bt.chalifour.2021.RdThe authors use genetic stock identification and otolith analyses to quantify estuarine habitat use by Chinook salmon (Oncorhynchus tshawytscha)-the Pacific salmon species considered most reliant on this habitat-in Canada's most productive salmon river, the Fraser River.
bt.chalifour.2021The data frame 91 × 8 contains the following columns:
| fishid | integer | fish identifier |
| habitat | character | habitat type |
| forklength_mm | numeric | fork length (mm) |
| side | character | otolith side (L or R) |
| sr_edge | numeric | sr/ca of otolith edge (mmol/mol) |
| ba_edge | numeric | ba/ca of otolith edge (umol/mol) |
| sr_core | numeric | sr/ca of otolith core (mmol/mol) |
| ba_core | numeric | ba/ca of otolith core (umol/mol) |
Sr:Ca at the otolith edge increases, and Ba:Ca at the otolith edge decreases with increasing residency in the estuary. This suggests that tidal fluctuations in the estuary and an ontogenetic shift outward towards more saline habitats influence otolith microchemistry over time as the fish reside in this estuarine environment.
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry)
Beam diameter: 30um
Scan speed: 5um/s
Reference materials: NIST611, NIST613, NIST615 (National Institutes of Standards and Technology glass standard)
Chalifour, L., Scott, D. C., MacDuffee, M., Stark, S., Dower, J. F., Beacham, T. D., ... & Baum, J. K. (2021). Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, British Columbia, a large urban estuary. Canadian Journal of Fisheries and Aquatic Sciences, 78(5), 539-550. https://doi.org/10.1139/cjfas-2020-0247
Sturrock, A. M., Wikert, J. D., Heyne, T., Mesick, C., Hubbard, A. E., Hinkelman, T. M., ... & Johnson, R. C. (2015). Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes. PLoS One, 10(5), e0122380.
Code and data availability are available at https://github.com/baumlab/Chalifour_etal_2021_CJFAS
Traversing the paper's information via Semantic Scholar ID a9b228af81e0e3ac67d0f621adbc10fc55b1fb1a using S2miner package
otolith, trace element, Sr/Ca, Ba/Ca
### copy data into 'dat'
dat <- bt.chalifour.2021
tibble::tibble(dat)
#> # A tibble: 91 × 8
#> fishid habitat forklength_mm side sr_edge ba_edge sr_core ba_core
#> <int> <chr> <int> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 762 Marsh 40 L 0.867 1.74 1.30 0.133
#> 2 767 Marsh 44 L 1.55 1.08 1.33 0.677
#> 3 933 Marsh 42 L 1.05 1.47 1.67 0.161
#> 4 4973 Marsh 63 L 0.775 1.71 0.827 0.522
#> 5 4985 Marsh 48 L 1.84 0.294 1.35 0.208
#> 6 4990 Sand flat 71 L 2.27 0.200 1.21 0.521
#> 7 4991 Sand flat 63 L 0.950 0.685 1.21 0.441
#> 8 4992 Sand flat 58 L 1.19 0.735 1.39 0.599
#> 9 4993 Sand flat 67 L 1.14 0.664 1.38 0.526
#> 10 5223 Sand flat 68 R 1.81 0.660 1.40 0.423
#> # ℹ 81 more rows
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### otolith core
ggplot(data = dat, aes(sr_core, ba_core)) +
geom_point(aes(col = habitat), show.legend = F, na.rm = T) +
facet_grid(. ~ habitat) +
xlab("Sr/Ca of otolith core (mmol/mol)") +
ylab("Ba/Ca of otolith core (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 edge
ggplot(data = dat, aes(sr_edge, ba_edge)) +
geom_point(aes(col = habitat), show.legend = F, na.rm = T) +
facet_grid(. ~ habitat) +
xlab("Sr/Ca of otolith edge (mmol/mol)") +
ylab("Ba/Ca of otolith edge (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")
)
}