bt.hill.2020.RdLA-ICP-MS was used to quantify seven elements (Mg, Mn, Cu, Zn, Sr, Ba, and Pb), along a continuous transect that ran from the ventral edge of the otolith through the core to the dorsal edge of each otolith, resulting in a time resolved model of the environmental exposure history of each fish.
bt.hill.2020The data frame 266,731 × 16 contains the following columns:
| river | character | river of capture |
| parent_river | character | parent river of capture |
| estuary | character | estuary of capture |
| state | character | state of capture |
| capt_yr | integer | year of capture |
| fishno | integer | fish id |
| sex | character | fish sex |
| elapsed_time | numeric | elapsed time of LA-ICP-MS |
| distance | numeric | distance from the ventral edge of the otolith through the core to the dorsal edge |
| mg_ca | numeric | Mg/Ca |
| mn_ca | numeric | Mn/Ca |
| cu_ca | numeric | Cu/Ca |
| zn_ca | numeric | Zn/Ca |
| sr_ca | numeric | Sr/Ca |
| ba_ca | numeric | Ba/Ca |
| pb_ca | numeric | Pb/Ca |
The dataset contains contains the raw chemistry data (results of LA-ICP-MS) for all 289 Hickory Shad (Alosa mediocris).
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry)
Beam diameter: 30um
Scan speed: 2-5um/s
Reference materials: NIST-610 (National Institutes of Standards and Technology glass standard)
Hill, C. R., Rulifson, R. A., & Halden, N. M. (2022). A quantitative approach to investigate natal philopatry in Hickory Shad (Alosa mediocris) using otolith chemistry. Fisheries Research, 249, 106232. https://doi.org/10.1016/j.fishres.2022.106232
Code and data availability are available at https://doi.org/10.5281/zenodo.4536534
Traversing the paper's information via Semantic Scholar ID 7690935e5be9a70157633875a316d7ba3d083205 using S2miner package
otolith, trace element, Sr/Ca, Mn/Ca, Mg/Ca, Ba/Ca, Pb/Ca, Cu/Ca
### copy data into 'dat'
dat <- bt.hill.2020
tibble::tibble(dat)
#> # A tibble: 266,731 × 16
#> river parent_river estuary state capt_yr fishno sex elapsed_time distance mg_ca mn_ca cu_ca zn_ca
#> <chr> <chr> <chr> <chr> <int> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Alt Alt AltSd GA 2017 786 F 0 0 0.05 0.43 0.63 0.04
#> 2 Alt Alt AltSd GA 2017 786 F 0.8 2.4 0.04 0.91 0.8 0.38
#> 3 Alt Alt AltSd GA 2017 786 F 1.6 4.8 0.05 0.5 0.4 1
#> 4 Alt Alt AltSd GA 2017 786 F 2.4 7.2 0.03 0.27 0.5 -0.03
#> 5 Alt Alt AltSd GA 2017 786 F 3.2 9.6 0.04 0.39 0.39 0.44
#> 6 Alt Alt AltSd GA 2017 786 F 4 12 0.02 0.57 0.18 -0.16
#> 7 Alt Alt AltSd GA 2017 786 F 4.8 14.4 0.03 0.66 0.54 0.38
#> 8 Alt Alt AltSd GA 2017 786 F 5.6 16.8 0.02 0.64 0.14 0.75
#> 9 Alt Alt AltSd GA 2017 786 F 6.4 19.2 0.03 0.8 0.1 -0.13
#> 10 Alt Alt AltSd GA 2017 786 F 7.2 21.6 0.03 0.37 0.43 0.16
#> # ℹ 266,721 more rows
#> # ℹ 3 more variables: sr_ca <dbl>, ba_ca <dbl>, pb_ca <dbl>
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### Sr/Ca profile figure
ggplot(data = dat, aes(distance, sr_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Sr/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
### Mg/Ca profile figure
ggplot(data = dat, aes(distance, mg_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Mg/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
### Cu/Ca profile figure
ggplot(data = dat, aes(distance, cu_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Cu/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
### Zn/Ca profile figure
ggplot(data = dat, aes(distance, zn_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Zn/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
### Ba/Ca profile figure
ggplot(data = dat, aes(distance, ba_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Ba/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
### Pb/Ca profile figure
ggplot(data = dat, aes(distance, pb_ca)) +
geom_line(aes(col = sex,group = fishno), show.legend = F) +
facet_grid(river ~ sex, scales = "free_y") +
ylab("Pb/Ca")+
xlab("Distance from the ventral edge of the otolith through the core to the dorsal edge") +
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")
)
}