Introductory Fisheries Analyses with R

Ogle, Derek H.

doi:10.1201/9781315371986

Cited by 261 publications

(284 citation statements)

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“…We used the package ‘AICcmodavg’ for model selection (Mazerolle, 2019) and ‘yarrr’ (Phillips, 2017) and ‘plot3D’ (Soetaert, 2019) for data visualization. ANCOVAs (type III) were performed using the ‘car’ package (Fow & Weisberg, 2019) together with the ‘FSA’ (Ogle, Wheeler, & Dinno, 2020) and ‘rcompanion’ (Mangiafico, 2020) R packages for Dunn’s tests and compact letter display for lists of comparisons. We managed phylogenetic data with ‘ape’ package (Paradis & Schliep, 2018) and phylogenetic signal was calculated with the ‘phytools’ package (Revell, 2012).…”

Section: Methodsmentioning

confidence: 99%

Body stoichiometry of heterotrophs: assessing drivers of interspecific variations in elemental composition

Andrieux

Signor

Guillou

et al. 2020

Preprint

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AimTo document how body stoichiometry of heterotrophs varies globally and to assess phylogenetic, trophic, habitat and body mass drivers of this interspecific variation in elemental composition, focusing on carbon (C), nitrogen (N) and phosphorus (P).LocationWorldwide.Time period1930 – 2018.Major taxa studiedAmphibians, fishes (Euteleosteomorpha and Otomorpha), invertebrates, mammals, microbes and sauropsids (birds and reptiles).MethodsWe compiled from the scientific literature a global database of body elemental composition of heterotrophs in marine, freshwater and terrestrial realms. We used model selection and ANCOVA analyses to investigate the proportion of variance in elemental composition explained by taxonomic groups, diet, habitat and body mass. We assessed the phylogenetic signal in body stoichiometry using Blomberg’s K and Pagel’s λ statistics. We assessed the phylogenetic structure of interspecific variation in body stoichiometry using mixed models with nested taxonomic levels as random factors. We finally assessed the co-variation in elemental composition using linear models.ResultsOur database currently gathers 17848 independent observations on 1491 species. Body elemental composition was found to be widely variable among species with the four assessed drivers significantly contributing to this variation. Taxonomic group is the strongest contributor to interspecific variance for the stoichiometric traits studied, followed by habitat, diet and body mass. More precisely, stoichiometric traits are generally variable at the three taxonomic levels studied (class, order and family), resulting in a significant but relatively modest phylogenetic signal. Finally, we found significant co-variation among the three body elemental contents, resulting in taxonomic group-specific C:N:P spectrums.Main conclusionsOur global synthesis of body stoichiometry of heterotrophs reveals a strong interspecific variability that is only modestly explained by the species attributes investigated: body mass, habitat and diet. It further reveals that this taxonomically structured residual variation in body stoichiometry seems to be constrained along taxonomic group-specific elemental spectrums.

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Section: Methodsmentioning

confidence: 99%

Body stoichiometry of heterotrophs: assessing drivers of interspecific variations in elemental composition

Andrieux

Signor

Guillou

et al. 2020

Preprint

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“…However, in many cases alternate growth functions, such as the Gompertz function (Campana and Jones ) or logistic function, are more appropriate for fitting age and length data (Zweifel and Lasker ; Katsanevakis and Maravelias ). The relationship between age and growth was evaluated using the VBGF, Gompertz growth function, and logistic growth function (Ogle ; Appendix Table A.1). Model selection with Akaike's information criterion corrected for small sample size (AIC c ; Burnham and Anderson ; Helidoniotis et al.…”

Section: Methodsmentioning

confidence: 99%

Otoliths Reveal Spawning Ecology and Early Life History of Sympatric Catostomids

Barkalow

Brandenburg

Platania

2020

N American J Fish Manag

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Differences in spawning ecology and early life history may influence the recruitment success of three sympatric catostomids in the Colorado River basin: the Bluehead Sucker Catostomus discobolus, Flannelmouth Sucker C. latipinnis, and federally endangered Razorback Sucker Xyrauchen texanus. In the San Juan River, all three species annually produce larvae, but only Bluehead and Flannelmouth suckers regularly recruit to the juvenile phase and older. Otolith microstructure analysis can determine age, growth rates, and spawning periodicity and may elucidate possible reasons for differences in recruitment among species. Larval suckers were collected from low-velocity habitats in the San Juan River in 2011; fish were measured, and ontogenetic phase and fish age were determined from otolith increment counts. Otolith age was used to determine hatch dates and spawning periodicity, calculate daily growth rates, and develop three candidate growth functions relating fish age and body length. Relative to Bluehead and Flannelmouth suckers, Razorback Suckers had a shorter spawning period, lower growth rate, and a higher proportion of the least developed ontogenetic phase. The small size of Razorback Suckers relative to other suckers may result in higher predation and lower prey acquisition, thus restricting their transition to more developed phases and limiting recruitment to the juvenile phase. Model ranking based on Akaike's information criterion (corrected for small sample size) was nearly identical for all growth functions. The early life history information we provide may guide flow releases in this regulated system to provide suitable backwater habitat and warmer water temperatures compatible with reproduction, growth, and survival of native catostomids, including the endangered Razorback Sucker. However, due to the limited temporal and geographic extent of samples used in this study, data presented herein are not inclusive of all conditions under which suckers may be present in the San Juan River.

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“…The entire procedure was repeated for each of the six landscape-season combinations. All analyses were conducted in R version 3.2.1 using packages MuMIn 30 , circular 31 , ascii 32 , raster 33 , sp 34 , rgdal 35 , rgeos 36 , FSA 37 , lme4 38 , beeswarm 39 and Hmisc 40 . Raw data are archived in Dryad (entry doi: xx.xxxx/dryad.xxxx).…”

Section: Methodsmentioning

confidence: 99%

Dancing bees evaluate agricultural forage resources as inferior to central urban land

Schürch

Leadbeater

2019

Preprint

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8Recent evidence suggests that flower-rich areas within cities could play an important role in 9 pollinator conservation, but direct comparison of agricultural and urban areas has proved challenging 10 to perform over large scales. Here we use the waggle dances of honeybees (Apis mellifera L.) to 11 evaluate floral resource availability over the entire season at deeply urban or agricultural sites. 12Through analysis of 3378 dances that were performed over two years by 20 colonies in SE England, 13 we show that foraging trip distance is consistently lower at urban sites across the entire season, 14 implying a higher availability of forage in heavily urbanized areas. Urban bees also collected nectar 15 with a higher mean sugar content. From the self-reported perspective of a generalist pollinator, the 16 modern agricultural landscapes that we studied provided insufficient and transient resources relative 17 to heavily urbanised areas, which may represent important refuges within an impoverished landscape. 18 19

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Introductory Fisheries Analyses with R

Cited by 261 publications

References 0 publications

Body stoichiometry of heterotrophs: assessing drivers of interspecific variations in elemental composition

Body stoichiometry of heterotrophs: assessing drivers of interspecific variations in elemental composition

Otoliths Reveal Spawning Ecology and Early Life History of Sympatric Catostomids

Dancing bees evaluate agricultural forage resources as inferior to central urban land

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