journal
https://read.qxmd.com/read/38463700/bison-a-bayesian-framework-for-inference-of-social-networks
#1
JOURNAL ARTICLE
Jordan D A Hart, Michael N Weiss, Daniel W Franks, Lauren J N Brent
Animal social networks are often constructed from point estimates of edge weights. In many contexts, edge weights are inferred from observational data, and the uncertainty around estimates can be affected by various factors. Though this has been acknowledged in previous work, methods that explicitly quantify uncertainty in edge weights have not yet been widely adopted, and remain undeveloped for many common types of data. Furthermore, existing methods are unable to cope with some of the complexities often found in observational data, and do not propagate uncertainty in edge weights to subsequent statistical analyses...
September 2023: Methods in Ecology and Evolution
https://read.qxmd.com/read/37876735/optimizing-insect-metabarcoding-using-replicated-mock-communities
#2
JOURNAL ARTICLE
Elzbieta Iwaszkiewicz-Eggebrecht, Emma Granqvist, Mateusz Buczek, Monika Prus, Jan Kudlicka, Tomas Roslin, Ayco J M Tack, Anders F Andersson, Andreia Miraldo, Fredrik Ronquist, Piotr Łukasik
1: 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, abundances, and biomass. 2: Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance...
April 2023: Methods in Ecology and Evolution
https://read.qxmd.com/read/36908682/principled-practical-flexible-fast-a-new-approach-to-phylogenetic-factor-analysis
#3
JOURNAL ARTICLE
Gabriel W Hassler, Brigida Gallone, Leandro Aristide, William L Allen, Max R Tolkoff, Andrew J Holbrook, Guy Baele, Philippe Lemey, Marc A Suchard
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic comparative methods seek to disentangle these relationships across the evolutionary history of a group of organisms. Unfortunately, most existing methods fail to accommodate high-dimensional data with dozens or even thousands of observations per taxon. Phylogenetic factor analysis offers a solution to the challenge of dimensionality. However, scientists seeking to employ this modeling framework confront numerous modeling and implementation decisions, the details of which pose computational and replicability challenges...
October 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/36340863/a-comparison-of-design-based-and-model-based-approaches-for-finite-population-spatial-sampling-and-inference
#4
JOURNAL ARTICLE
Michael Dumelle, Matt Higham, Jay M Ver Hoef, Anthony R Olsen, Lisa Madsen
The design-based and model-based approaches to frequentist statistical inference rest on fundamentally different foundations. In the design-based approach, inference relies on random sampling. In the model-based approach, inference relies on distributional assumptions. We compare the approaches in a finite population spatial context.We provide relevant background for the design-based and model-based approaches and then study their performance using simulated data and real data. The real data is from the United States Environmental Protection Agency's 2012 National Lakes Assessment...
September 1, 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/36250156/robitt-a-tool-for-assessing-the-risk-of-bias-in-studies-of-temporal-trends-in-ecology
#5
JOURNAL ARTICLE
Robin J Boyd, Gary D Powney, Fiona Burns, Alain Danet, François Duchenne, Matthew J Grainger, Susan G Jarvis, Gabrielle Martin, Erlend B Nilsen, Emmanuelle Porcher, Gavin B Stewart, Oliver J Wilson, Oliver L Pescott
Aggregated species occurrence and abundance data from disparate sources are increasingly accessible to ecologists for the analysis of temporal trends in biodiversity. However, sampling biases relevant to any given research question are often poorly explored and infrequently reported; this can undermine statistical inference. In other disciplines, it is common for researchers to complete 'risk-of-bias' assessments to expose and document the potential for biases to undermine conclusions. The huge growth in available data, and recent controversies surrounding their use to infer temporal trends, indicate that similar assessments are urgently needed in ecology...
