Data from: Intraspecific variation in color and carotenoids across environmental extremes in an African Cichlid
Data files
Mar 17, 2025 version files 60.61 MB
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Broodinfo.xlsx
9.97 KB
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Carotenoid_Fish_info.xlsx
20.51 KB
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Carotenoids_all.xlsx
71.64 KB
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Carotenoids_Plasmavolume.xlsx
9.62 KB
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Carotenoids_protein_upload.xlsx
15.40 KB
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Carotenoids_RearingInfo.xlsx
15.99 KB
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README.md
6.41 KB
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Rearing_Processing_Color.xlsx
18.89 KB
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Rearing_renamed.zip
60.39 MB
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Rearingspecfullspectrum.xlsx
48.32 KB
Abstract
Human activities frequently alter environmental conditions and affect the use of sexually selected traits like color in animals. However, the effects of environmental stressors are unlikely to be uniform across populations that experience different environments or between sexes. We aimed to understand the underlying genetic, environmental, and gene-by-environment contributions to color expression in males and females of a sexually dimorphic fish. Pseudocrenilabrus multicolor is a haplochromine cichlid found in environments that vary dramatically, particularly with respect to oxygen and turbidity levels. We reared fish from one swamp (hypoxic, clear) and one river (normoxic, turbid) population in a split-brood design (hypoxic/normoxic x clear/turbid) then quantified color and carotenoid concentrations. As expected in this sexually dimorphic species, females were far less colorful than males. In males, hypoxia and turbidity were drivers of traits associated with color, suggesting that color was modified under energetically or visually unfavorable conditions. Males in the hypoxic treatment from both populations were not as bright as males reared under normoxic conditions, which corresponds to results observed in wild fish. Males reared in turbid conditions were also marginally less bright along the ventral surface than males reared in clear water. Rearing under turbid conditions reduced carotenoid concentrations in male skin, but carotenoids were not correlated with spectral characteristics of male color. We did not find effects of population on color traits, suggesting that differences in color between wild populations are due to plastic rather than fixed genetic effects. Overall, we provide evidence that hypoxia and turbidity affect signaling traits, though the consequences for mating success remain to be determined.
This dataset includes color and carotenoid data of the cichlid Pseudocrenilabrus multicolor in response to rearing under hypoxic and turbid conditions. This dataset includes eight excel files and two R scripts, Spec_final.R and Carotenoids_rscript_final.R. Both scripts were analyzed using R version 4.3.0. Cells were left blank if a particular value could not be calculated for that individual.
Spec_final.R uses the input files: Rearing_Renamed.zip, Carotenoid_Fish_info.xlsx, Broodinfo.xlsx, and creates the file Rearingspecfullspectrum.xlsx, which is used in the next script.
Carotenoids_rscript_final.R uses the input files: Carotenoids_all.xlsx, Carotenoids_protein.xlsx, Broodinfo.xlsx, Carotenoids_Plasmavolume.xlsx, Rearingspecfullspectrum.xlsx, Carotenoid_Fish_info.xlsx, Rearing_Processing_Color.csv, Carotenoids_RearingInfo.xlsx
Description of the data and file structure
Rearing_Renamed.zip
This zip folder contains the jaz files that are analyzed in the R script. Jaz files can be viewed and were analyzed in R, but they can also be opened in a text editor or in excel. Each jaz file represents the spectral measurements for a single spot on an individual fish. Jaz files were used to derive the color values in the Rearingspecfullspectrum.xlsx file. Each file name contains information on the treatment (HC= hypoxic/clear, HT= hypoxic/turbid,NT=normoxic/turbid, NC= normoxic/clear), population (LWA= lwamunda swamp, NYA= nydabusole river), Fish ID, position name (Belly 1-3, Peduncle4, Blank, Dorsal, Lip), and position sequence (1-9). For example, file LWA_HC_JB193_Belly1_5.jaz contains the spectral data of the belly 1 position (the fifth measurement in the measurement sequence) for the fish JB193 which was a swamp fish in hypoxic/clear conditions.
Carotenoid_Fish_info.xlsx
This datasets includes basic information on fish such as their id, the tank they came from, sex, and size.
