rotl, an R package to interact with the Open Tree of Life data

Michonneau, François; Brown, James C.; Winter, David J.

doi:10.7287/peerj.preprints.1471v2

Cited by 47 publications

(49 citation statements)

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“…Phylogenetic and non‐phylogenetic models were fitted to investigate whether non‐independence due to the degree of relatedness between species influenced both the overall effects and their level of uncertainty. Phylogenetic relatedness was estimated based on existing phylogenies and taxonomic information from the Open Tree of Life, and any polytomies were resolved by randomisation [Hinchliff et al ., 2015; via R package ‘rotl’ v3.0.7 (Michonneau, Brown, & Winter, 2016); for the final phylogenetic tree see Appendix S5]. Branch lengths were estimated using Grafen's method [Grafen, 1989; via R package ‘ape’ v5.3 (Paradis & Schliep, 2019)], and were used to construct a phylogenetic variance–covariance relatedness matrix.…”

Section: Methodsmentioning

confidence: 99%

Poor nutritional condition promotes high‐risk behaviours: a systematic review and meta‐analysis

et al. 2020

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Animal behaviour can lead to varying levels of risk, and an individual's physical condition can alter the potential costs and benefits of undertaking risky behaviours. How risk‐taking behaviour depends on condition is subject to contrasting hypotheses. The asset protection principle proposes that individuals in better condition should be more risk averse, as they have higher future reproductive potential (i.e. more to lose). The state‐dependent safety hypothesis proposes that high‐condition individuals that are more likely to survive and maximise the benefits of risky situations may make apparently riskier choices, as their individual risk is in fact lower. We systematically searched for studies that experimentally manipulated animals’ nutritional or energetic condition through diet treatments, and subsequently measured risk‐taking behaviour in contexts relating to predation, novelty and exploration. Our meta‐analysis quantified condition effects on risk‐taking behaviour at both the mean and variance level. We preregistered our methods and hypotheses prior to conducting the study. Phylogenetic multilevel meta‐analysis revealed that the lower‐nutritional‐condition individuals showed on average ca. 26% greater tendency towards risk than high‐condition individuals (95% confidence interval: 15–38%; N = 126 studies, 1297 effect sizes). Meta‐regressions revealed several factors influencing the overall effect, such as the experimental context used to measure risk‐taking behaviour, and the life stage when condition was manipulated. Meta‐analysis of variance revealed no clear overall effect of condition on behavioural variance (on average ca. 3% decrease in variance in low‐ versus high‐condition groups; 95% confidence interval: −8 to 3%; N = 119 studies, 1235 effect sizes), however, the experimental context was an important factor influencing the strength and direction of the variance effect. Our comprehensive systematic review and meta‐analysis provide insights into the roles of state dependency and plasticity in intraspecific behavioural variation. While heterogeneity among effect sizes was high, our results show that poor nutritional state on average increases risk taking in ecological contexts involving predation, novelty and exploration.

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Section: Methodsmentioning

confidence: 99%

Poor nutritional condition promotes high‐risk behaviours: a systematic review and meta‐analysis

et al. 2020

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“…To control for phylogeny, we created a phylogenetic matrix of species in the dataset using the Open Tree of Life (Hinchliff et al., 2015). We used the ROTL package (Michonneau et al., 2016) to access the Open Tree of Life in R. ROTL does not calculate branch lengths for trees and thus we calculated these using the compute.brlen function in the APE package (Paradis et al., 2004). A correlation matrix of phylogenetic relatedness among species was then built using APE’s vcv function.…”

Section: Methodsmentioning

confidence: 99%

Species sensitivities to a global pollutant: A meta‐analysis on acoustic signals in response to anthropogenic noise

Kunc

Schmidt

2020

Global Change Biology

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Anthropogenically driven environmental changes affect our planet at an unprecedented rate. Among these changes are those in the acoustic environment caused by anthropogenic noise, which can affect both animals and humans. In many species, acoustic communication plays a crucial role to maintain social relationships by exchanging information via acoustic signals. However, how species relying on acoustic communication differ in their adjustments to anthropogenic noise is little understood. Yet, this is crucial because protecting species effectively depends on our capability to predict how species differ in their response to human‐induced environmental changes. Using a phylogenetically controlled meta‐analysis, we quantified differences in adjustments of acoustic signals to anthropogenic noise among species. The effect sizes included in the analysis were obtained from noise exposure experiments, as only carefully controlled experiments allow to establish cause‐and‐effect relationships. We found that animals changed acoustic signals when exposed to noise, but the magnitude and the direction of adjustments differed among species. Given the importance of communication in the animal kingdom, these adjustments can affect social relationships in many species. The diversity of responses among species highlights the necessity to assess the effect of environmental stressors not only for a few species, because an effect may be positive in one species but negative in another depending on the species’ biology. Thus, an effective conservation approach to protect different species is to preserve natural soundscapes of ecosystems to which species have adapted to by reducing or mitigating the emission of anthropogenic noise into the environment.

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“…In order to add value to the RPF data, phylogenetic relationships and variability indices also were assessed. The phylogenetic tree used in phylogenetic comparisons of RPF was generated from the National Center for Biotechnology Information (NCBI) database with R/ rotl (Michonneau et al ., ) and R/ ape (Paradis & Schliep, ). Groups included the Cupressaceae, or cypress family, as well as four groups within the Pinaceae, or pine family – the abietoid subfamily, the Pseudotsuga genus, the Pinus subgenus pinus and the Pinus subgenus strobus .…”

Section: Methodsmentioning

confidence: 99%

Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation

et al. 2020

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Summary Parenchyma cells in the xylem store nonstructural carbohydrates (NSC), providing reserves of energy that fuel woody perennials through periods of stress and/or limitations to photosynthesis. If the capacity for storage is subject to selection, then the fraction of wood occupied by living parenchyma should increase towards stressful environments. Ray parenchyma fraction (RPF) and seasonal NSC dynamics were quantified for 12 conifers and three oaks along a transect spanning warm dry foothills (500 m above sea level) to cold wet treeline (3250 m asl) in California's central Sierra Nevada. Mean RPF was lower for both conifer and oak species with warmer dryer ranges. RPF variability increased with elevation or in relation to associated climatic variables in conifers – treeline‐dominant Pinus albicaulis had the lowest mean RPF measured (c. 3.7%), but the highest environmentally standardized variability index. Conifer RPF variability was explained by environment, increasing predominantly towards cooler wetter range edges. In oaks, NSC was explained by environment – values increasing for evergreen and decreasing for deciduous oaks with elevation. Lastly, all species surveyed appear to prioritize filling available RPF with sugar to achieve molarities that balance reasonable tensions over starch to maximize stored carbon. RPF responds to environment but is unlikely to spatially constrain NSC storage.

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rotl, an R package to interact with the Open Tree of Life data

Cited by 47 publications

References 0 publications

Poor nutritional condition promotes high‐risk behaviours: a systematic review and meta‐analysis

Poor nutritional condition promotes high‐risk behaviours: a systematic review and meta‐analysis

Species sensitivities to a global pollutant: A meta‐analysis on acoustic signals in response to anthropogenic noise

Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation

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