mvabund– an R package for model‐based analysis of multivariate abundance data

Wang, Yi; Naumann, Ulrike; Wright, S.; Warton, David I.

doi:10.1111/j.2041-210x.2012.00190.x

Cited by 1,321 publications

(1,220 citation statements)

References 14 publications

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“…Bacterial OTUs correlated with seawater, whale blow or air samples were identified using Analysis of Variance (ANOVA) based on generalized linear models fit to the data (Wang et al, 2012). OTU diversity and abundance profiles for air and whale blow were significantly different (p < 0.05) from each other and bear little similarity with communities characteristic of the adjacent seawater.…”

Section: Next Generation Sequencing Resultsmentioning

confidence: 99%

“…The community structure dissimilarity between samples was observed with non-metric multidimensional scaling. Significant differences in communities sampled in seawater, UAV-captured air or whale blow samples were defined using generalized linear models within mvabund (Wang et al, 2012). Briefly, a negative binomial model was fit to the OTU abundance data and the sample grouping was analyzed using Analysis of Variance (ANOVA).…”

Section: Data Analysesmentioning

confidence: 99%

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An Economical Custom-Built Drone for Assessing Whale Health

Pirotta

Smith²,

Ostrowski

et al. 2017

Front. Mar. Sci.

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Drones or Unmanned Aerial Vehicles (UAVs) have huge potential to improve the safety and efficiency of sample collection from wild animals under logistically challenging circumstances. Here we present a method for surveying population health that uses UAVs to sample respiratory vapor, 'whale blow,' exhaled by free-swimming humpback whales (Megaptera novaeangliae), and coupled this with amplification and sequencing of respiratory tract microbiota. We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated 'blow' to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and dronecaptured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa. Whale-specific taxa included species and genera previously associated with the respiratory tracts or oral cavities of mammals (e.g., Pseudomonas, Clostridia, Cardiobacterium), as well as species previously isolated from dolphin or killer whale blowholes (Corynebacteria, others). Many examples of exogenous marine species were identified, including Tenacibaculum and Psychrobacter spp. that have been associated with the skin microbiota of marine mammals and fish and may include pathogens. This information provides a baseline of respiratory tract microbiota profiles of contemporary whale health. Customized UAVs are a promising new tool for marine megafauna research and may have broad application in cost-effective monitoring and management of whale populations worldwide.

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Section: Next Generation Sequencing Resultsmentioning

confidence: 99%

Section: Data Analysesmentioning

confidence: 99%

An Economical Custom-Built Drone for Assessing Whale Health

Pirotta

Smith²,

Ostrowski

et al. 2017

Front. Mar. Sci.

View full text Add to dashboard Cite

show abstract

“…An in-depth multivariate analysis was performed in order to evaluate dispersion effects between test groups by using the R package Bmvabund^selecting the Banova.manyglm^call. After checking model assumptions by plotting Bmeanvar^and Bmanyglmm atrixes, data was further processed as a Bnegative binomial^distribution, a typical option for abundance count data in the mvabund-package (Wang et al 2012). …”

Section: Resultsmentioning

confidence: 99%

Plasticity in the gut microbial community and uptake of Enterobacteriaceae (Gammaproteobacteria) in Bombus terrestris bumblebees’ nests when reared indoors and moved to an outdoor environment

et al. 2015

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-Bombus nests consisting of one queen, brood, and worker adults, are produced indoors for biological pollination in agriculture. In this study, we investigated the gut microbial community in workers of Bombus terrestris when the environment is stable (indoors) or variable (outdoors). When nests were reared indoors under standardized conditions, we identified a small gut microbial community consisting of Neisseriaceae , Orbaceae , Lactobacillaceae , and Bifidobacteriaceae , and the age of bumblebee nests and workers did not affect the alpha and beta diversity, confirming a stable microbiota. Secondly, when indoor-reared nests were moved to outdoors, we observed a major shift in the microbial community, especially in the newborn workers fully developed in the outdoor conditions, with a significant colonization of Enterobacteriaceae . Our new findings are discussed in relation to hostassociated core and non-core bacteria in bumblebees including possible implications for host functioning.Bombus terrestris / generalist pollinator / microbiota / plasticity / Enterobacteriaceae / reared bumblebees

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“…Analyses were performed using the R‐package mvabund (Wang, Neuman, Wright, & Warton, 2012). The response variable was binary (infective/noninfective), hence we used a binomial distribution of errors.…”

Section: Methodsmentioning

confidence: 99%

Spatio‐temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans

Bousset

Sprague

Thrall

et al. 2018

Evolutionary Applications

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Genetic, physiological and physical homogenization of agricultural landscapes creates ideal environments for plant pathogens to proliferate and rapidly evolve. Thus, a critical challenge in plant pathology and epidemiology is to design durable and effective strategies to protect cropping systems from damage caused by pathogens. Theoretical studies suggest that spatio‐temporal variation in the diversity and distribution of resistant hosts across agricultural landscapes may have strong effects on the epidemiology and evolutionary potential of crop pathogens. However, we lack empirical tests of spatio‐temporal deployment of host resistance to pathogens can be best used to manage disease epidemics and disrupt pathogen evolutionary dynamics in real‐world systems. In a field experiment, we simulated how differences in Brassica napus resistance deployment strategies and landscape connectivity influence epidemic severity and Leptosphaeria maculans pathogen population composition. Host plant resistance, spatio‐temporal connectivity [stubble loads], and genetic connectivity of the inoculum source [composition of canola stubble mixtures] jointly impacted epidemiology (disease severity) and pathogen evolution (population composition). Changes in population composition were consistent with directional selection for the ability to infect the host (infectivity), leading to changes in pathotype (multilocus phenotypes) and infectivity frequencies. We repeatedly observed decreases in the frequency of unnecessary infectivity, suggesting that carrying multiple infectivity genes is costly for the pathogen. From an applied perspective, our results indicate that varying resistance genes in space and time can be used to help control disease, even when resistance has already been overcome. Furthermore, our approach extends our ability to test not only for the efficacy of host varieties in a given year, but also for durability over multiple cropping seasons, given variation in the combination of resistance genes deployed.

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mvabund– an R package for model‐based analysis of multivariate abundance data

Cited by 1,321 publications

References 14 publications

An Economical Custom-Built Drone for Assessing Whale Health

An Economical Custom-Built Drone for Assessing Whale Health

Plasticity in the gut microbial community and uptake of Enterobacteriaceae (Gammaproteobacteria) in Bombus terrestris bumblebees’ nests when reared indoors and moved to an outdoor environment

Spatio‐temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans

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