotations produced by phenopype can be used as training data, thus presenting a stepping stone towards the application of deep learning architectures.
|
|
| 7. |
- Löfgren, Oskar, et al.
(författare)
-
Landscape history confounds the ability of the NDVI to detect fine-scale variation in grassland communities
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9:9, s. 2009-2018
-
Tidskriftsartikel (refereegranskat)abstract
- The NDVI is a remotely sensed vegetation index that is frequently used in ecological studies. There is, however, a lack of studies that evaluate the ability of the NDVI to detect fine-scale variation in grassland plant community composition and species richness. Ellenberg indicators characterize the environmental preferences of plant species—and community-mean Ellenberg values have been used to explore the environmental drivers of community assembly. We used variation partitioning to test the ability of satellite-based NDVI to explain community-mean Ellenberg nutrient (mN) and moisture (mF) indices, and the richness of habitat-specialist species in dry grasslands of different ages. The grasslands represent a gradient of decreasing soil nutrient status. If community composition is determined by the responses of individual species to the underlying environmental conditions and if, at the same time, community composition determines the optical characteristics of the vegetation canopy, then positive relationships between the NDVI and mN and mF are expected. Many grassland specialists are intolerant of nutrient-rich soils. If specialist richness is negatively related to soil-nutrient levels, then a negative association between the NDVI and specialist richness is expected. However, because grassland community composition is not only influenced by abiotic variables but also by other spatial and temporal drivers, we included spatial variables and grassland age in the statistical analyses. The NDVI explained the majority of the variation in mF, and also contributed to a substantial proportion of the variation in mN. However, variation in specialist richness and the lowest values of mN were explained by grassland age and spatial variables—but were poorly explained by the NDVI. Synthesis and applications. The NDVI showed a good ability to detect variation in plant community composition, and should provide a valuable tool for assessing fine-scale environmental variation in grasslands or for monitoring changes in grassland habitat properties. However, because the concentration of grassland specialists not only depends on environmental variables but also on the age and spatial context of the grasslands, the NDVI is unlikely to allow the identification of grasslands with high numbers of specialist species.
|
|
| 8. |
- Moller, Anders Pape, et al.
(författare)
-
Clutch-size variation in Western Palaearctic secondary hole-nesting passerine birds in relation to nest box design
- 2014
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:4, s. 353-362
-
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.
|
|
| 9. |
- Olsson, Ola, et al.
(författare)
-
Efficient, automated and robust pollen analysis using deep learning
- 2021
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12:5, s. 850-862
-
Tidskriftsartikel (refereegranskat)abstract
- Pollen analysis is an important tool in many fields, including pollination ecology, paleoclimatology, paleoecology, honey quality control, and even medicine and forensics. However, labour‐intensive manual pollen analysis often constrains the number of samples processed or the number of pollen analysed per sample. Thus, there is a desire to develop reliable, high‐throughput, automated systems. We present an automated method for pollen analysis, based on deep learning convolutional neural networks (CNN). We scanned microscope slides with fuchsine stained, fresh pollen and automatically extracted images of all individual pollen grains. CNN models were trained on reference samples (122,000 pollen grains, from 347 flowers of 83 species of 17 families). The models were used to classify images of different pollen grains in a series of experiments. We also propose an adjustment to reduce overestimation of sample diversity in cases where samples are likely to contain few species. Accuracy of a model for 83 species was 0.98 when all samples of each species were first pooled, and then split into a training and a validation set (splitting experiment). However, accuracy was much lower (0.41) when individual reference samples from different flowers were kept separate, and one such sample was used for validation of models trained on remaining samples of the species (leave‐one‐out experiment). We therefore combined species into 28 pollen types where a new leave‐one‐out experiment revealed an overall accuracy of 0.68, and recall rates >0.90 in most pollen types. When validating against 63,650 manually identified pollen grains from 370 bumblebee samples, we obtained an accuracy of 0.79, but our adjustment procedure increased this to 0.85. Validation through splitting experiments may overestimate robustness of CNN pollen analysis in new contexts (samples). Nevertheless, our method has the potential to allow large quantities of real pollen data to be analysed with reasonable accuracy. Although compiling pollen reference libraries is time‐consuming, this is simplified by our method, and can lead to widely accessible and shareable resources for pollen analysis.
|
|
| 10. |
- Pontarp, Mikael, et al.
