bt.young.2022.RdIn this study, the authors used stable isotope values of eye lenses to provide complimentary information on habitat utilization by a threatened cyprinid, Clear Lake Hitch (Lavinia exilicauda chi). Clear Lake Hitch inhabit a single lake (Clear Lake, Lake County, California) and utilize tributary streams for reproduction. Despite recent advances, there remain key uncertainties about Clear Lake Hitch habitat use. Analysis of d13C and d15N recorded in eye lenses demonstrates ontogenetic diet shifts that corresponded with shifts in habitat. Reconstruction of size-structured trophic and habitat information provides critical information to resource managers.
bt.young.2022The data frame 1,050 × 13 contains the following columns:
| fish_id | integer | an identifying number for the individual fish |
| eye_side | character | indicates which eye (left or right) the sample comes from |
| layer_number | integer | Indicates which layer of the eye was sampled. Layer 1 is the whole eye, and the highest number is the eye core |
| isotope | character | indicates which isotope was analyzed |
| dx_value | numeric | stable isotope value expressed in standard delta notation relative to a standard |
| width_mean | numeric | mean width of eye layer in micrometers (um) |
| species | character | species of the individual |
| species_code | character | three-to-four letter code indicating taxonomy of sampled individual |
| date | character | the date (MM/DD/YYYY) the sample was collected |
| latitude | numeric | the latitudinal coordinate that indicates the location of a sample (Datum is WGS 84) |
| longitude | numeric | the longitudinal coordinate that indicates the location of a sample (Datum is WGS 84) |
| standard_length | numeric | standard length in millimeters (mm) of individual |
| weight | numeric | weight in grams (g) of individual |
This dataset includes data from isotopic analysis of eye tissue from fish collected in Clear Lake, Lake County, California during June and July 2017. This data release includes all biological measurements and fish taxa included in the analysis.
Instrument: EA-IRMS (elemental analyzer–isotope ratio mass spectrometry)
Young, M. J., Larwood, V., Clause, J. K., Bell-Tilcock, M., Whitman, G., Johnson, R., & Feyrer, F. (2022). Eye lenses reveal ontogenetic trophic and habitat shifts in an imperiled fish, Clear Lake hitch (Lavinia exilicauda chi). Canadian Journal of Fisheries and Aquatic Sciences, 79(1), 21-30.
https://doi.org/10.1139/CJFAS-2020-0318
Data availability are available at http://dx.doi.org/10.5066/P98S3SBV
Traversing the paper's information via Semantic Scholar ID fec4b15688e13ab45b0bc28fa89be7aaa1f5ebe4 using S2miner package
eye lenses, stable isotope, d13C, d15N
### copy data into 'dat'
dat <- bt.young.2022
tibble::tibble(dat)
#> # A tibble: 1,050 × 13
#> fish_id eye_side layer_number isotope dx_value width_mean species species_code date latitude
#> <int> <chr> <int> <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl>
#> 1 1 L 1 d13C -23.7 2592 Lavinia exil… HCH 7/20… 39.0
#> 2 1 L 2 d13C -24.7 2341 Lavinia exil… HCH 7/20… 39.0
#> 3 1 L 3 d13C -23.0 1972. Lavinia exil… HCH 7/20… 39.0
#> 4 1 L 4 d13C -22.1 1866. Lavinia exil… HCH 7/20… 39.0
#> 5 1 L 5 d13C -22.2 1712 Lavinia exil… HCH 7/20… 39.0
#> 6 1 L 6 d13C -21.0 1582. Lavinia exil… HCH 7/20… 39.0
#> 7 1 L 7 d13C -20.6 1508. Lavinia exil… HCH 7/20… 39.0
#> 8 1 L 8 d13C -19.7 1400. Lavinia exil… HCH 7/20… 39.0
#> 9 1 L 9 d13C -18.1 1279 Lavinia exil… HCH 7/20… 39.0
#> 10 1 L 10 d13C -17.5 1166. Lavinia exil… HCH 7/20… 39.0
#> # ℹ 1,040 more rows
#> # ℹ 3 more variables: longitude <dbl>, standard_length <int>, weight <dbl>
if (FALSE) {
### load package
library(dplyr)
library(ggplot2)
### eye lenses d13C
ggplot(data = dat[which(dat$isotope == "d13C"),],aes(width_mean, dx_value)) +
geom_point(aes(group = fish_id,colour = species),shape = 1, size = 2,
show.legend = F, na.rm = T)+
geom_line(aes(group = fish_id, colour = species),
show.legend = F, na.rm = T) +
facet_grid(eye_side ~ species, scales = "free_y") +
xlab("Mean width of eye layer in micrometers (um)") +
ylab(expression(delta * ""^13 * "C" * " (‰)")) +
theme_bw() +
theme(
panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(colour = "black"),
text = element_text(size = 10), legend.title = element_blank(),
plot.title = element_text(face = "bold")
)
### eye lenses d15N
ggplot(data = dat[which(dat$isotope == "d15N"),],aes(width_mean, dx_value)) +
geom_point(aes(group = fish_id,colour = species),shape = 1, size = 2,
show.legend = F, na.rm = T)+
geom_line(aes(group = fish_id, colour = species),
show.legend = F, na.rm = T) +
facet_grid(eye_side ~ species, scales = "free_y") +
xlab("Mean width of eye layer in micrometers (um)") +
ylab(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")
)
}