| 1. |
- Auffret, Alistair G., et al.
(författare)
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HistMapR : Rapid digitization of historical land-use maps in R
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:11, s. 1453-1457
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Tidskriftsartikel (refereegranskat)abstract
- Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision. Comparing land use between maps from different time periods allows estimation of the magnitude of habitat change in an area. However, digitizing historical maps manually is time-consuming and analyses of change are usually carried out at small spatial extents or at low resolutions. HistMapR contains a number of functions that can be used to semi-automatically digitize historical land use according to a map's colours, as defined by the RGB bands of the raster image. We test the method on different historical land-use map series and compare results to manual digitizations. Digitization is fast, and agreement with manually digitized maps of around 80-90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.
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| 2. |
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| 3. |
- Dapporto, Leonardo, et al.
(författare)
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Comparing population patterns for genetic and morphological markers with uneven sample sizes. An example for the butterfly Maniola jurtina
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:8, s. 834-843
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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.
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| 4. |
- 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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| 5. |
- 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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| 6. |
- Humphreys, Aelys M., et al.
(författare)
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Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:11, s. 1366-1375
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Tidskriftsartikel (refereegranskat)abstract
- There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. We simulated >32000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns.
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| 7. |
- Iwaszkiewicz-Eggebrecht, Elzbieta, et al.
(författare)
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Optimizing insect metabarcoding using replicated mock communities
- 2023
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 14:4, s. 1130-1146
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Tidskriftsartikel (refereegranskat)abstract
- Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundance and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization? and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalize better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for the presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
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| 8. |
- Lennox, Robert J., et al.
(författare)
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Positioning aquatic animals with acoustic transmitters
- 2023
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 14:10, s. 2514-2530
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Forskningsöversikt (refereegranskat)abstract
- Geolocating aquatic animals with acoustic tags has been ongoing for decades, relying on the detection of acoustic signals at multiple receivers with known positions to calculate a 2D or 3D position, and ultimately recreate the path of an aquatic animal from detections at fixed stations.This method of underwater geolocation is evolving with new software and hardware options available to help investigators design studies and calculate positions using solvers based predominantly on time-difference-of-arrival and time-of-arrival.We provide an overview of the considerations necessary to implement positioning in aquatic acoustic telemetry studies, including how to design arrays of receivers, test performance, synchronize receiver clocks and calculate positions from the detection data. We additionally present some common positioning algorithms, including both the free open-source solvers and the ‘black-box’ methods provided by some manufacturers for calculating positions.This paper is the first to provide a comprehensive overview of methods and considerations for designing and implementing better positioning studies that will support users, and encourage further knowledge advances in aquatic systems.
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| 9. |
- Maciute, Adele, et al.
(författare)
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A microsensor-based method for measuring respiration of individual nematodes
- 2021
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12:10, s. 1841-1847
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Tidskriftsartikel (refereegranskat)abstract
- Meiofauna (invertebrates that pass through a 1-mm mesh sieve, but are retained on a 40-µm mesh) represent the most abundant and diverse animal group on Earth, but empirical evidence of their role in benthic respiration, production and carbon cycling across ecosystems is not well documented. Moreover, how meiofauna respond to changing oxygen conditions is poorly understood. We further developed an incubation system, in which oxygen and temperature conditions are easily controlled and single meiofaunal nematode respiration is resolved in glass capillary tubes, using Clark-type oxygen microsensor. We performed the respiration measurements after exposing nematodes to different ambient oxygen concentrations, which resulted in 3–60µM O2 during hypoxic and 80–210µM O2 during oxic incubations in close proximity to the respective nematodes. Individual nematode respiration rates ranged from 0.02 to 1.30nmol O2 ind.−1day−1 and were 27% lower during hypoxic than oxic incubations. Rates derived from established allometric relations were on average fourfold higher than our direct measurements. The presented method is suitable for single nematode respiration measurements and can be adapted to a wide range of experimental conditions. Therefore, it can be used to assess meiofauna contribution to ecosystem processes and investigate species-specific responses to changing environmental conditions, for example, oxygen stress, increasing water temperature.
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| 10. |
- May, Michael R., et al.
(författare)
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A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:8, s. 947-959
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Tidskriftsartikel (refereegranskat)abstract
- The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction approximate to 23Ma. This new approach - the CPP on Mass-Extinction Times (CoMET) model - provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
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