| 81. |
- 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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| 82. |
- 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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| 83. |
- Shafer, Aaron B. A., et al.
(författare)
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Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:8, s. 907-917
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Tidskriftsartikel (refereegranskat)abstract
- 1. Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure precise and unbiased interpretation. 2. To test the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, F-IS, coverage, mapping and genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, pi, Het(obs), F-IS, F-ST, N-e and m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio T-s/T-v and Mendelian mismatch rates of known parent-offspring trios). 3. We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing F-IS and T-s/T-v. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site frequency spectrum was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null expectations were best met by reference-based approaches, although contingent on the specific criteria. 4. We recommend that RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.
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| 84. |
- Shefferson, Richard P., et al.
(författare)
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lefko3 : Analysing individual history through size-classified matrix population models
- 2021
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 12:2, s. 378-382
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Tidskriftsartikel (refereegranskat)abstract
- 1. The histories of individuals impact the dynamics of their populations. Matrix projection models (MPMs) are used to analyse population dynamics, but are not structured to incorporate these influences. Historical MPMs (hMPM) were developed to incorporate these impacts, but their complexity has left them little used. We developed r package lefko3 to provide simple, quick methods to estimate and analyse hMPMs, as well as ahistorical MPMs.2. Package lefko3 handles the entire workflow from dataset organization to the construction and analysis of hMPMs. Dataset management functions reorganize most demographic data formats, and matrix creation functions estimate both raw and function-based matrices. Vital rates may be modelled as mixed or generalized linear models, with model selection protocols involving current best practices.3. The core kernels are binaries allowing even matrices with over 10,000 rows and columns to be estimated quickly without parallelization. We also include functions to conduct basic deterministic projection analyses.4. Package lefko3, available on CRAN, dramatically reduces the difficulties in testing the impacts of individual history on population dynamics. We provide three vignettes to showcase how hMPMs can be developed and analysed.
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| 85. |
- Singer, Alexander, et al.
(författare)
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Dating past colonization events to project future species distributions
- 2019
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 10, s. 471-480
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge on the colonization process is important to understand and project future species distributions. The classic method to quantify colonization rates is time-consuming, as it requires recording infrequent colonization events during extensive, repeated surveys. We present the novel "dating-based approach" that requires one complete survey of species occurrence and estimates of subpopulation ages to back-date colonization events. These data allow statistical reconstruction of a virtual, repeated survey to estimate colonization rates in response to environmental covariates or connectivity. With only 30% of survey effort, the dating-based approach provided similar estimates of rate and distance of dispersal of a metapopulation of the epiphytic moss Neckera pennata as the classic approach relying on long-term surveys. Projections of the number of colonization events during the next 100 years differed by only 2.3% (95%-credible interval: [-1.9%; 7.1%]) between methods. The dating-based approach is applicable across spatial scales and promises enhanced species distribution models with urgently needed quantitative dispersal information.
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| 86. |
- Skarin, Anna
(författare)
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Modelling group dynamic animal movement
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5, s. 190-199
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Tidskriftsartikel (refereegranskat)abstract
- Group dynamics are a fundamental aspect of many species' movements. The need to adequately model individuals' interactions with other group members has been recognized, particularly in order to differentiate the role of social forces in individual movement from environmental factors. However, to date, practical statistical methods, which can include group dynamics in animal movement models, have been lacking. We consider a flexible modelling framework that distinguishes a group-level model, describing the movement of the group's centre, and an individual-level model, such that each individual makes its movement decisions relative to the group centroid. The basic idea is framed within the flexible class of hidden Markov models, extending previous work on modelling animal movement by means of multistate random walks. While in simulation experiments parameter estimators exhibit some bias in non-ideal scenarios, we show that generally the estimation of models of this type is both feasible and ecologically informative. We illustrate the approach using real movement data from 11 reindeer (Rangifer tarandus). Results indicate a directional bias towards a group centroid for reindeer in an encamped state. Though the attraction to the group centroid is relatively weak, our model successfully captures group-influenced movement dynamics. Specifically, as compared to a regular mixture of correlated random walks, the group dynamic model more accurately predicts the non-diffusive behaviour of a cohesive mobile group. As technology continues to develop, it will become easier and less expensive to tag multiple individuals within a group in order to follow their movements. Our work provides a first inferential framework for understanding the relative influences of individual versus group-level movement decisions. This framework can be extended to include covariates corresponding to environmental influences or body condition. As such, this framework allows for a broader understanding of the many internal and external factors that can influence an individual's movement.