(författare)
-
Inferring community assembly processes from macroscopic patterns using dynamic eco-evolutionary models and Approximate Bayesian Computation (ABC)
- 2019
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 10:4, s. 450-460
-
Forskningsöversikt (refereegranskat)abstract
- Statistical techniques exist for inferring community assembly processes from community patterns. Habitat filtering, competition, and biogeographical effects have, for example, been inferred from signals in phenotypic and phylogenetic data. The usefulness of current inference techniques is, however, debated as a mechanistic and causal link between process and pattern is often lacking, and evolutionary processes and trophic interactions are ignored.Here, we revisit the current knowledge on community assembly across scales and, in line with several reviews that have outlined challenges associated with current inference techniques, we identify a discrepancy between the current paradigm of eco-evolutionary community assembly and current inference techniques that focus mainly on competition and habitat filtering. We argue that trait-based dynamic eco-evolutionary models in combination with recently developed model fitting and model evaluation techniques can provide avenues for more accurate, reliable, and inclusive inference. To exemplify, we implement a trait-based, spatially explicit eco-evolutionary model and discuss steps of model modification, fitting, and evaluation as an iterative approach enabling inference from diverse data sources.Through a case study on inference of prey and predator niche width in an eco-evolutionary context, we demonstrate how inclusive and mechanistic approaches-eco-evolutionary modelling and Approximate Bayesian Computation (ABC)-can enable inference of assembly processes that have been largely neglected by traditional techniques despite the ubiquity of such processes.Much literature points to the limitations of current inference techniques, but concrete solutions to such limitations are few. Many of the challenges associated with novel inference techniques are, however, already to some extent resolved in other fields and thus ready to be put into action in a more formal way for inferring processes of community assembly from signals in various data sources.
|
|
| 11. |
- Radersma, Reinder, et al.
(författare)
-
A new permutation technique to explore and control for spatial autocorrelation
- 2015
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 6:9, s. 1026-1033
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Permutation tests are important in ecology and evolution as they enable robust analysis of small sample sizes and control for various forms of dependencies among observations. A common source of dependence is spatial autocorrelation. Accounting for spatial autocorrelation is often crucial, because many ecological and evolutionary processes are spatially restricted, such as gene flow, dispersal, mate choice, inter-and intraspecific competition, mutualism and predation. 2. Here we discuss various ways of controlling for spatial autocorrelation in permutation tests; we highlight their particular properties and assumptions and introduce a new permutation technique which explores and controls for spatial autocorrelation: the floating grid permutation technique (FGPT). 3. The FGPT is a method to randomize observations with known geographical locations. Within the randomization process, the probability an observation is assigned to any of the spatial locations is a negative function of the distance between its original and assigned location. The slope of this function depends on a preset parameter, and by exploring its parameter space, non-random ecological and evolutionary processes can be both assessed and controlled at multiple spatial scales. 4. We show that the FGPT has acceptable type-I-error rates. We applied the FGPT to simulated univariate and bivariate data sets in which both negative and positive spatial autocorrelation were present. In comparison with a method that uses eigenvector decomposition to separate negative from positive spatial autocorrelation, the FGPT performed better for negative spatial autocorrelation alone, equal for positive spatial autocorrelation alone and equal or slightly worse for simultaneous negative and positive spatial autocorrelation. For the bivariate data, it performed equally to a bootstrapping technique in which sampling probabilities were weighted by distance. The FGPT benefits from a large flexibility for application to bivariate (e.g. dyadic interactions) and multivariate observations (e.g. genetic marker-based relatedness measures) and has a large freedom in the choice of test statistic. It also has the potential to identify two spatial autocorrelation patterns, even if both result in positive spatial autocorrelation, given that they operate at different spatial scales. 5. The Floating Grid Permutation Technique is available as the R-package fgpt in CRAN.
|
|
| 12. |
|
|
| 13. |
|
|
| 14. |
- Mukherjee, Nibedita, et al.
(författare)
-
Comparison of techniques for eliciting views and judgements in decision‐making
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 54-63
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Decision-making is a complex process that typically includes a series of stages: identifying the issue, considering possible options, making judgements and then making a decision by combining information and values. The current status quo relies heavily on the informational aspect of decision-making with little or no emphasis on the value positions that affect decisions.2. There is increasing realization of the importance of adopting rigorous methods for each stage such that the information, views and judgements of stakeholders and experts are used in a systematic and repeatable manner. Though there are several methodological textbooks which discuss a plethora of social science techniques, it is hard to judge the suitability of any given technique for a given decision problem.3. In decision-making, the three critical aspects are “what” decision is to be made, “who” makes the decisions and “how” the decisions are made. The methods covered in this paper focus on “how” decisions can be made. We compare six techniques: Focus Group Discussion (FGD), Interviews, Q methodology, Multi-criteria Decision Analysis (MCDA), Nominal Group Technique and the Delphi technique specifically in the context of biodiversity conservation. All of these techniques (with the exception of MCDA) help in understanding human values and the underlying perspectives which shape decisions.4. Based on structured reviews of 423 papers covering all six methods, we compare the conceptual and logistical characteristics of the methods, and map their suitability for the different stages of the decision- making process. While interviews and FGD are well-known, techniques such the Nominal Group technique and Q methodology are relatively under- used. In situations where conflict is high, we recommend using the Q methodology and Delphi technique to elicit judgements. Where conflict is low, and a consensus is needed urgently, the Nominal Group technique may be more suitable.5. We present a nuanced synthesis of methods aimed at users. The comparison of the different techniques might be useful for project managers, academics or practitioners in the planning phases of their projects and help in making better informed methodological choices.
|
|
| 15. |
- Silvestro, Daniele, et al.
