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Methods in Ecology and Evolution

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https://www.readbyqxmd.com/read/29861885/using-multi-response-models-to-investigate-pathogen-coinfections-across-scales-insights-from-emerging-diseases-of-amphibians
#1
William E Stutz, Andrew R Blaustein, Cheryl J Briggs, Jason T Hoverman, Jason R Rohr, Pieter T J Johnson
Associations among parasites affect many aspects of host-parasite dynamics, but a lack of analytical tools has limited investigations of parasite correlations in observational data that are often nested across spatial and biological scales.Here we illustrate how hierarchical, multiresponse modeling can characterize parasite associations by allowing for hierarchical structuring, offering estimates of uncertainty, and incorporating correlational model structures. After introducing the general approach, we apply this framework to investigate coinfections among four amphibian parasites (the trematodes Ribeiroia ondatrae and Echinostoma spp...
April 2018: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29892335/an-efficient-extension-of-n-mixture-models-for-multi-species-abundance-estimation
#2
Juan Pablo Gomez, Scott K Robinson, Jason K Blackburn, José Miguel Ponciano
In this study we propose an extension of the N-mixture family of models that targets an improvement of the statistical properties of rare species abundance estimators when sample sizes are low, yet typical for tropical studies. The proposed method harnesses information from other species in an ecological community to correct each species' estimator. We provide guidance to determine the sample size required to estimate accurately the abundance of rare tropical species when attempting to estimate the abundance of single species...
February 2018: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29755717/patternize-an-r-package-for-quantifying-colour-pattern-variation
#3
Steven M Van Belleghem, Riccardo Papa, Humberto Ortiz-Zuazaga, Frederik Hendrickx, Chris D Jiggins, W Owen McMillan, Brian A Counterman
The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms. patternize is an R package that quantifies variation in color patterns obtained from image data. patternize first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration...
February 2018: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29576862/a-method-for-analysing-small-samples-of-floral-pollen-for-free-and-protein-bound-amino-acids
#4
Daniel Stabler, Eileen F Power, Anne M Borland, Jeremy D Barnes, Geraldine A Wright
Pollen provides floral visitors with essential nutrients including proteins, lipids, vitamins and minerals. As an important nutrient resource for pollinators, including honeybees and bumblebees, pollen quality is of growing interest in assessing available nutrition to foraging bees. To date, quantifying the protein-bound amino acids in pollen has been difficult and methods rely on large amounts of pollen, typically more than 1 g. More usual is to estimate a crude protein value based on the nitrogen content of pollen, however, such methods provide no information on the distribution of essential and non-essential amino acids constituting the proteins...
February 2018: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29456829/processing-of-acceleration-and-dive-data-on-board-satellite-relay-tags-to-investigate-diving-and-foraging-behaviour-in-free-ranging-marine-predators
#5
Sam L Cox, Florian Orgeret, Mathieu Gesta, Charles Rodde, Isaac Heizer, Henri Weimerskirch, Christophe Guinet
Biologging technologies are changing the way in which the marine environment is observed and monitored. However, because device retrieval is typically required to access the high-resolution data they collect, their use is generally restricted to those animals that predictably return to land. Data abstraction and transmission techniques aim to address this, although currently these are limited in scope and do not incorporate, for example, acceleration measurements which can quantify animal behaviours and movement patterns over fine-scales...
January 2018: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29263778/identifying-consistent-allele-frequency-differences-in-studies-of-stratified-populations
#6
R Axel W Wiberg, Oscar E Gaggiotti, Michael B Morrissey, Michael G Ritchie
With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply...
December 2017: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/29104749/a-guide-to-null-models-for-animal-social-network-analysis
#7
Damien R Farine
Null models are an important component of the social network analysis toolbox. However, their use in hypothesis testing is still not widespread. Furthermore, several different approaches for constructing null models exist, each with their relative strengths and weaknesses, and often testing different hypotheses.In this study, I highlight why null models are important for robust hypothesis testing in studies of animal social networks. Using simulated data containing a known observation bias, I test how different statistical tests and null models perform if such a bias was unknown...
October 2017: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28989596/the-automated-root-exudate-system-ares-a-method-to-apply-solutes-at-regular-intervals-to-soils-in-the-field
#8
Luis Lopez-Sangil, Charles George, Eduardo Medina-Barcenas, Ali J Birkett, Catherine Baxendale, Laëtitia M Bréchet, Eduard Estradera-Gumbau, Emma J Sayer
Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions, but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field...