July 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35915739/circular-linear-copulae-for-animal-movement-data
#6
JOURNAL ARTICLE
Florian H Hodel, John R Fieberg
Animal movement is often modelled in discrete time, formulated in terms of steps taken between successive locations at regular time intervals. Steps are characterized by the distance between successive locations ( step lengths ) and changes in direction ( turn angles ). Animals commonly exhibit a mix of directed movements with large step lengths and turn angles near 0 when travelling between habitat patches and more wandering movements with small step lengths and uniform turn angles when foraging. Thus, step lengths and turn angles will typically be cross-correlated...
May 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35909503/introducing-the-combined-atlas-framework-for-large-scale-web-based-data-visualization-the-glonaf-atlas-of-plant-invasion
#7
JOURNAL ARTICLE
Sebastian C Hancock, Franz Essl, Menno-Jan Kraak, Wayne Dawson, Holger Kreft, Petr Pyšek, Jan Pergl, Mark van Kleunen, Patrick Weigelt, Marten Winter, Georg Gartner, Bernd Lenzner
Large-scale biodiversity data, for example, on species distribution and richness information, are being mobilized and becoming available at an increasing rate. Interactive web applications like atlases have been developed to visualize available datasets and make them accessible to a wider audience. Web mapping tools are changing rapidly, and different underlying concepts have been developed to visualize datasets at a high cartographic standard.Here, we introduce the Combined Atlas Framework for the development of interactive web atlases for ecological data visualization...
May 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35910299/ecological-inference-using-data-from-accelerometers-needs-careful-protocols
#8
JOURNAL ARTICLE
Baptiste Garde, Rory P Wilson, Adam Fell, Nik Cole, Vikash Tatayah, Mark D Holton, Kayleigh A R Rose, Richard S Metcalfe, Hermina Robotka, Martin Wikelski, Fred Tremblay, Shannon Whelan, Kyle H Elliott, Emily L C Shepard
Accelerometers in animal-attached tags are powerful tools in behavioural ecology, they can be used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, using data repositories to draw ecological inference requires a good understanding of the error introduced according to sensor type and position on the study animal and protocols for error assessment and minimisation.Using laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), a proxy for energy expenditure, in human participants...
April 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/37920569/argos-a-toolkit-for-tracking-multiple-animals-in-complex-visual-environments
#9
JOURNAL ARTICLE
Subhasis Ray, Mark A Stopfer
Automatically tracking the positions of multiple animals is often necessary for studying behaviours. This task involves multiple object tracking, a challenging problem in computer vision. Recent advances in machine learning applied to video analysis have been helpful for animal tracking. However, existing tools work well only in homogeneous environments with uniform illumination, features rarely found in natural settings. Moreover, available algorithms cannot effectively process discontinuities in animal motion such as sudden jumps, thus requiring laborious manual review...
March 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35873757/permutation-tests-for-hypothesis-testing-with-animal-social-network-data-problems-and-potential-solutions
#10
JOURNAL ARTICLE
Damien R Farine, Gerald G Carter
Permutation tests are widely used to test null hypotheses with animal social network data, but suffer from high rates of type I and II error when the permutations do not properly simulate the intended null hypothesis.Two common types of permutations each have limitations. Pre-network (or datastream) permutations can be used to control 'nuisance effects' like spatial, temporal or sampling biases, but only when the null hypothesis assumes random social structure. Node (or node-label) permutation tests can test null hypotheses that include nonrandom social structure, but only when nuisance effects do not shape the observed network...
January 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35873756/the-features-and-processes-underpinning-high-quality-data-generation-in-participatory-research-and-engagement-activities
#11
JOURNAL ARTICLE
Phoebe R Maund, Jacob W Bentley, Gail E Austen, Katherine N Irvine, Robert Fish, Martin Dallimer, Zoe G Davies
Participatory approaches are widely used by researchers to gather data and insight about how the environment is perceived, valued and used. The participatory activities may be creating information as part of curiosity-driven blue-skies research or to inform policy/practise decision-making.The quality and usability of data derived from participatory approaches are heavily influenced by how activities are conducted. We share a set of features and processes that underpin the generation of high-quality data, based on our collective experience of developing and undertaking participatory activities with an environmental and conservation focus...