(författare)
-
Measurement errors should always be incorporated in phylogenetic comparative analysis
- 2015
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 6:3, s. 340-346
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of continuous traits is the central component of comparative analyses in phylogenetics, and the comparison of alternative models of trait evolution has greatly improved our understanding of the mechanisms driving phenotypic differentiation. Several factors influence the comparison of models, and we explore the effects of random errors in trait measurement on the accuracy of model selection. We simulate trait data under a Brownian motion model (BM) and introduce different magnitudes of random measurement error. We then evaluate the resulting statistical support for this model against two alternative models: Ornstein-Uhlenbeck (OU) and accelerating/decelerating rates (ACDC). Our analyses show that even small measurement errors (10%) consistently bias model selection towards erroneous rejection of BM in favour of more parameter-rich models (most frequently the OU model). Fortunately, methods that explicitly incorporate measurement errors in phylogenetic analyses considerably improve the accuracy of model selection. Our results call for caution in interpreting the results of model selection in comparative analyses, especially when complex models garner only modest additional support. Importantly, as measurement errors occur in most trait data sets, we suggest that estimation of measurement errors should always be performed during comparative analysis to reduce chances of misidentification of evolutionary processes.
|
|
| 16. |
- Silvestro, Daniele, et al.
(författare)
-
PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data
- 2014
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 5:10, s. 1126-1131
-
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 .
|
|
| 17. |
- Zizka, Alexander, 1986, et al.
(författare)
-
CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
- 2019
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 10:5, s. 744-751
-
Tidskriftsartikel (refereegranskat)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
|
|
| 18. |
- Bowlin, Melissa, et al.
(författare)
-
The effects of geolocator drag and weight on the flight ranges of small migrants
- 2010
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 1:4, s. 398-402
-
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.
|
|
| 19. |
- Lisovski, Simeon, et al.
(författare)
-
Geolocation by light: accuracy and precision affected by environmental factors
- 2012
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 3:3, s. 603-612
-
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.
|
|
| 20. |
- Sahlin, Ullrika, et al.
(författare)
-
A benefit analysis of screening for invasive species - base-rate uncertainty and the value of information
- 2011
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 2:5, s. 500-508
-
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.
|
|
| 21. |
- Adem Esmail, Blal, 1982-, et al.
(författare)
-
Multi-criteria decision analysis for nature conservation : A review of 20 years of applications
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 42-53
-
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.
|
|
| 22. |
- Arnoldi, Jean-Francois, et al.
(författare)
-
Invasions of ecological communities : Hints of impacts in the invaders growth rate
- 2022
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 13:1, s. 167-182
-
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.
|
|
| 23. |
- Auffret, Alistair G., et al.
(författare)
-
HistMapR : Rapid digitization of historical land-use maps in R
- 2017
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:11, s. 1453-1457
-
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.
|
|
| 24. |
|
|
| 25. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
-
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
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
-
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.
|
|
| 26. |
- Bradter, Ute, et al.
(författare)
-
Can opportunistically collected Citizen Science data fill a data gap for habitat suitability models of less common species?
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 1667-1678
-
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.
|
|
| 27. |
- Byrnes, J. E. K., et al.
(författare)
-
Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions
- 2014
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:2, s. 111-124
-
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.
|
|
| 28. |
- Campione, Nicolas E., et al.
(författare)
-
Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions
- 2014
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:9, s. 913-923
-
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.
|
|
| 29. |
- Carvalho, J., et al.
(författare)
-
poolHelper: An R package to help in designing Pool-Seq studies
- 2023
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:9, s. 2300-2307
-
Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing of pooled samples (Pool-seq) is an important tool in population genomics and molecular ecology. In Pool-seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates, influencing downstream analysis. When designing Pool-seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximise the accuracy of allele frequency estimates while minimising the sequencing effort. We describe a novel tool to simulate single nucleotide polymorphism (SNP) data using coalescent theory and account for sources of uncertainty in Pool-seq. We introduce an R package, poolHelper, enabling users to simulate Pool-seq data under different combinations of average depth of coverage and pool size, accounting for unequal individual contributions and sequencing errors, modelled by adjustable parameters. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool-seq. poolHelper enables users to simulate multiple combinations of pooling errors, average depth of coverage, pool sizes and number of pools to assess how they influence the error of sample allele frequencies and expected heterozygosity. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool-seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. This can help users to define an effective sampling design by using those combinations of parameters that minimise the sequencing effort. The poolHelper package provides tools for performing simulations with different combinations of parameters (e.g. pool size, depth of coverage, unequal individual contribution) before sampling and generating data, allowing users to define sampling schemes based on simulations. This allows researchers to focus on the best sampling scheme to answer their research questions. poolHelper is comprehensively documented with examples to guide effective use.
|
|
| 30. |
- Certain, Grégoire, et al.
(författare)
-
How do MAR(1) models cope with hidden nonlinearities in ecological dynamics?
