bt.limburg.2015.RdOtolith chemistry is often useful for tracking provenance of fishes, as well as examining migration histories. Whereas elements such as strontium and barium correlate well with salinity and temperature, experiments that examine manganese uptake as a function of these parameters have found no such correlation. Instead, dissolved manganese is available as a redox product, and as such, is indicative of low-oxygen conditions. Here the authors present evidence for thatmechanism in a range of habitats frommarine to freshwater, across species, and also present ancillary proxies that support the mechanism as well.
bt.limburg.2015The data frame 13,843 × 10 contains the following columns:
| fish_id | integer | fish identifier |
| species | character | scientic name |
| common_name | character | common name |
| system | character | location of capture |
| status | character | habitat of capture (Normoxic or Hypoxic) |
| distance | integer | distance from otolith core, microns |
| mn_ca | numeric | otolith mn:ca |
These data are transects of Mn:Ca ratios measured on otoliths of 19 Atlantic croaker Micropogonias undulatus, 20 Baltic flounder Platichthys flesus , and 12 yellow perch (YP) Perca flavescens . Negative distances on some transects are data extracted from longer transects that went "edge to edge" on an otolith, crossing the core, which was designated as zero. Data collected to the left of the core were by default given negative distance values. Mn and Ca are expressed in mass, not molar, ratios.
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry)
Beam diameter: 35-75um
Scan speed: 3-5um/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)
Limburg, K. E., Walther, B. D., Lu, Z., Jackman, G., Mohan, J., Walther, Y., ... & Schmitt, A. K. (2015). In search of the dead zone: use of otoliths for tracking fish exposure to hypoxia. Journal of Marine Systems, 141, 167-178.
https://doi.org/10.1016/J.JMARSYS.2014.02.014
Data availability are available at https://ars.els-cdn.com/content/image/1-s2.0-S0924796314000438-mmc1.pdf
Traversing the paper's information via Semantic Scholar ID 1d926323b07c59e8808b0c36d61d06b3a56c1454 using S2miner package
otolith, trace element, Mn/Ca
### copy data into 'dat'
dat <- bt.limburg.2015
tibble::tibble(dat)
#> # A tibble: 13,843 × 7
#> fish_id species common_name system status distance mn_ca
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 0 0.000007
#> 2 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 3 0.000009
#> 3 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 5 0.000005
#> 4 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 8 0.000012
#> 5 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 11 0.000007
#> 6 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 13 0.000014
#> 7 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 16 0.00001
#> 8 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 19 0.000009
#> 9 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 21 0.000007
#> 10 MU086 C6 Micropogonias undulatus Atlantic croaker Gulf of Mexico Normoxic 24 0.000019
#> # ℹ 13,833 more rows
if (FALSE) {
### load package
library(dplyr)
library(ggplot2)
### otolith sr/ca
ggplot(data = dat, aes(distance, mn_ca*1000)) +
geom_line(aes(colour = species, group = fish_id), show.legend = F, na.rm = T) +
facet_grid(species ~ status, scales = "free_y") +
xlab("Distance from otolith core, microns") +
ylab("Otolith Mn/Ca (x1000)") +
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")
)
}