bt.carlisle.2015.RdA novel combination of stable isotope analysis of vertebral annuli, Bayesian mixing models, isoscapes and electronic tag data is used to reconstruct ontogenetic patterns of habitat and resource use in a pelagic apex predator, the salmon shark.
bt.carlisle.2015The data frame 251 × 8 contains the following columns:
| fish_id | character | shark identifier |
| sex | character | shark sex |
| date | character | date of capture |
| plc | numeric | precaudal length (cm) |
| age | integer | age (years) ,vertebrae from each annulus, including inside the birthmark representing in utero growth (age U), -1 represent U |
| sample_id | character | sample id |
| d15n | numeric | carbon isotope ratio of shark vertebrae |
| d13c | numeric | nitrogen isotope ratio of shark vertebrae |
This dataset contains measured isotope values (expressed in ‰) for shark (shortfin mako shark Isurus oxyrinchus and sandbar shark Carcharhinus plumbeus) tooth collagen, for individual teeth across different rows and tooth positions.
Instrument: EA-IRMS (elemental analyzer–isotope ratio mass spectrometry)
Carlisle, A. B., Goldman, K. J., Litvin, S. Y., Madigan, D. J., Bigman, J. S., Swithenbank, A. M., ... & Block, B. A. (2015). Stable isotope analysis of vertebrae reveals ontogenetic changes in habitat in an endothermic pelagic shark. Proceedings of the Royal Society B: Biological Sciences, 282(1799), 20141446.
https://doi.org/10.1098/rspb.2014.1446
Traversing the paper's information via Semantic Scholar ID 4d57b5713b276fe341e8928ce0c6dcabd6356d79 using S2miner package
vertebrae, stable isotope, d13c, d15n
### copy data into 'dat'
dat <- bt.carlisle.2015
tibble::tibble(dat)
#> # A tibble: 251 × 8
#> fish_id sex date plc age sample_id d13c d15n
#> <chr> <chr> <chr> <int> <int> <chr> <dbl> <dbl>
#> 1 shark_1 F 2007-08-03 192 -1 1-U -15.5 15.0
#> 2 shark_1 F 2007-08-03 192 0 1-0 -16.7 12.8
#> 3 shark_1 F 2007-08-03 192 1 1-1 -16.8 14.7
#> 4 shark_1 F 2007-08-03 192 2 1-2 -16.4 13.1
#> 5 shark_1 F 2007-08-03 192 3 1-3 -16.4 13.3
#> 6 shark_1 F 2007-08-03 192 4 1-4 -15.7 15.1
#> 7 shark_1 F 2007-08-03 192 5 1-5 -18.1 15.7
#> 8 shark_1 F 2007-08-03 192 6 1-6 -16.3 13.9
#> 9 shark_1 F 2007-08-03 192 7 1-7 -15.7 13.0
#> 10 shark_1 F 2007-08-03 192 8 1-8 -15.3 13.5
#> # ℹ 241 more rows
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### d13C profile figure
ggplot(data = dat, aes(age, d13c)) +
geom_line(aes(col = fish_id), show.legend = F, linewidth = 0.02, na.rm = T) +
geom_point(aes(col = fish_id), show.legend = F, na.rm = T) +
facet_wrap(. ~ sex) +
labs(
x = "Age (years)",
y = expression(delta * ""^13 * "C" * " (‰)")
) +
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")
)+
scale_x_continuous(breaks = c(-1:14),labels = c("U",0:14))
### d15N profile figure
ggplot(data = dat, aes(age, d15n)) +
geom_line(aes(col = fish_id), show.legend = F, linewidth = 0.02, na.rm = T) +
geom_point(aes(col = fish_id), show.legend = F, na.rm = T) +
facet_wrap(. ~ sex) +
labs(
x = "Age (years)",
y = expression(delta * ""^15 * "N" * " (‰)")
) +
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")
)+
scale_x_continuous(breaks = c(-1:14),labels = c("U",0:14))
}