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Methods in Ecology and Evolution

Lars Rönnegård, S Eryn McFarlane, Arild Husby, Takeshi Kawakami, Hans Ellegren, Anna Qvarnström
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...
July 2016: Methods in Ecology and Evolution
Natalie Cooper, Gavin H Thomas, Richard G FitzJohn
Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods.Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them...
June 2016: Methods in Ecology and Evolution
Gemma G R Murray, Fang Wang, Ewan M Harrison, Gavin K Paterson, Alison E Mather, Simon R Harris, Mark A Holmes, Andrew Rambaut, John J Welch
'Dated-tip' methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of 'temporal signal' are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable.We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin-resistant Staphylococcus aureus (to show how particular problems arise with real-world data sets)...
January 2016: Methods in Ecology and Evolution
Richard J Reynolds, Gustavo de Los Campos, Scott P Egan, James R Ott
No abstract text is available yet for this article.
January 2016: Methods in Ecology and Evolution
Kevin Schneider, Stephan Koblmüller, Kristina M Sefc
The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time...
November 11, 2015: Methods in Ecology and Evolution
Jolyon Troscianko, Martin Stevens
Quantitative measurements of colour, pattern and morphology are vital to a growing range of disciplines. Digital cameras are readily available and already widely used for making these measurements, having numerous advantages over other techniques, such as spectrometry. However, off-the-shelf consumer cameras are designed to produce images for human viewing, meaning that their uncalibrated photographs cannot be used for making reliable, quantitative measurements. Many studies still fail to appreciate this, and of those scientists who are aware of such issues, many are hindered by a lack of usable tools for making objective measurements from photographs...
November 2015: Methods in Ecology and Evolution
Hyun S Gweon, Anna Oliver, Joanne Taylor, Tim Booth, Melanie Gibbs, Daniel S Read, Robert I Griffiths, Karsten Schonrogge
Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables.Here, we introduce PIPITS, an open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables...
August 2015: Methods in Ecology and Evolution
Christian Rutz, Michael B Morrissey, Zackory T Burns, John Burt, Brian Otis, James J H St Clair, Richard James
Growing interest in the structure and dynamics of animal social networks has stimulated efforts to develop automated tracking technologies that can reliably record encounters in free-ranging subjects. A particularly promising approach is the use of animal-attached 'proximity loggers', which collect data on the incidence, duration and proximity of spatial associations through inter-logger radio communication. While proximity logging is based on a straightforward physical principle - the attenuation of propagating radio waves with distance - calibrating systems for field deployment is challenging, since most study species roam across complex, heterogeneous environments...
June 2015: Methods in Ecology and Evolution
Tim C D Lucas, Elizabeth A Moorcroft, Robin Freeman, J Marcus Rowcliffe, Kate E Jones
Wildlife monitoring technology is advancing rapidly and the use of remote sensors such as camera traps and acoustic detectors is becoming common in both the terrestrial and marine environments. Current methods to estimate abundance or density require individual recognition of animals or knowing the distance of the animal from the sensor, which is often difficult. A method without these requirements, the random encounter model (REM), has been successfully applied to estimate animal densities from count data generated from camera traps...
May 2015: Methods in Ecology and Evolution
Carolina Pardo-Diaz, Camilo Salazar, Chris D Jiggins
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability...
April 2015: Methods in Ecology and Evolution
Nathan D Merchant, Kurt M Fristrup, Mark P Johnson, Peter L Tyack, Matthew J Witt, Philippe Blondel, Susan E Parks
1. Many organisms depend on sound for communication, predator/prey detection and navigation. The acoustic environment can therefore play an important role in ecosystem dynamics and evolution. A growing number of studies are documenting acoustic habitats and their influences on animal development, behaviour, physiology and spatial ecology, which has led to increasing demand for passive acoustic monitoring (PAM) expertise in the life sciences. However, as yet, there has been no synthesis of data processing methods for acoustic habitat monitoring, which presents an unnecessary obstacle to would-be PAM analysts...