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 1975-1995
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Multivariate autoregressive (MAR) models are an increasingly popular technique to infer interaction strengths between species in a community and to predict the community response to environmental change. The most commonly employed MAR(1) models, with one time lag, can be viewed either as multispecies competition models with Gompertz density dependence or, more generally, as a linear approximation of more complex, nonlinear dynamics around stable equilibria. This latter interpretation allows for broader applicability, but may come at a cost in terms of interpretation of estimates and reliability of both short- and long-term predictions.2. We investigate what these costs might be by fitting MAR(1) models to simulated 2-species competition, consumer-resource and host-parasitoid systems, as well as a larger food web influenced by the environment. We review how MAR(1) coefficients can be interpreted and evaluate how reliable are estimates of interaction strength, rank, or sign; accuracy of short-term forecasts; as well as the ability of MAR(1) models to predict the long-term responses of communities submitted to environmental change such as PRESS perturbations.3. The net effects of species j on species i are usually (90%-95%) well recovered in terms of sign or rank, with the notable exception of overcompensatory dynamics. In actual values, net effects of species j on species i are not well recovered when the underlying dynamics are nonlinear. MAR(1) models are better at making short-term qualitative forecasts (next point going up or down) than at predicting long-term responses to environmental perturbations, which can be severely over- as well as underestimated.4. We conclude that when applying MAR(1) models to ecological data, inferences on net effects among species should be limited to signs, or the Gompertz assumption should be tested and discussed. This particular assumption on density-dependence (log-linearity) is also required for unbiased long-term predictions. Overall, we think that MAR(1) models are highly useful tools to resolve and characterize community dynamics, but we recommend to use them in conjunction with alternative, nonlinear models resembling the ecological context in order to improve their interpretation in specific applications.
|
|
| 31. |
- Chapron, Guillaume
(författare)
-
Complex decisions made simple: a primer on stochastic dynamic programming
- 2013
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4, s. 872-884
-
Tidskriftsartikel (refereegranskat)abstract
- 5. Stochastic dynamic programming is a powerful technique to make decisions in presence of uncertainty about biological stochastic systems changing through time. We hope this review will provide an entry point into the technical literature about SDP and will improve its application in ecology.
|
|
| 32. |
- Choquet, Remi, et al.
(författare)
-
Estimating demographic parameters from capturerecapture data with dependence among individuals within clusters
- 2013
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:5, s. 474-482
-
Tidskriftsartikel (refereegranskat)abstract
- Two-level data, in which level-1 units or individuals are nested within level-2 units or clusters, are very common in natural populations. However, very few multilevel analyses are conducted for data with imperfect detection of individuals. Multilevel analyses are important to quantify the variability at each level of the data. In this study, we present two-level analyses for estimating demographic parameters from data with imperfect detection of individuals and with a source of individual variability that is nested within a source of cluster variability. This method allows separating and quantifying the phenotypic plasticity or facultative behavioural responses from the evolutionary responses. We illustrate our approach using data from studies of a long-lived perennially monogamous seabird, the Cory's shearwater (Calonectris diomedea) and a patchy population of collared flycatchers (Ficedula albicollis). We demonstrate the existence of dependence in recapture probability between paired individuals in the Cory's shearwater. In addition, we show that family structure has no influence on parentoffspring resemblance in collared flycatchers dispersal. The new method is implemented in program e-surge which is freely available from the internet.
|
|
| 33. |
- Cirtwill, Alyssa, et al.
(författare)
-
A quantitative framework for investigating the reliability of empirical network construction
- 2019
-
Ingår i: Methods in Ecology and Evolution. - : WILEY. - 2041-210X. ; 10:6, s. 902-911
-
Tidskriftsartikel (refereegranskat)abstract
- Descriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. For interactions that have not been observed, most datasets will not contain enough information for the ecologist to be confident that unobserved interactions truly did not occur. Here, we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction. We then outline a framework to quantify the uncertainty around each interaction by combining data on observed co-occurrences with prior knowledge. We illustrate this framework using perhaps the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions. This uncertainty can, however, be constrained with informative priors. This uncertainty scaled up to summary measures of network structure such as connectance and nestedness. Even with informative priors, we are likely to miss many interactions that may occur rarely or under different local conditions. Overall, we demonstrate the importance of acknowledging the uncertainty inherent in network studies, and the utility of treating interactions as probabilities in pinpointing areas where more study is needed. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change network analyses and yield greater realism.
|
|
| 34. |
- Dapporto, Leonardo, et al.
(författare)
-
Comparing population patterns for genetic and morphological markers with uneven sample sizes. An example for the butterfly Maniola jurtina
- 2014
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:8, s. 834-843
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Integrating genetic and/or phenotypic traits at population level is considered a fundamental approach in the study of evolutionary processes, systematics, biogeography and conservation. But combining the two types of data remain a complex task, mostly due to the high, and sometimes different, sample sizes required for reliable assessments of community traits. Data availability has been increasing in recent years, thanks to online resources, but it is uncommon that different types of markers are available for any given specimen. 2. We provide new R functions aimed at directly correlating traits at population level, even if data sets only overlap partially. The new functions are based on a modified Procrustes algorithm that minimizes differences between bidimensional ordinations of two different markers, based on a subsample of specimens for which both characters are known. To test the new functions, we used a molecular and morphological data set comprising Mediterranean specimens of the butterfly Maniola jurtina. 3. By using this method, we have been able to maximize similarities between genotypic and phenotypic configurations obtained after principal coordinate analysis for the model species and evaluated their degree of correlation at both individual and population level. The new recluster. procrustes function retained the information of the relative importance of different morphological variables in determining the observed ordinations and preserved it in the transformed configurations. This allowed calculating the best combination of morphological variables mirroring genetic relationships among specimens and populations. Finally, it was possible to analyse the modality and variance of the phenotypic characters correlated with the genetic structure among populations. 4. The genetic and phenotypic markers displayed high overall correlation in the study area except in the contact zone, where discrepancies for particular populations were detected. Interestingly, such discrepancies were spatially structured, with southern populations displaying typical western morphotype and eastern haplotypes, while the opposite occurred in the northern populations. The methodology here described can be applied to any number and type of traits for which bidimensional configurations can be obtained, and opens new possibilities for datamining and formeta-analyses combining existing data sets in biogeography, systematics and ecology.
