DOI: 10.5061/dryad.6m905qg59
title: Data from: Intraspecific variation in color and carotenoids across environmental extremes in an African Cichlid

description: 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.
description: These data were collected using photographs and a
 spectrophotomer. Data were analyazed and processed in R.
description: Data can be viewed using excel and analyzed in R.
description: # Intraspecific Variation in Color and Carotenoids Across Environmental
 Extremes 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.](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.