Fish: Fish id number
Reartank: The tank the fish was reared in
TL: Total length, length from tip of snout to end of tail in cm
SL: Standard length, length from tip of snout to caudal pedunce in cm
Sex: F= female, M= male
Brooding: Was fish brooding at time of sampling (Y= Yes, N= No, NA= Not applicable for males)
Broodinfo.xlsx
This dataset includes the name of the brood from each reartank
Reartank: The tank the fish was reared in
Brood: The name of the fish brood to keep track of sibling identity
Carotenoids_all.xlsx
This dataset contains information on the HPLC runs that are used to calculate carotenoid concentrations
Sample: Sample type (skin or gonad)
Fish: Fish id number
Rtime: HPLC retention time
Area: HPLC area under curve, used to calculate carotenoid concentration
Type: Type of carotenoid (keto-carotenoid or other)
Notes: any notes on sample, left empty if there was nothing to note
Carotenoids protein upload.xlsx
This dataset contains information on the protein concentration in each sample.
Fish: Fish id number
Sample: Sample type (skin or gonad)
Absorbance: absorbance measured by spectrophotomer
Dilution: the amount the protein was diluted by
Protein_dilutioncorrectedugperml: the protein concentration (g/mL)
Carotenoids_Plasmavolume.xlsx
This dataset has the amount of plasma that was used to run the HPLC
Fish: Fish id number
Plasmaul: Volume of plasma in L
Rearingspecfullspectrum.xlsx
This dataset contains various color descriptors generated from the Pavo R package. Cells are empty if a particular value couldn’t be computed for that individual (i.e., they didn’t have a distinct spectral peak). For more detailed description of each color descriptor see Pavo’s manual: https://book.colrverse.com/spectral-shape-descriptors.html.
B1:Total brightness across entire spectral range, %
B2: Mean brightness, mean reflectance across spectral range %
B3: Reflectance max, reflectance at wavelength of maximum reflectance %
S1U: Chroma, Relative contribution of a spectral range to total brightness (300-400nm)
S1V:Chroma, Relative contribution of a spectral range to total brightness (400-415 nm)
S1B:Chroma, Relative contribution of a spectral range to total brightness (400-510 nm)
S1G:Chroma, Relative contribution of a spectral range to total brightness (510-605 nm)
S1Y:Chroma, Relative contribution of a spectral range to total brightness (550-625 nm)
S1R:Chroma, Relative contribution of a spectral range to total brightness (605-lambdamax nm)
S2: Spectral Saturation (Rmax/Rmin)
S3: Chroma: Reflectance over the Rmax+-50nm range divided by B1
S4: Spectral Purity: calculated by approximating the derivative of the spectral curve
S5: Chroma: measure of saturation, Similar in design to segment classification measures
S6: Contrast: Rmax-Rmin %
S7: Spectral Saturation: Difference between the relative reflectance before and after the wavelength
at which reflectance is halfway between its minimum (Rmin) and its maximum (Rmax)
S8: Chroma, measure of saturation (Rmax-Rmin)/B2
S9: Carotenoid Chroma, (R700- R450)/R700
S10:Peaky Chroma,(Rmax - Rmin)/B2 x |bmaxneg|. Should be used with properly smoothed
curves
H1: Hue, wavelength at maximum reflectance, nm
H2: Hue, Wavelength at bmaxneg, nm
H3: Hue, wavelength at lambda Rmid,nm
H4: Hue, arctan(By-Bb/Br-Bg), Similar in design to segment classification measures
H5: Hue, wavelength at bmax
Fish: full fish name (includes code for population and treatment in addition to fish id number)
RT: Rearing treatment, HC= hypoxic/clear, HT= Hypoxic/turbid, NC= Normoxic/clear, NT= Normoxic/Turbid
Population: Fish population of origin, LWA= lwamunda swamp, NYA= Nydabusole river
FishID: Fish id number
Rearing_Processing_Color.csv
This dataset contains the color measurements of each fish (percent red or yellow coloration)
Fish: Fish id number
Yellow: % Yellow coloration
Red: % Red coloration
Carotenoids_RearingInfo.xlsx
Basic information on rearing treatment and population for each fish.
Fish: Fish id number
Pop: Fish population, LWA= lwamunda swamp, NYA= nydabusole river
Treatment:Rearing treatment, HC= hypoxic/clear, HT= Hypoxic/turbid, NC= Normoxic/clear, NT= Normoxic/Turbid
Code/Software
This data was analyzed using R. The package Pavo was used to analyze spectrograhpic data.
These data were collected using photographs and a spectrophotomer. Data were analyazed and processed in R.
Data can be viewed using excel and analyzed in R.