bt.altenritter.2018.2019.RdConsequences of sub-lethal hypoxia exposure for teleosts tracked with biogeochemical markers: a trans-basin comparison.
bt.altenritter.2018.2019The data frame 820,891 × 9 contains the following columns:
| fish_id | character | fish identifier,number of each individual fish |
| distance | numeric | otolith transect distance traversed by laser; distance across the otolith (um) |
| mg_m24 | numeric | concentration of Magnesium isotope 24, parts per million (ppm) |
| mg_m25 | numeric | concentration of Magnesium isotope 25, parts per million (ppm) |
| mn_m55 | numeric | concentration of Manganese isotope 55, parts per million (ppm) |
| sr_m88 | numeric | concentration of Strontium isotope 88, parts per million (ppm) |
| in_115 | numeric | concentration of Indium isotope 115, parts per million (ppm) |
| i_m127 | numeric | concentration of Iodine isotope 127, parts per million (ppm) |
| ba_m138 | numeric | concentration of Barium isotope 138, parts per million (ppm) |
Geochemical concentrations (ppm) of six elements measured in otoliths of Atlantic croaker sampled on board of the R/V Oregon II during the NOAA Seamap Fall Groundfish Survey of 2014 (Oct 10 to Nov 4) and 2015 (Oct 8 to Nov 22).
Otolith element concentrations for each individual fish (labeled as “HMU ####”) were measured at the University of Austin, Jackson School of Geosciences using laser ablation inductively coupled mass spectrometry. Standard reference materials included a National Institutes of Standards and Technology glass standard (NIST-612) and a United States Geological Survey microanalytical carbonate standard pressed pellet (MACS-3). Otolith element concentrations were quantified along the longest dorso-ventral axis spanning the core (i.e. hatch) to the edge (i.e. death). Please reference Altenritter et al. (2018) and Altenritter and Walther (2019) for detailed information on sampling and analysis, instrumentation, and data processing.
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry)
Beam diameter: 25um
Scan speed: 5um/s
Reference materials: NIST-612 (National Institutes of Standards and Technology glass standard) and MACS-3 (United States Geological Survey microanalytical carbonate standard pressed pellet)
Altenritter, M. E., & Walther, B. D. (2019). The Legacy of Hypoxia: Tracking Carryover Effects of Low Oxygen Exposure in a Demersal Fish Using Geochemical Tracers. Transactions of the American Fisheries Society, 148(3), 569–583. https://doi.org/10.1002/tafs.10159
Altenritter, M., Cohuo, A., & Walther, B. (2018). Proportions of demersal fish exposed to sublethal hypoxia revealed by otolith chemistry. Marine Ecology Progress Series, 589, 193–208. https://doi.org/10.3354/meps12469
Data availability are available at https://www.bco-dmo.org/dataset/784969
Data availability are available at https://doi.org/10.26008/1912/bco-dmo.784969.1
Traversing the paper's information via Semantic Scholar ID 959aa4c423a8e4a052877c672889f51c3ebda532;
eabf95501fd3accc84e69120dfb2a15e0570f436 using S2miner package
otolith, trace element, Sr/Ba, Mn, Mg, I, In
### copy data into 'dat'
dat <- bt.altenritter.2018.2019
tibble::tibble(dat)
#> # A tibble: 820,891 × 9
#> fish_id distance mg_m24 mg_m25 mn_m55 sr_m88 in_115 i_m127 ba_m138
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 HMU593 0 43.9 47.4 12.3 2644. 26.5 -18.7 8.05
#> 2 HMU593 2.54 36.2 39.9 7.52 1948. -13.5 24.2 6.93
#> 3 HMU593 5.07 32.5 25.7 9.32 2114. 186. 15.9 6.72
#> 4 HMU593 7.61 42.4 31.8 8.41 2219. -53.5 18.7 7.99
#> 5 HMU593 10.1 38.7 52.1 8.17 2384. 66.5 19.2 6.07
#> 6 HMU593 12.7 37.8 31.7 8.80 1882. -13.5 12.6 5.96
#> 7 HMU593 15.2 44.7 30.3 9.31 1981. 26.5 15.4 5.13
#> 8 HMU593 17.8 55.6 50.5 6.95 1729. 26.5 8.47 4.51
#> 9 HMU593 20.3 37.6 40.3 7.10 1707. -53.5 18.1 5.19
#> 10 HMU593 22.8 37.3 26.9 6.74 2058. -53.5 19.4 3.69
#> # ℹ 820,881 more rows
if (FALSE) {
### load package
library(dplyr)
library(ggplot2)
### otolith Sr/Ba
ggplot(data = dat, aes(distance, sr_m88/ba_m138)) +
geom_line(aes(group = fish_id), show.legend = F, na.rm = T) +
xlab("Distance across the otolith (um)") +
ylab("otolith sr/ba") +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
### otolith Mg24/Mg25
ggplot(data = dat, aes(distance, mg_m24/mg_m25)) +
geom_line(aes(group = fish_id), show.legend = F, na.rm = T) +
xlab("Distance across the otolith (um)") +
ylab(expression(Mg * ""^24 * "/" * Mg * ""^25)) +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
}