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| 87. |
- Skov Nielsen, Cecilie
(författare)
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Isotopic methods for non-destructive assessment of carbon dynamics in shrublands under long-term climate change manipulation
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 866-880
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Forskningsöversikt (refereegranskat)abstract
- 1. Long-term climate change experiments are extremely valuable for studying ecosystem responses to environmental change. Examination of the vegetation and the soil should be non-destructive to guarantee long-term research. In this paper, we review field methods using isotope techniques for assessing carbon dynamics in the plant-soil-air continuum, based on recent field experience and examples from a European climate change manipulation network.2. Eight European semi-natural shrubland ecosystems were exposed to warming and drought manipulations. One field site was additionally exposed to elevated atmospheric CO2. We discuss the isotope methods that were used across the network to evaluate carbon fluxes and ecosystem responses, including: (1) analysis of the naturally rare isotopes of carbon (C-13 and C-14) and nitrogen (N-15); (2) use of in situ pulse labelling with (CO2)-C-13, soil injections of C-13- and N-15-enriched substrates, or continuous labelling by free air carbon dioxide enrichment (FACE) and (3) manipulation of isotopic composition of soil substrates (C-14) in laboratory-based studies.3. The natural C-14 signature of soil respiration gave insight into a possible long-term shift in the partitioning between the decomposition of young and old soil carbon sources. Contrastingly, the stable isotopes C-13 and N-15 were used for shorter-term processes, as the residence time in a certain compartment of the stable isotope label signal is limited. The use of labelled carbon-compounds to study carbon mineralisation by soil micro-organisms enabled to determine the long-term effect of climate change on microbial carbon uptake kinetics and turnover.4. Based on the experience with the experimental work, we provide recommendations for the application of the reviewed methods to study carbon fluxes in the plant-soil-air continuum in climate change experiments. C-13-labelling techniques exert minimal physical disturbances, however, the dilution of the applied isotopic signal can be challenging. In addition, the contamination of the field site with excess C-13 or C-14 can be a problem for subsequent natural abundance (C-14 and C-13) or label studies. The use of slight changes in carbon and nitrogen natural abundance does not present problems related to potential dilution or contamination risks, but the usefulness depends on the fractionation rate of the studied processes.
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| 88. |
- Spens, Johan, et al.
(författare)
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Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol : advantage of enclosed filter
- 2017
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 8:5, s. 635-645
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Tidskriftsartikel (refereegranskat)abstract
- Aqueous environmental DNA (eDNA) is an emerging efficient non-invasive tool for species inventory studies. To maximize performance of downstream quantitative PCR (qPCR) and next-generation sequencing (NGS) applications, quality and quantity of the starting material is crucial, calling for optimized capture, storage and extraction techniques of eDNA. Previous comparative studies for eDNA capture/storage have tested precipitation and open' filters. However, practical enclosed' filters which reduce unnecessary handling have not been included. Here, we fill this gap by comparing a filter capsule (Sterivex-GP polyethersulfone, pore size 022m, hereafter called SX) with commonly used methods. Our experimental set-up, covering altogether 41 treatments combining capture by precipitation or filtration with different preservation techniques and storage times, sampled one single lake (and a fish-free control pond). We selected documented capture methods that have successfully targeted a wide range of fauna. The eDNA was extracted using an optimized protocol modified from the DNeasy((R)) Blood & Tissue kit (Qiagen). We measured total eDNA concentrations and Cq-values (cycles used for DNA quantification by qPCR) to target specific mtDNA cytochrome b (cyt b) sequences in two local keystone fish species. SX yielded higher amounts of total eDNA along with lower Cq-values than polycarbonate track-etched filters (PCTE), glass fibre filters (GF) or ethanol precipitation (EP). SX also generated lower Cq-values than cellulose nitrate filters (CN) for one of the target species. DNA integrity of SX samples did not decrease significantly after 2weeks of storage in contrast to GF and PCTE. Adding preservative before storage improved SX results. In conclusion, we recommend SX filters (originally designed for filtering micro-organisms) as an efficient capture method for sampling macrobial eDNA. Ethanol or Longmire's buffer preservation of SX immediately after filtration is recommended. Preserved SX capsules may be stored at room temperature for at least 2weeks without significant degradation. Reduced handling and less exposure to outside stress compared with other filters may contribute to better eDNA results. SX capsules are easily transported and enable eDNA sampling in remote and harsh field conditions as samples can be filtered/preserved on site.