|
|
| 35. |
- Dettki, Holger
(författare)
-
A standardisation framework for bio-logging data to advance ecological research and conservation
- 2021
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12, s. 996-1007
-
Tidskriftsartikel (refereegranskat)abstract
- Bio-logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio-logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio-logging data into research and management recommendations.We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy-of-use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security.We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing.Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter-governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio-logging data formats across all fields in animal ecology.
|
|
| 36. |
- Edler, Daniel, et al.
(författare)
-
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
- 2021
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 12:2, s. 373-377
-
Tidskriftsartikel (refereegranskat)abstract
- raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to setup and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one-click model testing to select the best substitution models using ModelTest-NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML-NG, which provides new functionality and higher performance on large datasets. raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML. © 2020 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society
|
|
| 37. |
- Eklöf, Anna, 1976-, et al.
(författare)
-
Secondary extinctions in food webs : a Bayesian network approach
- 2013
-
Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 4:8, s. 760-770
-
Tidskriftsartikel (refereegranskat)abstract
- Ecological communities are composed of populations connected in tangled networks of ecological interactions. Therefore, the extinction of a species can reverberate through the network and cause other (possibly distantly connected) species to go extinct as well. The study of these secondary extinctions is a fertile area of research in ecological network theory.However, to facilitate practical applications, several improvements to the current analytical approaches are needed. In particular, we need to consider that (i) species have different ‘a priori’ probabilities of extinction, (ii) disturbances can simultaneously affect several species, and (iii) extinction risk of consumers likely grows with resource loss. All these points can be included in dynamical models, which are, however, difficult to parameterize.Here we advance the study of secondary extinctions with Bayesian networks. We show how this approach can account for different extinction responses using binary – where each resource has the same importance – and quantitative data – where resources are weighted by their importance. We simulate ecological networks using a popular dynamical model (the Allometric Trophic Network model) and use it to test our method.We find that the Bayesian network model captures the majority of the secondary extinctions produced by the dynamical model and that consumers’ responses to species loss are best modelled using a nonlinear sigmoid function. We also show that an approach based exclusively on food web structure loses power when species at higher trophic levels are preferentially lost. Because the loss of apex predators is unfortunately widespread, the results highlight a serious limitation of studies on network robustness.
|
|
| 38. |
- Ekström, Magnus, 1966-, et al.
(författare)
-
Estimating density from presence/absence data in clustered populations
- 2020
-
Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 11:3, s. 390-402
-
Tidskriftsartikel (refereegranskat)abstract
- Inventories of plant populations are fundamental in ecological research and monitoring, but such surveys are often prone to field assessment errors. Presence/absence (P/A) sampling may have advantages over plant cover assessments for reducing such errors. However, the linking between P/A data and plant density depends on model assumptions for plant spatial distributions. Previous studies have shown, for example, how that plant density can be estimated under Poisson model assumptions on the plant locations. In this study, new methods are developed and evaluated for linking P/A data with plant density assuming that plants occur in clustered spatial patterns. New theory was derived for estimating plant density under Neyman-Scott-type cluster models such as the Matern and Thomas cluster processes. Suggested estimators, corresponding confidence intervals and a proposed goodness-of-fit test were evaluated in a Monte Carlo simulation study assuming a Matern cluster process. Furthermore, the estimators were applied to plant data from environmental monitoring in Sweden to demonstrate their empirical application. The simulation study showed that our methods work well for large enough sample sizes. The judgment of what is' large enough' is often difficult, but simulations indicate that a sample size is large enough when the sampling distributions of the parameter estimators are symmetric or mildly skewed. Bootstrap may be used to check whether this is true. The empirical results suggest that the derived methodology may be useful for estimating density of plants such as Leucanthemum vulgare and Scorzonera humilis. By developing estimators of plant density from P/A data under realistic model assumptions about plants' spatial distributions, P/A sampling will become a more useful tool for inventories of plant populations. Our new theory is an important step in this direction.
|
|
| 39. |
- Falster, Daniel S., et al.
