bt.saboret.2019.RdIt is shown that early life environment can have multiple effects on adult performance and ecology, with the potential for lifetime fitness trade‐offs associated with life history, and that even relatively minor variation in rearing conditions may be enough to generate individual variation in natural populations.
bt.saboret.2019The data frame 142 × 21 contains the following columns:
| id | character | fish identifier |
| type | character | fish were used for two distinct set of analysis, referred to as behaviour or diet |
| sex | character | fish sex |
| site | character | site of capture |
| trap | character | trap name |
| utm59e | integer | east GPS coordinates of capture in Universal Transverse Mercator 59 system |
| utm59n | integer | north GPS coordinates of capture in Universal Transverse Mercator 59 system |
| cluster | character | cluster of fish according to their capture locations: UL (upstream lake), NL (north lake), EL (east lake), SL (south lake), DL (downstream lake) |
| length | numeric | total length (mm) |
| weight | numeric | weight (g) |
| gonade_w | numeric | gonad weight (g) |
| srlarvae | numeric | sr/ca (mmol.mol^(-1)) of otolith core (larval environment) |
| balarvae | numeric | ba/ca (mmol.mol^(-1)) of otolith core (larval environment) |
| sradult | numeric | sr/ca (mmol.mol^(-1)) of otolith edge (adult environment) |
| baadult | numeric | ba/ca (mmol.mol^(-1)) of otolith edge (adult environment) |
| increment1 | numeric | distance from the otolith core to the metamorphosis check (mm) |
| increment2_4 | numeric | distance from otolith annulus i-1 to annulus i (mm) |
| otolithradius | numeric | distance from the otolith core to the edge (mm), measured independently |
| age | integer | estimated age based on annuli numbers |
The dataset contains otolith microchemistry of common bullies (Gobiomorphus cotidianus) collected on February 12-13 2018 in lake Waipori system, South Island, New Zealand. NA indicates missing data.
Instrument: Q-ICP-MS (quadrupole inductively coupled plasma mass spectrometry);IRMS (isotope ratio mass spectrometer)
Beam diameter: 90um
Reference materials: NIST-610,NIST-612 (National Institutes of Standards and Technology glass standard) and MACS-3 (United States Geological Survey microanalytical carbonate standard pressed pellet)
Saboret, G., & Ingram, T. (2019). Carryover effects of larval environment on individual variation in a facultatively diadromous fish. Ecology and Evolution, 9(18), 10630-10643. https://doi.org/10.1002/ece3.5582
Data availability are available at https://doi.org/10.5061/dryad.852h5m8
Traversing the paper's information via Semantic Scholar ID f6cde67aebe2af146d831b61c472f17b393b4dbe using S2miner package
otolith, trace element, Sr/Ca, Ba/Ca
### copy data into 'dat'
dat <- bt.saboret.2019
tibble::tibble(dat)
#> # A tibble: 142 × 21
#> id type sex site trap utm59e utm59n cluster length weight gonade_w srlarvae balarvae
#> <chr> <chr> <chr> <chr> <chr> <int> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 L4RY Behaviour NA Waipori NA NA NA NA 52.7 NA NA 0.852 0.00177
#> 2 U2LO Behaviour M Upstream NA NA NA UL 55.0 NA NA 1.02 0.00164
#> 3 L12VY Behaviour M Waipori NA NA NA NA 48.4 NA NA 0.996 0.00158
#> 4 U2VY Behaviour NA Upstream NA NA NA UL 52.1 NA NA 0.913 0.00111
#> 5 L11LY Behaviour F Waipori NA NA NA NA 54.9 NA NA 0.989 0.00202
#> 6 U1RY Behaviour M Upstream NA NA NA UL 47.0 NA NA 0.856 0.00201
#> 7 L13VY Behaviour F Waipori NA NA NA NA 51.0 NA NA 1.18 0.00214
#> 8 U1LO2 Behaviour M Upstream NA NA NA UL NA NA NA NA NA
#> 9 L1VY Behaviour M Waipori NA NA NA NA 48.1 NA NA 0.899 0.00157
#> 10 D1LO Behaviour F Downstr… NA NA NA DL 49.9 NA NA 1.05 0.00191
#> # ℹ 132 more rows
#> # ℹ 8 more variables: sradult <dbl>, baadult <dbl>, increment1 <dbl>, increment2 <dbl>,
#> # increment3 <dbl>, increment4 <dbl>, otolithradius <dbl>, age <int>
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
library(tidyr)
### Sr/Ca profile figure
dat[, c(1, 3, 12, 14)] |> pivot_longer(
cols = srlarvae:sradult,
names_to = "life_history",
values_to = "sr_ca"
) -> dat1
dat1$life_history <- ifelse(dat1$life_history == "sradult", "Otolith edge", "Otolith core")
ggplot(data = dat1, aes(life_history, sr_ca)) +
geom_boxplot(aes(col = sex), show.legend = F, na.rm = T) +
facet_grid(. ~ sex) +
ylab("Sr/Ca (mmol.mol^(-1))") +
xlab("") +
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
dat[, c(1, 3, 13, 15)] |> pivot_longer(
cols = balarvae:baadult,
names_to = "life_history",
values_to = "ba_ca"
) -> dat2
dat2$life_history <- ifelse(dat2$life_history == "Baadult", "Otolith edge", "Otolith core")
ggplot(data = dat2, aes(life_history, ba_ca)) +
geom_boxplot(aes(col = Sex), show.legend = F, na.rm = T) +
facet_grid(. ~ Sex) +
ylab("Ba/Ca (mmol.mol^(-1))") +
xlab("") +
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")
)
}