January 2022: Methods in Ecology and Evolution
https://read.qxmd.com/read/35874973/the-geodiv-r-package-tools-for-calculating-gradient-surface-metrics
#12
JOURNAL ARTICLE
Annie C Smith, Kyla M Dahlin, Sydne Record, Jennifer K Costanza, Adam M Wilson, Phoebe L Zarnetske
The geodiv r package calculates gradient surface metrics from imagery and other gridded datasets to provide continuous measures of landscape heterogeneity for landscape pattern analysis. geodiv is the first open-source, command line toolbox for calculating many gradient surface metrics and easily integrates parallel computing for applications with large images or rasters (e.g. remotely sensed data). All functions may be applied either globally to derive a single metric for an entire image or locally to create a texture image over moving windows of a user-defined extent...
November 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/35874972/study-becomes-insight-ecological-learning-from-machine-learning
#13
JOURNAL ARTICLE
Qiuyan Yu, Wenjie Ji, Lara Prihodko, C Wade Ross, Julius Y Anchang, Niall P Hanan
The ecological and environmental science communities have embraced machine learning (ML) for empirical modelling and prediction. However, going beyond prediction to draw insights into underlying functional relationships between response variables and environmental 'drivers' is less straightforward. Deriving ecological insights from fitted ML models requires techniques to extract the 'learning' hidden in the ML models.We revisit the theoretical background and effectiveness of four approaches for deriving insights from ML: ranking independent variable importance (Gini importance, GI; permutation importance, PI; split importance, SI; and conditional permutation importance, CPI), and two approaches for inference of bivariate functional relationships (partial dependence plots, PDP; and accumulated local effect plots, ALE)...
November 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/35874971/alpaca-a-fast-and-accurate-computer-vision-approach-for-automated-landmarking-of-three-dimensional-biological-structures
#14
JOURNAL ARTICLE
Arthur Porto, Sara Rolfe, A Murat Maga
Landmark-based geometric morphometrics has emerged as an essential discipline for the quantitative analysis of size and shape in ecology and evolution. With the ever-increasing density of digitized landmarks, the possible development of a fully automated method of landmark placement has attracted considerable attention. Despite the recent progress in image registration techniques, which could provide a pathway to automation, three-dimensional (3D) morphometric data are still mainly gathered by trained experts...
November 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/34888025/a-machine-learning-approach-for-classifying-and-quantifying-acoustic-diversity
#15
JOURNAL ARTICLE
Sara C Keen, Karan J Odom, Michael S Webster, Gregory M Kohn, Timothy F Wright, Marcelo Araya-Salas
1. Assessing diversity of discretely varying behavior is a classical ethological problem. In particular, the challenge of calculating an individuals' or species' vocal repertoire size is often an important step in ecological and behavioral studies, but a reproducible and broadly applicable method for accomplishing this task is not currently available. 2. We offer a generalizable method to automate the calculation and quantification of acoustic diversity using an unsupervised random forest framework. We tested our method using natural and synthetic datasets of known repertoire sizes that exhibit standardized variation in common acoustic features as well as in recording quality...
July 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/34262682/rasterdiv-an-information-theory-tailored-r-package-for-measuring-ecosystem-heterogeneity-from-space-to-the-origin-and-back
#16
JOURNAL ARTICLE
Duccio Rocchini, Elisa Thouverai, Matteo Marcantonio, Martina Iannacito, Daniele Da Re, Michele Torresani, Giovanni Bacaro, Manuele Bazzichetto, Alessandra Bernardi, Giles M Foody, Reinhard Furrer, David Kleijn, Stefano Larsen, Jonathan Lenoir, Marco Malavasi, Elisa Marchetto, Filippo Messori, Alessandro Montaghi, Vítězslav Moudrý, Babak Naimi, Carlo Ricotta, Micol Rossini, Francesco Santi, Maria J Santos, Michael E Schaepman, Fabian D Schneider, Leila Schuh, Sonia Silvestri, Petra Ŝímová, Andrew K Skidmore, Clara Tattoni, Enrico Tordoni, Saverio Vicario, Piero Zannini, Martin Wegmann
Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms...