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| 89. |
- Stoffel, Martin A., et al.
(författare)
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inbreedR : an R package for the analysis of inbreeding based on genetic markers
- 2016
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 7:11, s. 1331-1339
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Tidskriftsartikel (refereegranskat)abstract
- Heterozygosity-fitness correlations (HFCs) have been widely used to explore the impact of inbreeding on individual fitness. Initially, most studies used small panels of microsatellites, but more recently with the advent of next-generation sequencing, large SNP datasets are becoming increasingly available and these provide greater power and precision to quantify the impact of inbreeding on fitness. Despite the popularity of HFC studies, effect sizes tend to be rather small. One reason for this may be low variation in inbreeding levels among individuals. Using genetic markers, it is possible to measure variance in inbreeding through the strength of correlation in heterozygosity across marker loci, termed identity disequilibrium (ID). ID can be quantified using the measure g2, which is also a central parameter in HFC theory that can be used within a wider framework to estimate the direct impact of inbreeding on both marker heterozygosity and fitness. However, no software exists to calculate g2 for large SNP datasets nor to implement this framework. inbreedR is an R package that provides functions to calculate g2 based on microsatellite and SNP markers with associated P-values and confidence intervals. Within the framework of HFC theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness. Finally, inbreedR implements user-friendly simulations to explore the precision and magnitude of estimates based on different numbers of genetic markers. We hope this package will facilitate good practice in the analysis of HFCs and help to deepen our understanding of inbreeding effects in natural populations.
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| 90. |
- Ståhl, Göran, et al.
(författare)
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Informative plot sizes in presence-absence sampling of forest floor vegetation
- 2017
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Ingår i: Methods in Ecology and Evolution. - Hoboken : British Ecological Society. - 2041-210X. ; 8:10, s. 1284-1291
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Tidskriftsartikel (refereegranskat)abstract
- 1. Plant communities are attracting increased interest in connection with forest and landscape inventories due to society’s interest in ecosystem services. However, the acquisition of accurate information about plant communities poses several methodological challenges. Here, we investigate the use of presence-absence sampling with the aim to monitor state and change in plant density. We study what plot sizes are informative, i.e. the estimators should have as high precision as possible.2. Plant occurrences were modelled through different Poisson processes and tests were developed for assessing the plausibility of the model assumptions. Optimum plot sizes were determined by minimizing the variance of the estimators. While state estimators of similar kind as ours have been proposed in previous studies, our tests and change estimation procedures are new.3. We found that the most informative plot size for state estimation is 1.6 divided by the plant density, i.e. if the true density is 1 plant per square metre the optimum plot size is 1.6 square metres. This is in accordance with previous findings. More importantly, the most informative plot size for change estimation was smaller and depended on the change patterns. We provide theoretical results as well as some empirical results based on data from the Swedish National Forest Inventory.4. Use of too small or too large plots resulted in poor precision of the density (and density change) estimators. As a consequence, a range of different plot sizes would be required for jointly monitoring both common and rareplants using presence-absence sampling in monitoring programmes.
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