March 2015: Methods in Ecology and Evolution
Paul C D Johnson, Sarah J E Barry, Heather M Ferguson, Pie Müller, Holger Schielzeth
'Will my study answer my research question?' is the most fundamental question a researcher can ask when designing a study, yet when phrased in statistical terms - 'What is the power of my study?' or 'How precise will my parameter estimate be?' - few researchers in ecology and evolution (EE) try to answer it, despite the detrimental consequences of performing under- or over-powered research. We suggest that this reluctance is due in large part to the unsuitability of simple methods of power analysis (broadly defined as any attempt to quantify prospectively the 'informativeness' of a study) for the complex models commonly used in EE research...
February 2015: Methods in Ecology and Evolution
Olga Chernomor, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika Henzinger, Arndt von Haeseler
Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.Depending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action...
January 2015: Methods in Ecology and Evolution
Robert B Thorpe, Will J F Le Quesne, Fay Luxford, Jeremy S Collie, Simon Jennings
Implementation of an ecosystem approach to fisheries requires advice on trade-offs among fished species and between fisheries yields and biodiversity or food web properties. However, the lack of explicit representation, analysis and consideration of uncertainty in most multispecies models has limited their application in analyses that could support management advice.We assessed the consequences of parameter uncertainty by developing 78 125 multispecies size-structured fish community models, with all combinations of parameters drawn from ranges that spanned parameter values estimated from data and literature...
January 2015: Methods in Ecology and Evolution
Bram Vrancken, Philippe Lemey, Andrew Rambaut, Trevor Bedford, Ben Longdon, Huldrych F Günthard, Marc A Suchard
Phylogenetic signal quantifies the degree to which resemblance in continuously-valued traits reflects phylogenetic relatedness. Measures of phylogenetic signal are widely used in ecological and evolutionary research, and are recently gaining traction in viral evolutionary studies. Standard estimators of phylogenetic signal frequently condition on data summary statistics of the repeated trait observations and fixed phylogenetics trees, resulting in information loss and potential bias. To incorporate the observation process and phylogenetic uncertainty in a model-based approach, we develop a novel Bayesian inference method to simultaneously estimate the evolutionary history and phylogenetic signal from molecular sequence data and repeated multivariate traits...
January 1, 2015: Methods in Ecology and Evolution
Loïc Chalmandrier, Tamara Münkemüller, Vincent Devictor, Sébastien Lavergne, Wilfried Thuiller
The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties...
January 1, 2015: Methods in Ecology and Evolution
Jussi Laitila, Atte Moilanen, Federico M Pouzols
Biodiversity offsetting, which means compensation for ecological and environmental damage caused by development activity, has recently been gaining strong political support around the world. One common criticism levelled at offsets is that they exchange certain and almost immediate losses for uncertain future gains. In the case of restoration offsets, gains may be realized after a time delay of decades, and with considerable uncertainty. Here we focus on offset multipliers, which are ratios between damaged and compensated amounts (areas) of biodiversity...
November 2014: Methods in Ecology and Evolution
Finlay Scott, Julia L Blanchard, Ken H Andersen
Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed to capture fish community dynamics useful for assessing the community impacts of fishing.We present mizer, an R package for implementing dynamic size spectrum ecological models of an entire aquatic community subject to fishing...
October 2014: Methods in Ecology and Evolution
Cuong Q Tang, Aelys M Humphreys, Diego Fontaneto, Timothy G Barraclough, Emmanuel Paradis
Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods...
October 2014: Methods in Ecology and Evolution
Paul Cd Johnson, Robert B O'Hara
Nakagawa & Schielzeth extended the widely used goodness-of-fit statistic R (2) to apply to generalized linear mixed models (GLMMs). However, their R (2) GLMM method is restricted to models with the simplest random effects structure, known as random intercepts models. It is not applicable to another common random effects structure, random slopes models.I show that R (2) GLMM can be extended to random slopes models using a simple formula that is straightforward to implement in statistical software. This extension substantially widens the potential application of R (2) GLMM...
September 2014: Methods in Ecology and Evolution
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