bt.enomoto.2022.RdJapanese jack mackerel (Trachurus japonicus) is distributed in the semi-demersal layer of the continental shelf of the East China Sea (ECS), whereas their larvae are distributed on the surface. Notably, a smooth vertical habitat layer shift (HLS) to a deeper layer during their juvenile stage is crucial for the survival of this species. To elucidate the timing of the HLS, the authors analyzed the otolith oxygen stable isotope ratio (oto_d18O), which increases at lower temperatures and higher salinity (the conditions that the fish experience in the deeper layers of the ECS), at a high temporal resolution of minimum 5 days intervals.
bt.enomoto.2022The data frame 740 × 8 contains the following columns:
| fish_id | character | fish identifier |
| sample_id | character | sample identifier |
| year | integer | year of capture |
| sample_number | integer | number of sample |
| area | integer | area of capture |
| d18o | numeric | oxygen isotope ratio relative to VPDB in permil |
| d18o_sd | numeric | standard deviation of oxygen isotope ratio relative to VPDB in permil |
| age | numeric | centered daily age (dph) |
Summary on sampling data, biological information, and d18O otolith analyses of 78 Japanese jack mackerel Trachurus japonicus.
Instrument: IRMS (isotope ratio mass spectrometer)
Enomoto, M., Ito, S. I., Takahashi, M., Sassa, C., Higuchi, T., & Shirai, K. (2022). Vertical habitat shifts of juvenile jack mackerel estimated using otolith oxygen stable isotope. Progress in Oceanography, 208, 102897. https://doi.org/10.1016/j.pocean.2022.102897
Traversing the paper's information via Semantic Scholar ID fb5a0cb084eba0790bc291b22d6d26a51ed10db2 using S2miner package
otolith, stable isotope, d18O
### copy data into 'dat'
dat <- bt.enomoto.2022
tibble::tibble(dat)
#> # A tibble: 740 × 8
#> fish_id sample_id year sample_number area d18o d18o_sd age
#> <chr> <chr> <int> <int> <chr> <dbl> <dbl> <dbl>
#> 1 KM091406 KM091406-1 2009 6 central East China Sea NA 0.114 10.5
#> 2 KM091406 KM091406-2 2009 6 central East China Sea NA 0.114 25.5
#> 3 KM091406 KM091406-3 2009 6 central East China Sea -0.489 0.114 35.5
#> 4 KM091406 KM091406-4 2009 6 central East China Sea -0.257 0.114 45.5
#> 5 KM091406 KM091406-5 2009 6 central East China Sea -0.349 0.114 55.5
#> 6 KM091406 KM091406-6 2009 6 central East China Sea -0.363 0.114 65.5
#> 7 KM091406 KM091406-7 2009 6 central East China Sea -0.357 0.114 75.5
#> 8 KM091611 KM091611-1 2009 11 central East China Sea NA 0.131 10.5
#> 9 KM091611 KM091611-2 2009 11 central East China Sea -0.932 0.131 25.5
#> 10 KM091611 KM091611-3 2009 11 central East China Sea -0.325 0.131 33
#> # ℹ 730 more rows
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### d18O profile figure
ggplot(data = dat, aes(age, d18o)) +
geom_line(aes(col = area, group = fish_id), show.legend = F, linewidth = 0.02, na.rm = T) +
geom_point(aes(col = area, group = fish_id), show.legend = F, na.rm = T) +
facet_wrap(. ~ area) +
labs(
x = ("Age (dph)"),
y = (expression(delta * ""^18 * "O" * " (‰)"))
) +
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")
)
}