bt.hermann.2016.RdThe results of this study suggested that Brachyplatystoma filamentosum did not enter the estuary during its life history, and introduced what should be a productive line of research desperately needed to better understand the migrations of these unique and imperilled fishes.
bt.hermann.2016The data frame 7,035 × 6 contains the following columns:
| sampleid | character | fish identifier |
| species | character | species studied |
| distance | numeric | distance from fish otolith cores-edge transects (unit: micron) |
| value | character | Laser ablation–inductively coupled plasma mass spectrometry raw value |
| oto_element | character | trace element: Ba, Sr, Ca, Mn |
| locality | character | locality of captured |
Laser ablation–inductively coupled plasma mass spectrometry raw data (background- and drift-corrected) for Brachyplatystoma rousseauxii (Ecuador and Colombia), Brachyplatystoma filamentosum (Colombia), and six Prochilodus nigricans. Data include Ca, Sr, and Ba for both Brachyplatystoma species and localities, and Ca, Ba, and Mn for all six P. nigricans.
Instrument: LA-ICP-MS (laser ablation-inductively coupled plasma mass spectrometry);SXFM (scanning x-ray fluorescence imaging)
Hermann, T. W., Stewart, D. J., Limburg, K. E., & Castello, L. (2016). Unravelling the life history of Amazonian fishes through otolith microchemistry. Royal Society open science, 3(6), 160206. http://dx.doi.org/10.1098/rsos.160206
Data availability are available at https://doi.org/10.5061/dryad.8kd35
Traversing the paper's information via Semantic Scholar ID 73c934cff5baaa29235d0388b4f14133c95415f7 using S2miner package
otolith, trace element, Sr/Ca, Mn/Ca, Ba/Ca
### copy data into 'dat'
dat <- bt.hermann.2016
tibble::tibble(dat)
#> # A tibble: 7,035 × 6
#> sampleid species distance value oto_element locality
#> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 BR1 Brachyplatystoma rousseauxii 0 487371. Ca Ecuador
#> 2 BR1 Brachyplatystoma rousseauxii 7.59 827141. Ca Ecuador
#> 3 BR1 Brachyplatystoma rousseauxii 15.2 1025308 Ca Ecuador
#> 4 BR1 Brachyplatystoma rousseauxii 22.8 476471. Ca Ecuador
#> 5 BR1 Brachyplatystoma rousseauxii 30.4 860977. Ca Ecuador
#> 6 BR1 Brachyplatystoma rousseauxii 37.9 638388 Ca Ecuador
#> 7 BR1 Brachyplatystoma rousseauxii 45.5 665656. Ca Ecuador
#> 8 BR1 Brachyplatystoma rousseauxii 53.1 609487. Ca Ecuador
#> 9 BR1 Brachyplatystoma rousseauxii 60.7 759480. Ca Ecuador
#> 10 BR1 Brachyplatystoma rousseauxii 68.3 509173. Ca Ecuador
#> # ℹ 7,025 more rows
table(dat$species)
#>
#> Brachyplatystoma filamentosum Brachyplatystoma rousseauxii Prochilodus nigricans
#> 1125 3612 2298
if (FALSE) {
### trace element profile figure
library(dplyr)
library(tidyr)
library(ggplot2)
### Brachyplatystoma rousseauxii
dat[which(dat$species == "Brachyplatystoma rousseauxii" &
dat$locality == "Ecuador"), ]
B_rousseauxii |>
pivot_wider(
names_from = oto_element,
values_from = value
) |>
ggplot(aes(distance, (Ba / Ca) * 1000)) +
geom_line(aes(col = locality), show.legend = F, linewidth = 0.02, na.rm = T) +
labs(
x = (expression(
paste("Distance from fish otolith cores – edge transects (", mu, "m)",
sep = ""))),
y = ("(Ba/Ca)x1000")
) +
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")
)
B_rousseauxii |>
pivot_wider(
names_from = oto_element,
values_from = value
) |>
ggplot(aes(distance, (Sr / Ca) * 1000)) +
geom_line(aes(col = locality), show.legend = F, linewidth = 0.02, na.rm = T) +
labs(
x = (expression(
paste("distance from fish otolith cores – edge transects (", mu, "m)",
sep = ""))),
y = ("Sr/Ca")
) +
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")
)
}