June 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/34249305/a-novel-fluorescence-and-dna-combination-for-versatile-long-term-marking-of-mosquitoes
#17
JOURNAL ARTICLE
Roy Faiman, Benjamin J Krajacich, Leland Graber, Adama Dao, Alpha Seydou Yaro, Ousmane Yossi, Zana Lamissa Sanogo, Moussa Diallo, Djibril Samaké, Daman Sylla, Moribo Coulibaly, Salif Kone, Sekou Goita, Mamadou B Coulibaly, Olga Muratova, Ashley McCormack, Bronner P Gonçalves, Jennifer Hume, Patrick Duffy, Tovi Lehmann
Current mark-release-recapture methodologies are limited in their ability to address complex problems in vector biology, such as studying multiple groups overlapping in space and time. Additionally, limited mark retention, reduced post-marking survival and the large effort in marking, collection and recapture all complicate effective insect tracking.We have developed and evaluated a marking method using a fluorescent dye (SmartWater® ) combined with synthetic DNA tags to informatively and efficiently mark adult mosquitoes using an airbrush pump and nebulizer...
June 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/34858566/medi-macronutrient-extraction-and-determination-from-invertebrates-a-rapid-cheap-and-streamlined-protocol
#18
JOURNAL ARTICLE
Jordan P Cuff, Shawn M Wilder, Maximillian P T G Tercel, Rhiannon Hunt, Somoye Oluwaseun, Paige S Morley, Rafael A Badell-Grau, Ian P Vaughan, James R Bell, Pablo Orozco-terWengel, William O C Symondson, Carsten T Müller
Macronutrients, comprising carbohydrates, proteins and lipids, underpin many ecological processes, but their quantification in ecological studies is often inaccurate and laborious, requiring large investments of time and bulk samples, which make individual-level studies impossible. This study presents Macronutrient Extraction and Determination from Invertebrates (MEDI), a protocol for the direct, rapid and relatively low-cost determination of macronutrient content from single small macroinvertebrates.Macronutrients were extracted by a sequential process of soaking in 1:12 chloroform:methanol solution to remove lipid and then solubilising tissue in 0...
April 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/33889377/quantifying-carbon-in-tree-bark-the-importance-of-bark-morphology-and-tree-size
#19
JOURNAL ARTICLE
Mathias Neumann, Michael J Lawes
Bark contributes approximately 20% to the total above-ground biomass of trees, yet bark is not properly accounted for when estimating carbon sequestered by trees. Current allometric functions estimate tree volume from diameter measured over the bark, and derive bark density and carbon content from estimates for wood. As the bark density of hardwood species is 40%-50% lower than the wood density, but nearly equivalent in conifers, bark carbon is overestimated for most species. The latter is further exacerbated by variation in bark volume with bark surface morphology...
April 2021: Methods in Ecology and Evolution
https://read.qxmd.com/read/35464674/common-datastream-permutations-of-animal-social-network-data-are-not-appropriate-for-hypothesis-testing-using-regression-models
#20
JOURNAL ARTICLE
Michael N Weiss, Daniel W Franks, Lauren J N Brent, Samuel Ellis, Matthew J Silk, Darren P Croft
1. Social network methods have become a key tool for describing, modelling, and testing hypotheses about the social structures of animals. However, due to the non-independence of network data and the presence of confounds, specialized statistical techniques are often needed to test hypotheses in these networks. Datastream permutations, originally developed to test the null hypothesis of random social structure, have become a popular tool for testing a wide array of null hypotheses in animal social networks...
February 2021: Methods in Ecology and Evolution
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