(författare)
-
plant : A package for modelling forest trait ecology and evolution
- 2016
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:2, s. 136-146
-
Tidskriftsartikel (refereegranskat)abstract
- Population dynamics in forests are strongly size-structured: larger plants shade smaller plants while also expending proportionately more energy on building and maintaining woody stems. Although the importance of size structure for demography is widely recognized, many models either omit it entirely or include only coarse approximations. Here, we introduce the plant package, an extensible framework for modelling size- and trait-structured demography, ecology and evolution in simulated forests. At its core, plant is an individual-based model where plant physiology and demography are mediated by traits. Individual plants from multiple species can be grown in isolation, in patches of competing plants or in metapopulations under a disturbance regime. These dynamics can be integrated into metapopulation-level estimates of invasion fitness and vegetation structure. Because fitness emerges as a function of traits, plant provides a novel arena for exploring eco-evolutionary dynamics. plant is an open source R package and is available at . Accessed from R, the core routines in plant are written in C++. The package provides for alternative physiologies and for capturing trade-offs among parameters. A detailed test suite is provided to ensure correct behaviour of the code. plant provides a transparent platform for investigating how physiological rules and functional trade-offs interact with competition and disturbance regimes to influence vegetation demography, structure and diversity.
|
|
| 40. |
- Farage, C., et al.
(författare)
-
Identifying flow modules in ecological networks using Infomap
- 2021
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 12:5, s. 778-786
-
Tidskriftsartikel (refereegranskat)abstract
- Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system. Although many ecological networks describe flows, such as biomass flows in food webs or disease transmission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics. Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers to analyse their networks with Infomap, we introduce the open-source R package infomapecology. Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.
|
|
| 41. |
- Farage, Carmel, et al.
(författare)
-
Identifying flow modules in ecological networks using Infomap
- 2021
-
Ingår i: Methods in Ecology and Evolution. - London : British Ecology Society. - 2041-210X. ; 12:5, s. 778-786
-
Tidskriftsartikel (refereegranskat)abstract
- Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system. Although many ecological networks describe flows, such as biomass flows in food webs or disease transmission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics. Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers to analyse their networks with Infomap, we introduce the open-source R package infomapecology. Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.
|
|
| 42. |
- Gaboriau, T., et al.
(författare)
-
A multi-platform package for the analysis of intra- and interspecific trait evolution
- 2020
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 11:11, s. 1439-1447
-
Tidskriftsartikel (refereegranskat)abstract
- Evolutionary forces affect the distribution of phenotypes both within and among species. Yet, at the macro-evolutionary scale, the evolution of intraspecific variance is rarely considered. Here, we present an r and a BEAST 2 implementation that extends the JIVE (Joint inter- and Intraspecific Variance Evolution) model aimed at the analysis of continuous trait evolution at both inter- and intraspecific level. Using a hierarchical Bayesian approach, we implemented a range of models for continuous trait evolution that operate independently on species means and variances along a phylogeny. The package uses Markov chain Monte Carlo for the inference of parameters and the evaluation of model fit. JIVE is available in the bite (Bayesian Integrative models of Trait Evolution) r package, as well as in BEAST 2. The two implementations offer the same continuous trait evolutionary models, but differ in their use and types of analyses. The r implementation allows for faster analyses by taking the phylogeny as data, while providing graphical and statistical functions as part of tools for model comparison, result parsing and summary, and plotting. In the BEAST 2 implementation, the species tree is a parameter, and both its topology and divergence times are jointly estimated with trait model parameters. The bite package and the BEAST 2 implementation introduce new frameworks within comparative phylogenetics that explicitly model intraspecific variance. These tools allow users to tackle long-standing questions in evolutionary biology, such as the identification of key evolutionary processes determining niche conservatism, niche partitioning, and life-history strategies. © 2020 British Ecological Society
|
|
| 43. |
- Goodman, Rosa
(författare)
-
Estimation of above-ground biomass of large tropical trees with terrestrial LiDAR
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 223-234
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Tropical forest biomass is a crucial component of global carbon emission estimations. However, calibration and validation of such estimates require accurate and effective methods to estimate in situ above-ground biomass (AGB). Present methods rely on allometric models that are highly uncertain for large tropical trees. Terrestrial laser scanning (TLS) tree modelling has demonstrated to be more accurate than these models to infer forest AGB. Nevertheless, applying TLS methods on tropical large trees is still challenging. We propose a method to estimate AGB of large tropical trees by three-dimensional (3D) tree modelling of TLS point clouds.2. Twenty-nine plots were scanned with a TLS in three study sites (Peru, Indonesia and Guyana). We identified the largest tree per plot (mean diameter at breast height of 73.5cm), extracted its point cloud and calculated its volume by 3D modelling its structure using quantitative structure models (QSM) and converted to AGB using species-specific wood density. We also estimated AGB using pantropical and local allometric models. To assess the accuracy of our and allometric methods, we harvest the trees and took destructive measurements.3. AGB estimates by the TLS-QSM method showed the best agreement in comparison to destructive harvest measurements (28.37% coefficient of variation of root mean square error [CV-RMSE] and concordance correlation coefficient [CCC] of 0.95), outperforming the pantropical allometric models tested (35.6%-54.95% CV-RMSE and CCC of 0.89-0.73). TLS-QSM showed also the lowest bias (overall underestimation of 3.7%) and stability across tree size range, contrasting with the allometric models that showed a systematic bias (overall underestimation ranging 15.2%-35.7%) increasing linearly with tree size. The TLS-QSM method also provided accurate tree wood volume estimates (CV RMSE of 23.7%) with no systematic bias regardless the tree structural characteristics.4. Our TLS-QSM method accounts for individual tree biophysical structure more effectively than allometric models, providing more accurate and less biased AGB estimates for large tropical trees, independently of their morphology. This non-destructive method can be further used for testing and calibrating new allometric models, reducing the current under-representation of large trees in and enhancing present and past estimates of forest biomass and carbon emissions from tropical forests.
