| 41. |
- Falster, Daniel S., et al.
(författare)
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plant : A package for modelling forest trait ecology and evolution
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:2, s. 136-146
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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.
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| 42. |
- 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
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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.
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| 43. |
- Farage, Carmel, et al.
(författare)
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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.
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| 44. |
- Gaboriau, T., et al.
(författare)
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A multi-platform package for the analysis of intra- and interspecific trait evolution
- 2020
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 11:11, s. 1439-1447
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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
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| 45. |
- Goodman, Rosa
(författare)
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Estimation of above-ground biomass of large tropical trees with terrestrial LiDAR
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 223-234
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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.
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| 46. |
- Gorokhova, Elena
(författare)
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Individual growth as a non-dietary determinant of the isotopic niche metrics
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9:2, s. 269-277
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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.
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| 47. |
- Gril, Eva, et al.
(författare)
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Slope and equilibrium : A parsimonious and flexible approach to model microclimate
- 2023
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:3, s. 885-897
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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.
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| 48. |
- Göthe, Emma
(författare)
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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.
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| 49. |
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| 50. |
- Hasegawa, Shun
(författare)
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Using plant, microbe, and soil fauna traits to improve the predictive power of biogeochemical models
- 2019
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 10, s. 146-157
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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.
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