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| 2. |
- Moller, Anders Pape, et al.
(författare)
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Clutch-size variation in Western Palaearctic secondary hole-nesting passerine birds in relation to nest box design
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:4, s. 353-362
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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.
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| 3. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 4. |
- Campione, Nicolas E., et al.
(författare)
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Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:9, s. 913-923
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Tidskriftsartikel (refereegranskat)abstract
- Body mass is strongly related to both physiological and ecological properties of living organisms. As a result, generating robust, broadly applicable models for estimating body mass in the fossil record provides the opportunity to reconstruct palaeobiology and investigate evolutionary ecology on a large temporal scale. A recent study provided strong evidence that the minimum circumference of stylopodial elements (humerus and femur) is conservatively associated with body mass in living quadrupeds. Unfortunately, this model is not directly applicable to extinct bipeds, such as non-avian dinosaurs. This study presents a new equation that mathematically corrects the quadruped equation for use in bipeds. It is derived from the systemic difference in the circumference-to-area scaling relationship of two circles (hypothetical quadruped) and one circle (hypothetical biped), which represent the cross-section of the main weight-bearing limb bones. When applied to a newly constructed data set of femoral circumferences and body masses in living birds, the new equation reveals errors that are significantly lower than other published equations, but significantly higher than the error inherent in the avian data set. Such errors, however, are expected given the unique overall femoral circumference-body mass scaling relationship found in birds. Body mass estimates for a sample of bipedal dinosaurs using the new model are consistent with recent estimates based on volumetric life reconstructions, but, in contrast, this equation is simpler to use, with the concomitant potential to provide a wider set of body mass estimates for extinct bipeds. Although it is evident that no one estimation model is flawless, the combined use of the corrected quadrupedal equations and the previously published quadrupedal equation offer a consistent approach with which to estimate body masses in both quadrupeds and bipeds. These models have implications for conducting large-scale macroevolutionary analyses of body size throughout the evolutionary history of terrestrial vertebrates, and, in particular, across major changes in body plan, such as the evolution of bipedality in archosaurs and quadrupedality in dinosaurs.
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| 5. |
- Choquet, Remi, et al.
(författare)
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Estimating demographic parameters from capturerecapture data with dependence among individuals within clusters
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:5, s. 474-482
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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.
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| 6. |
- Jutfelt, Fredrik, et al.
(författare)
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Two-current choice flumes for testing avoidance and preference in aquatic animals
- 2017
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Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 8:3, s. 379-390
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Forskningsöversikt (refereegranskat)abstract
- Aquatic chemical ecology is an important and growing field of research that involves understanding how organisms perceive and respond to chemical cues in their environment. Research assessing the preference or avoidance of a water source containing specific chemical cues has increased in popularity in recent years, and a variety of methods have been described in the scientific literature. Two-current choice flumes have seen the greatest increase in popularity, perhaps because of their potential to address the broadest range of research questions.Here, we review the literature on two-current choice flumes and show that there is a clear absence of standardized methodologies that make comparisons across studies difficult. Some of the main issues include turbulent flows that cause mixing of cues, inappropriate size of choice arenas for the animals, short experiments with stressed animals, failure to report how experiment and researcher biases were eliminated, general underreporting of methodological details, underutilization of collected data and inappropriate data analyses.In this review, we present best practice guidelines on how to build, test and use two-current choice flumes to measure the behavioural responses of aquatic animals to chemical cues, and provide blueprints for flume construction. The guidelines include steps that can be taken to avoid problems commonly encountered when using two-current choice flumes and analysing the resulting data.This review provides a set of standards that should be followed to ensure data quality, transparency and replicability in future studies in this field.
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| 7. |
- Kass, Jamie M., et al.
(författare)
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ENMeval 2.0 : Redesigned for customizable and reproducible modeling of species’ niches and distributions
- 2021
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Ingår i: Methods in Ecology and Evolution. - : John Wiley & Sons. - 2041-210X. ; 12:9, s. 1602-1608
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Tidskriftsartikel (refereegranskat)abstract
- Quantitative evaluations to optimize complexity have become standard for avoiding overfitting of ecological niche models (ENMs) that estimate species’ potential geographic distributions. ENMeval was the first R package to make such evaluations (often termed model tuning) widely accessible for the Maxent algorithm. It also provided multiple methods for partitioning occurrence data and reported various performance metrics.Requests by users, recent developments in the field, and needs for software compatibility led to a major redesign and expansion. We additionally conducted a literature review to investigate trends in ENMeval use (2015–2019).ENMeval 2.0 has a new object-oriented structure for adding other algorithms, enables customizing algorithmic settings and performance metrics, generates extensive metadata, implements a null-model approach to quantify significance and effect sizes, and includes features to increase the breadth of analyses and visualizations. In our literature review, we found insufficient reporting of model performance and parameterization, heavy reliance on model selection with AICc and low utilization of spatial cross-validation; we explain how ENMeval 2.0 can help address these issues.This redesigned and expanded version can promote progress in the field and improve the information available for decision-making.
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| 8. |
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| 9. |
- Rönnegård, Lars, et al.
(författare)
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Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:7, s. 792-799
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Tidskriftsartikel (refereegranskat)abstract
- 1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.
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| 10. |
- Schliep, Klaus, et al.
(författare)
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Intertwining phylogenetic trees and networks
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:10, s. 1212-1220
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Tidskriftsartikel (refereegranskat)abstract
- 1. The fields of phylogenetic tree and network inference have dramatically advanced in the past decade, but independently with few attempts to bridge them.2. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks.3. This includes: (i) identifying and labelling equivalent tree branches and network edges, (ii) transferring tree branch support to network edges, and (iii) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges.4. ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and inferences.
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