|
|
| 44. |
- Gorokhova, Elena
(författare)
-
Individual growth as a non-dietary determinant of the isotopic niche metrics
- 2018
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9:2, s. 269-277
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Quantitative analytical approaches for isotopic niche analysis in the trophic diversity studies are proliferating rapidly; however, the assumptions behind the isotopic niche applications are rarely tested. One of the main assumptions is independence of the niche metrics and physiological status of the animals. The aim of this experimental study was to test the relationship between growth and Layman's metrics of isotopic niche in consumers eating the same food but in different quantities and growing at different rates.2. Based on research indicating that individual variability in isotopic fractionation increases under suboptimal conditions, I hypothesized that a group of consumers originating from the same population and exposed to food limitation would have greater estimates of the niche breadth and diversity as a result of higher inter-individual variability in growth rate and stable isotope signatures than in non-limiting feeding conditions. This hypothesis was tested using Baltic mysids Neomysis integer fed isotopically uniform diet under laboratory conditions and analysing individual growth and stable isotope signature in concert.3. As hypothesized, mysid growth rate was a significant negative predictor of most niche metrics. These effects were related to both increased inter-individual variability and higher trophic fractionation in malnourished animals, whereas in actively growing mysids, lower fractionation was observed together with lower values for niche size, isotopic range and trophic diversity.4. These findings challenge how we interpret the intrapopulation isotopic variance and evaluate isotopic evidence of individual specialization and call for integrated approaches for isotopic niche and growth assessment.
|
|
| 45. |
- Gril, Eva, et al.
(författare)
-
Slope and equilibrium : A parsimonious and flexible approach to model microclimate
- 2023
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:3, s. 885-897
-
Tidskriftsartikel (refereegranskat)abstract
- Most statistical models of microclimate focus on the difference or ‘offset’ between standardized air temperatures (macroclimate) and those of a specific habitat such as forest understorey, grassland or under a log. However, these offsets can fluctuate from positive to negative over a single day such that common practice consists in aggregating data into daily mean, minimum and maximum before modelling monthly offsets for each summary statistic. Here, we propose a more parsimonious and flexible approach relying on just two parameters: the slope and equilibrium. The slope captures the linear relationship between microclimate and macroclimate, while the equilibrium is the point at which microclimate equals macroclimate. Although applicable to other habitats, we demonstrate the relevance of our method by focusing on forest understoreys.We installed temperature sensors at 1-m height inside forest stands and in nearby open grasslands equipped with standardized weather stations, across 13 sites in France spanning a wide climatic gradient. From a year of hourly temperatures and for each sensor, we established relationships between microclimate and macroclimate temperatures using two linear mixed-effects models, during the leaf-on (May–November) and leaf-off period (December–April). We extracted the monthly equilibrium and slope for each sensor, and used another set of linear mixed-effects models to investigate their main determinants.The slope was chiefly determined by stand structure variables interacting with the leaf-on/leaf-off period: stand type (conifer vs broadleaf); shade-casting ability; stand age; dominant height; stem density; and cover of the upper and lower shrub layer. In contrast, forest structure had no explanatory power on the equilibrium. We found the equilibrium to be positively related to mean macroclimate temperature, interacting with the open/forest habitat.The method introduced here overcomes several shortcomings of modelling microclimate offsets. By demonstrating that the slope and equilibrium vary in predictable ways, we have established a general linkage between microclimate and macroclimate temperatures that can be applied to any location or time if we know the mean macroclimate temperature (equilibrium) and buffering or amplifying capacity of the habitat (slope). We also warn about methodological biases due to the reference used for macroclimate.
