Introductory Fisheries Analyses with R

Ogle, Derek H.

doi:10.1201/b19232

Cited by 174 publications

(203 citation statements)

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“…We tested the null hypothesis, which says that for each variable there were no significant differences between our sites. For statistically different groups (mound, pit, control) for each variable we used a post-hoc two-sided Dunn test with correction for multiple comparisons according to the Bonferroni method (Dinno 2016;Ogle 2016). For all tests the level of significance has been accepted to p-value=0.05.…”

Section: Resultsmentioning

confidence: 99%

Deciphering the history of forest disturbance and its effects on landforms and soils – lessons from a pit-and-mound locality at Rogowa Kopa, Sudetes, SW Poland

Pawlik

Musielok

Migoń³

et al. 2017

Bulletin of Geography. Physical Geography Series

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Abstract. The historical dimension of pit-and-mound topography has been studied at the Mt Rogowa Kopa locality, Stołowe Mountains, SW Poland. This site represents one of the best developed regional examples of hummocky forest floor relief due to widespread tree uprooting and subsequent degradation of root plates. Through map analysis and dendrochronology the disturbance history was traced to at least the 1930s and, most likely, a strong wind episode from 1933 was the reason for the forest calamity that resulted in the nearly total destruction of the original stand. However, the affected forest was a planted Norway spruce monoculture, introduced and managed until at least the beginning of the 20 th century, and not a natural forest. The windthrow niche was then used by beech, whose individuals preferentially chose mounds to grow, conserving the hummocky microtopography. Changes in soil evolutionary pathways brought about by wind-driven disturbance include both haploidisation (rejuvenation) and horizonation (differentiation). Evidence of soil rejuvenation includes a decrease in organic carbon content and an increase in pH in the upper parts of soils developed on mounds relative to the pH of undisturbed references soils. Soil texture was relatively homogenised in pits and mounds. Dating of the pit-and-mound microrelief by means of soil properties (organic carbon content, iron forms) was only partly successful. Although the young age of pits and mounds is evident, the actual age inferred from soil properties was underestimated by a few tens of years. Evaluation of factors potentially controlling the propensity to widespread treethrow suggests that the type of forest is a far more important variable than local abiotic factors of bedrock geology, regolith characteristics, and slope inclination.

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Section: Resultsmentioning

confidence: 99%

Deciphering the history of forest disturbance and its effects on landforms and soils – lessons from a pit-and-mound locality at Rogowa Kopa, Sudetes, SW Poland

Pawlik

Musielok

Migoń³

et al. 2017

Bulletin of Geography. Physical Geography Series

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“…Goodness of fit was evaluated with the Hosmer-Lemeshow test [26]. We also used a bootstrap routine [27] to develop confidence intervals for days at large when 50% of the fish had either one-or-more or two-or-more sutures.…”

Section: Methodsmentioning

confidence: 99%

Estimating incision healing rate for surgically implanted acoustic transmitters from recaptured fish

et al. 2017

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Background: Intracoelomic implantation of electronic tags has become a common method in fishery research, but rarely are fish examined by scientists after release to understand the extent that surgical incisions have healed. Walleye (Sander vitreus) are a valuable, highly exploited fishery resource in the Laurentian Great Lakes. Here, fishery capture of walleye with internal acoustic transmitters combined with a high reward program provided multiple opportunities to examine photographs and quantify the status of surgical incisions. Walleye (n = 926) from reef and river spawning populations in Lake Erie and Lake Huron were implanted with acoustic transmitters during spring spawning events from 2011 to 2016. Incisions were closed with polydioxanone monofilament using two to three interrupted sutures. Out of 276 recaptured fish, 60 incision sites were clearly visible in photographs, and these were scored by two independent readers for incision closure, inflammation, and the presence of sutures.Results: While incision sites were completely closed by 61 days post-release (95% CI 44-94), sutures remained for up to 866 days. Sutures were expelled serially during a protracted period, and the probability of observing at least one suture in a recaptured fish declined below 50% after 673 days (95% CI 442-1016). Inflammation at the incision increased during the first 71 days and then declined monotonically, remaining detectable at low levels. Conclusion:Our results emphasized that sutures remained in free-ranging fish past the time when they were beneficial for incision healing. Most dissolvable sutures have been designed for use in endotherms where the body temperature and internal milieu differ dramatically from the conditions experienced by fishes in temperate climates. Identification of new suture materials for fish that facilitate healing while absorbing or dissolving in a reasonable period (e.g., a few weeks to three months) in colder temperatures (e.g., <12 °C) would be beneficial to mitigate potential adverse impacts from inflammation at the incision.

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“…(1) was achieved by a generalised nonlinear least-squares routine from the nlme library (Pinheiro et al 2014) for the software R (R Core Team 2016), by which heterogeneous errors were accounted for and assumptions of the full model (fitted on data from natural beds and culture plots together) were met by the data. Growth between mussels on natural beds and culture plots was compared following the likelihood methodology of Kimura (1980) and its implementation by Ogle (2015a), with the help of the FSA package for R (Ogle 2015b). In this method, a complex model with all parameters of the VBGF different for natural beds and culture plots are compared to simpler nested models, with 1 or more VBGF parameters in common.…”

Section: Growthmentioning

confidence: 99%

Population dynamics of subtidal blue mussels Mytilus edulis and the impact of cultivation

Stralen¹,

Wijsman²,

Herman³

et al. 2017

Aquacult. Environ. Interact.

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Fishery on subtidal mussel beds and subsequent relying on culture plots in the same system is a common practice in bottom mussel culture. We address factors that determine the population dynamics of subtidal blue mussels Mytilus edulis L. and to what extent total (natural plus cultured) subtidal mussel biomass in the system is affected by fishery practices. Mussel size and density of spatially segregated natural and cultured subtidal mussel populations in the western Wadden Sea were measured over time in 2 field studies. Spatial patterns in survival rates showed better spat survival in areas with lower salinity and lower density of sea stars Asterias rubens. This suggests that mussel survival is negatively related to sea star distribution which is to a large extent controlled by salinity. The Asterias−Mytilus relation in the Wadden Sea is an example of the concept that environmental stress determines the successes of the prey by affecting the prey− predator relationship. Natural beds that escape predation are found at lower salinities, and mussels on these beds showed low growth rates, also because of lower food quality in these areas. Mussel culture is strongly affecting the population dynamics of the subtidal mussel population, through relay of mussels from natural mussel beds to culture plots. This activity increases mussel growth and survival, because food quality on culture plots is high and predation is controlled. Despite harvesting, mussel biomass production on culture plots was higher than on natural mussel beds, enhancing total subtidal mussel stock.

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Introductory Fisheries Analyses with R

Cited by 174 publications

References 0 publications

Deciphering the history of forest disturbance and its effects on landforms and soils – lessons from a pit-and-mound locality at Rogowa Kopa, Sudetes, SW Poland

Deciphering the history of forest disturbance and its effects on landforms and soils – lessons from a pit-and-mound locality at Rogowa Kopa, Sudetes, SW Poland

Estimating incision healing rate for surgically implanted acoustic transmitters from recaptured fish

Population dynamics of subtidal blue mussels Mytilus edulis and the impact of cultivation

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