September 2017: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28943999/measuring-site-fidelity-and-spatial-segregation-within-animal-societies
#9
Thomas O Richardson, Luca Giuggioli, Nigel R Franks, Ana B Sendova-Franks
Animals often display a marked tendency to return to previously visited locations that contain important resources, such as water, food, or developing brood that must be provisioned. A considerable body of work has demonstrated that this tendency is strongly expressed in ants, which exhibit fidelity to particular sites both inside and outside the nest. However, thus far many studies of this phenomena have taken the approach of reducing an animal's trajectory to a summary statistic, such as the area it covers...
August 2017: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28503291/how-many-more-sample-size-determination-in-studies-of-morphological-integration-and-evolvability
#10
Mark Grabowski, Arthur Porto
1. The variational properties of living organisms are an important component of current evolutionary theory. As a consequence, researchers working on the field of multivariate evolution have increasingly used integration and evolvability statistics as a way of capturing the potentially complex patterns of trait association and their effects over evolutionary trajectories. Little attention has been paid, however, to the cascading effects that inaccurate estimates of trait covariance have on these widely used evolutionary statistics...
May 2017: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28239442/integral-projection-models-for-host-parasite-systems-with-an-application-to-amphibian-chytrid-fungus
#11
Mark Q Wilber, Kate E Langwig, A Marm Kilpatrick, Hamish I McCallum, Cheryl J Briggs
Host parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites.We illustrate how Integral Projection Models (IPM)s provide a novel, elegant modeling framework to represent both types of pathogens. We build a simple host-parasite IPM that tracks both the number of susceptible and infected hosts and the distribution of parasite burdens in infected hosts...
October 2016: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28008347/tree-centric-mapping-of-forest-carbon-density-from-airborne-laser-scanning-and-hyperspectral-data
#12
Michele Dalponte, David A Coomes
Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated...
October 2016: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/27800150/immunoglobulin-detection-in-wild-birds-effectiveness-of-three-secondary-anti-avian-igy-antibodies-in-direct-elisas-in-41-avian-species
#13
Carol A Fassbinder-Orth, Travis E Wilcoxen, Tiffany Tran, Raoul K Boughton, Jeanne M Fair, Erik K Hofmeister, Jennifer L Grindstaff, Jen C Owen
Immunological reagents for wild, non-model species are limited or often non-existent for many species.In this study, we compare the reactivity of a new anti-passerine IgY secondary antibody with existing secondary antibodies developed for use with birds. Samples from 41 species from the following six avian orders were analysed: Anseriformes (1 family, 1 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2 species) and Suliformes (1 family, 1 species)...
October 2016: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/27478587/increasing-the-power-of-genome-wide-association-studies-in-natural-populations-using-repeated-measures-evaluation-and-implementation
#14
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
https://www.readbyqxmd.com/read/27499839/shedding-light-on-the-dark-side-of-phylogenetic-comparative-methods
#15
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
https://www.readbyqxmd.com/read/27110344/the-effect-of-genetic-structure-on-molecular-dating-and-tests-for-temporal-signal
#16
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
https://www.readbyqxmd.com/read/26949509/modelling-heterogeneity-among-fitness-functions-using-random-regression
#17
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
https://www.readbyqxmd.com/read/27066216/hext-a-software-supporting-tree-based-screens-for-hybrid-taxa-in-multilocus-data-sets-and-an-evaluation-of-the-homoplasy-excess-test
#18
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
https://www.readbyqxmd.com/read/27076902/image-calibration-and-analysis-toolbox-a-free-software-suite-for-objectively-measuring-reflectance-colour-and-pattern
#19
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
https://www.readbyqxmd.com/read/27867467/high-throughput-monitoring-of-wild-bee-diversity-and-abundance-via-mitogenomics
#20
Min Tang, Chloe J Hardman, Yinqiu Ji, Guanliang Meng, Shanlin Liu, Meihua Tan, Shenzhou Yang, Ellen D Moss, Jiaxin Wang, Chenxue Yang, Catharine Bruce, Tim Nevard, Simon G Potts, Xin Zhou, Douglas W Yu
Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline.We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees...
September 2015: Methods in Ecology and Evolution
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