|
|
| 46. |
- Göthe, Emma
(författare)
-
A new paradigm for biomonitoring: an example building on the Danish Stream Plant Index
- 2017
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8, s. 297-307
-
Tidskriftsartikel (refereegranskat)abstract
- Despite intensive efforts for more than a decade to develop Water Framework-compliant assessment systems, shortcomings continue to appear. In particular, the lack of reference conditions has hindered the development of assessment systems capturing the heart of the Water Framework Directive (WFD) - that ecological status should be set as the deviation from the natural, undisturbed condition. Recently, the Danish Stream Plant Index (DSPI) was developed. This system contrasts existing systems in that it builds on an expert interpretation of the normative definitions of ecological status classes in the WFD without taking pressure-impact relationships into account. Here, we substantiate the approach taken in the development of DSPI and examine whether the DSPI class decreases with increasing level of anthropogenic stress and, additionally, whether the deviation from the natural undisturbed condition increases with decreasing DSPI class sensu WFD using trait composition of plant assemblages from Danish streams around year 1900 as a reference. We furthermore examine the trait composition of the vegetation in sites classified into different DSPI status classes to explore whether predictable patterns exist that can be used to identify the ultimate cause(s) of failure to meet ecological goals and help guide the selection of appropriate mitigation measures. We observed that DSPI declined with several parameters indicative of environmental stress in Danish streams and, furthermore, that the deviation from the natural undisturbed condition regarding the trait composition of plant communities declined with increasing DSPI, implying that the trait composition of plant communities in the high DSPI status class was most similar to those occurring in Danish streams around year 1900. We also found that trait characteristics capable of disentangling important stressors in Danish streams varied consistently among sites classified into different DSPI classes.Based on our findings, we call for new thinking. We suggest that more effort should be directed at describing reference conditions and interpreting the normative definitions of good, moderate, poor and bad instead of focusing solely on developing assessment systems using pressure-impact frameworks. We find this particularly important with respect to streams as these are seldom impacted by only a single stressor.
|
|
| 47. |
|
|
| 48. |
- Hasegawa, Shun
(författare)
-
Using plant, microbe, and soil fauna traits to improve the predictive power of biogeochemical models
- 2019
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 10, s. 146-157
-
Tidskriftsartikel (refereegranskat)abstract
- Process-based models describing biogeochemical cycling are crucial tools to understanding long-term nutrient dynamics, especially in the context of perturbations, such as climate and land-use change. Such models must effectively synthesize ecological processes and properties. For example, in terrestrial ecosystems, plants are the primary source of bioavailable carbon, but turnover rates of essential nutrients are contingent on interactions between plants and soil biota. Yet, biogeochemical models have traditionally considered plant and soil communities in broad terms. The next generation of models must consider how shifts in their diversity and composition affect ecosystem processes. One promising approach to synthesize plant and soil biodiversity and their interactions into models is to consider their diversity from a functional trait perspective. Plant traits, which include heritable chemical, physical, morphological and phenological characteristics, are increasingly being used to predict ecosystem processes at a range of scales, and to interpret biodiversity-ecosystem functional relationships. There is also emerging evidence that the traits of soil microbial and faunal communities can be correlated with ecosystem functions such as decomposition, nutrient cycling, and greenhouse gas production. Here, we draw on recent advances in measuring and using traits of different biota to predict ecosystem processes, and provide a new perspective as to how biotic traits can be integrated into biogeochemical models. We first describe an explicit trait-based model framework that operates at small scales and uses direct measurements of ecosystem properties; second, an integrated approach that operates at medium scales and includes interactions between biogeochemical cycling and soil food webs; and third, an implicit trait-based model framework that associates soil microbial and faunal functional groups with plant functional groups, and operates at the Earth-system level. In each of these models, we identify opportunities for inclusion of traits from all three groups to reduce model uncertainty and improve understanding of biogeochemical cycles. These model frameworks will generate improved predictive capacity of how changes in biodiversity regulate biogeochemical cycles in terrestrial ecosystems. Further, they will assist in developing a new generation of process-based models that include plant, microbial, and faunal traits and facilitate dialogue between empirical researchers and modellers.
|
|
| 49. |
- Hauffe, T., et al.
(författare)
-
A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
- 2022
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 13:6, s. 1201-1213
-
Tidskriftsartikel (refereegranskat)abstract
- Speciation, dispersal and extinction govern the spatial and temporal dynamics of biodiversity. The fossil record offers the opportunity to directly estimate range expansion and contraction via dispersal and extinction, respectively. However, due to the incomplete occurrence record, determining the dynamics of these processes and the biotic and abiotic factors influencing them remains challenging. The dispersal-extinction-sampling (DES) model infers dispersal and extinction rates from present and past geographical ranges of taxa while accounting for the incompleteness of the fossil record via jointly estimated sampling rates. Here, we expand the DES framework to a new suite of models that (a) incorporate heterogeneity in fossil sampling across taxa, (b) reconstruct diversity trajectories through time and across regions, and (c) link rates of range evolution with biotic and abiotic covariates. These models integrate the effects of competitive interaction, traits and environmental change on dispersal and extinction while controlling for phylogenetic effects through higher level taxonomy. We validate our framework through simulations and find that likelihood-based model testing has the power to discriminate among models with or without biotic and abiotic effects on dispersal and extinction. Among the tested models, we found that trait-dependent models yielded the most accurate parameter estimates. We then assess the factors influencing geographical range evolution for Eurasian and North American terrestrial carnivores. We identify substantial variation in the fossil sampling rates of carnivore genera and find that global cooling increased their extinction risk while their dispersal rate varied among families and increased with larger body size. The expanded suite of DES models for fossil biogeography is a powerful tool to test hypotheses about the factors influencing geographical range evolution using fossil data.
|
|
| 50. |
- Hsiang, Allison
(författare)
-
AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction
- 2017
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X.
-
Tidskriftsartikel (refereegranskat)abstract
- Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage- scale morphological data.We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms.
|
|
