bt.feyrer.2020.RdThis study examined the habitat ecology of two lagoon species, the endangered Tidewater Goby (Eucyclogobius newberryi) and the Prickly Sculpin (Cottus asper) by reconstructing individual life histories from patterns in the concentration of the element Sr (as ratioed to Ca; Sr:Ca) in otoliths.Specific objectives were to (1) elucidate any movements of individual fishes among three primary habitat components of typical bar-built lagoon systems: coastal ocean, brackish lagoon, and freshwater watershed streams, and (2) determine if either species exhibited a standard life history as defined by a prototypical otolith Sr:Ca chronology, which could be indicative of a standard range of salinity or temperature occupied through ontogeny.
bt.feyrer.2020The data frame 5,734 × 11 contains the following columns:
| fish_id | integer | fish identifier |
| distance | numeric | distance from the core to the edge of otolith (microns) |
| value | numeric | Sr:Ca or Mn:Ca |
| element | character | trace element |
| common_name | character | species common name |
| scientific_name | character | species scientific name |
| location | character | location of capture |
| date | character | date of capture |
| standard_length | numeric | standard length (mm) |
| weight | numeric | fish weight (g) |
| otolith_radius | numeric | otolith_radius (microns) |
This dataset contains otolith elemental raw data of two coastal lagoon fishes from around the perimeter of Rodeo Lagoon following a hypoxia-induced fish kill that occurred on 08 August 2016. Additional Prickly Sculpins were collected on 12 April 2016 from Rodeo Lagoon using a beach seine and from Rodeo Creek using a minnow trap. In total, 14 Tidewater Gobies (mean standard length = 40 mm, standard deviation = 2) and 10 Prickly Sculpins (mean standard length = 62 mm, standard deviation = 12) were examined.
Instrument: SXFM (scanning x-ray fluorescence imaging)
Feyrer, F., Young, M., Fong, D., Limburg, K., & Johnson, R. (2020). Cryptic Lives of Conspicuous Animals: Otolith Chemistry Chronicles Life Histories of Coastal Lagoon Fishes. Frontiers in Marine Science, 7, 417.
https://doi.org/10.3389/fmars.2020.00417
Data availability are available at https://doi.org/10.5066/P9PZMELL
Traversing the paper's information via Semantic Scholar ID 57c668a6b12ca55f2534f448db15ddbe8212c2f9 using S2miner package
otolith, trace element, Sr/Ca, Mn/Ca
### copy data into 'dat'
dat <- bt.feyrer.2020
tibble::tibble(dat)
#> # A tibble: 5,734 × 11
#> fish_id distance value element common_name scientific_name location date standard_length weight
#> <int> <int> <dbl> <chr> <chr> <chr> <chr> <chr> <int> <dbl>
#> 1 6 0 0.00389 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 2 6 1 0.00395 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 3 6 2 0.00393 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 4 6 3 0.00393 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 5 6 4 0.00395 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 6 6 5 0.00405 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 7 6 6 0.00402 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 8 6 7 0.00398 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 9 6 8 0.00394 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> 10 6 9 0.00411 Sr_Ca Tidewater G… " Eucyclogobiu… Rodeo L… 8/16… 38 0.64
#> # ℹ 5,724 more rows
#> # ℹ 1 more variable: otolith_radius <dbl>
if (FALSE) {
### load package
library(dplyr)
library(ggplot2)
### otolith sr/ca
ggplot(data = dat[which(dat$element == "Sr_Ca" & dat$value < 0.02), ],
aes(distance, value)) +
geom_line(aes(colour = common_name, group = fish_id), show.legend = F, na.rm = T) +
facet_grid(common_name ~ ., scales = "free_y") +
xlab("Distance from the core to the edge of otolith (mm)") +
ylab("Otolith 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")
)
### otolith mn/ca
ggplot(data = dat[which(dat$element == "Mn_Ca" & dat$value < 0.001),],
aes(distance, value)) +
geom_line(aes(colour = common_name, group = fish_id), show.legend = F, na.rm = T) +
facet_grid(common_name ~ ., scales = "free_y") +
xlab("Distance from the core to the edge of otolith (mm)") +
ylab("Otolith Mn: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")
)
}