bt.mohan.2022.RdOtolith biominerals of large Pacific bluefin tuna Thunnus orientalis (PBT) collected from the western, eastern, and south Pacific Ocean, were analyzed for a suite of trace elements across calcified/proteinaceous growth zones to investigate patterns across ontogeny.
bt.mohan.2022The data frame 246,375 × 11 contains the following columns:
| pbt_id | character | pacific bluefin tuna Thunnus orientalis identifier |
| distance | numeric | distance from otolith core to edge (um) |
| value | numeric | otolith element(E):Ca (Ba/Ca in umol/mol; Li/Ca in umol/mol; Mg/Ca in umol/mol; Mn/Ca in umol/mol; Sr/Ca in mmol/mol; Zn/Ca in umol/mol ) |
| elements | character | trace element |
| date | character | date of capture |
| ocean | character | ocean of capture |
| region | character | region of capture |
| sex | character | fish sex |
| fl | numeric | fork length (cm) |
| age | character | estimated age (year) |
| gg_weight | integer | gilled and gutted (gg) weight (kg) |
Elemental profiles of individual Pacific bluefin tuna Thunnus orientalis (PBT) otoliths collected from the Eastern Pacific (EPO), Western Pacific (WPO) and South Pacific (SPO); different colored lines represent individual fish from each region.
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry)
Beam diameter: 50um
Scan speed: 5um/s
Reference materials: NIST-612 (National Institutes of Standards and Technology glass standard) andMACS-3 (United States Geological Survey microanalytical carbonate standard pressed pellet)
Mohan, J. A., Dewar, H., Snodgrass, O. E., Miller, N. R., Tanaka, Y., Ohshimo, S., ... & Wells, R. D. (2022). Otolith geochemistry reflects life histories of Pacific bluefin tuna. Plos one, 17(10), e0275899. https://doi.org/10.1371/journal.pone.0275899
Traversing the paper's information via Semantic Scholar ID 21574f9994add809b1d6c495a60d706ce070a552 using S2miner package
otolith, trace element, Ba/Ca, Li/Ca, Mg/Ca, Mn/Ca, Sr/Ca, Zn/Ca
### copy data into 'dat'
dat <- bt.mohan.2022
tibble::tibble(dat)
#> # A tibble: 246,375 × 11
#> pbt_id distance value elements date ocean region sex fl age gg_weight
#> <chr> <dbl> <dbl> <chr> <int> <chr> <chr> <chr> <int> <int> <int>
#> 1 EP01 0 3.20 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 2 EP01 2.02 3.42 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 3 EP01 4.03 3.67 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 4 EP01 6.05 3.89 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 5 EP01 8.06 3.89 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 6 EP01 10.1 4.10 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 7 EP01 12.1 3.89 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 8 EP01 14.1 3.92 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 9 EP01 16.1 3.73 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> 10 EP01 18.1 3.64 Li_Ca 20170920 East Pacific San Deigo, Califr… M 197 9 156
#> # ℹ 246,365 more rows
if (FALSE) {
### load package
library(dplyr)
library(ggplot2)
### Otolith ba/ca
ggplot(data = dat[which(dat$elements == "Ba_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Ba/Ca (umol/mol)") +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
### Otolith li/ca
ggplot(data = dat[which(dat$elements == "Li_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Li/Ca (umol/mol)") +
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 mg/ca
ggplot(data = dat[which(dat$elements == "Mg_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Mg/Ca (umol/mol)") +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
### Otolith mn/ca
ggplot(data = dat[which(dat$elements == "Mn_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Mn/Ca (umol/mol)") +
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 sr/ca
ggplot(data = dat[which(dat$elements == "Sr_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Sr/Ca (mmol/mol)") +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
### Otolith zn/ca
ggplot(data = dat[which(dat$elements == "Zn_Ca"), ], aes(distance, value)) +
geom_line(aes(colour = ocean, group = pbt_id), show.legend = F, na.rm = T) +
facet_grid(ocean ~ ., scales = "free_y") +
xlab("Distance from otolith core to edge (um)") +
ylab("Otolith Zn/Ca (umol/mol)") +
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")
)
}