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Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations

Citation

Fuller, Rebecca et al. (2022), Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations, Dryad, Dataset, https://doi.org/10.5061/dryad.f4qrfj6xk

Abstract

The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained.  Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both.  Color patterns in male bluefin killifish provoke both types of questions.  Red and yellow morphs are common in all populations.  Blue males are more common in tannin-stained swamps relative to clear springs.  Here we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns.  We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.

Methods

There are two primary data sets here.

Data set #1: Color morph frequences across treatments:

In this study, we conducted a series of crosses between males and females from a spring and a swamp population. For each population, we attempted to get 2 males that were represented of 4 major color patterns (see column 8). We also attempted to cross the male with two separate dams (usually denoted as dam a and dam b). For each sire-dam combination, we sought to obtain 50 eggs which were divided between two tanks: one with clear water that mimicked springs and the other with tea-stained water that mimicked swamps.  We raised the individuals to adulthood and scored them for coloration. From these, we examined the effects of cross, male color pattern, and water treatment (i.e., lighting environment) on the expression of male coloration.

Data Set #2: Downwelling irradiance data:

Downwelling irradiance spectrum from the Everglades site (26 Mile Bend) and the Wakulla River.  Spectra were collected in May and June 2017 with an Ocean Optics S2000 spectrophotometer.  The spectrophotometer was calibrated with a deuterium-halogen light source. Spectra were taken with an Ocean Optics cosine-corrector attached to a patch cord. Multiple spectra were taken slightly above the water surface (0 cm), slightly below the water surface (1 cm) and at 38 cm depth.  Measurements were taken at sunny conditions in the mid-morning. Replicate spectra were averaged at for each combination of depth and population.

Usage Notes

Meta-Data for Data Associated with the Article “Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations

Explanations for the data in the file “Killifish_plasticity.csv”.

In this study, we conducted a series of crosses between males and females from a spring and a swamp population. For each population, we attempted to get 2 males that were represented of 4 major color patterns (see column 8). We also attempted to cross the male with two separate dams (usually denoted as dam a and dam b). For each sire-dam combination, we sought to obtain 50 eggs which were divided between two tanks: one with clear water that mimicked springs and the other with tea-stained water that mimicked swamps.  We raised the individuals to adulthood and scored them for coloration. From these, we examined the effects of cross, male color pattern, and water treatment (i.e., lighting environment) on the expression of male coloration.

The R scripts ‘Killifish_plasticity_Fulleretal_script1.R, Killifish_plasticity_Fulleretal_script2.R, Killifish_plasticity_Fulleretal_script3.R, and Killifish_plasticity_Fulleretal_script4.R refer to these data’.

Column 1: “tank” – This is the code that was given to each tank of fish. It reflects the sire ID (as a number), the dam ID (as a letter), and whether the fish were held in tea or clear water.

Column 2: “sire” – The sire numerical code.

Column 3: “dam” – The ID of the dam as an alphabetical code.

Column 4: “malepop” – Whether the sire was from the spring or the swamp population.

Column 5: “femalepop” – Whether the dam was from the spring or the swamp population.

Column 6: “cross” – This indicates the combination of the male and female population of origin.  There were 4 cross types: (1) swamp male x swamp female “swmxswf”, (2) swamp male x spring female “swmxspf”, (3) spring male x swamp female “spmxswf”, and (4) swamp male x swamp female “swmxswf”.

Column 7: “water” – Whether the fish were reared in clear or tea-stained water

Column 8: “malecolorpattern” – This indicates the color pattern of the sire.  There were four potential color patterns: (1) males with a red rear dorsal fin and solid red anal fin, “rr”(see supplemental figure 1a), (2) males with a yellow rear dorsal fin and yellow red anal fin, “yy”(see supplemental figure 1b), (3) males with a red rear dorsal fin and solid blue anal fin, “rb”(see supplemental figure 1e), (4) males with a yellow rear dorsal fin and solid blue anal fin, “yb”(see supplemental figure 1f).

Column 9: “Color_blue” – Whether or not the sire had a solid blue anal fin. ‘rb’ and ‘yb’ males were coded as ‘blue’; ‘rr’ and ‘yy’ males were coded as ‘not blue’.

Column 10: “swamp_other” – Whether or not the cross involved both a swamp sire and dam.  “swmxswf” crosses were denoted as “swamp”. The other three cross types, which involved spring sires and/or dams were denoted as “other”.

Column 11: “females” – total number of females

Column 12: “totalmaleswithcolor” – the number of males in the tank for whom we could record the color pattern.

Column 13: “totalsolidred” – The total number of males in the tank with solid red anal fins.

Column 14: “totalsolidblue” – The total number of males in the tank with solid blue anal fins. This includes males C, D, E, F, L, M, and P from supplemental figure 1.

Column 15: “totalsolidyellow” – The total number of males with solid yellow anal fins. This includes males B and K from supplemental figure 1.

Column 16: “totalanyyellow” – The total number of males with any yellow on their rear dorsal, anal, or pelvic fins.  This includes males B, D, F, H, J, K, and L from supplemental figure 1.      

Column 17: “ totalanyred” – The total number of males with any red on their rear dorsal, anal, or pelvic fins. This includes males A, C, E, G, and I from supplemental figure 1.

Column 18: “totalanyblue” – The total number of males with any blue on their anal fins. This includes males C, D, E, F, L, M, P, G, H, I, J, and O from supplemental figure 1.

Column 19: “totalsolidorange” – The total number of males with solid orange anal fins.

Column 20: “totalanyorange “ – The total number of males with any orange on their rear dorsal, anal, or pelvic fins. This includes males N and O from supplemental figure 1.

Column 21: “totalred_blue_combo” – The total number of males with a combination of red and blue on their anal fins. This includes males G and I from supplemental figure 1.

Column 22: “totalyellow_blue_combo” – The total number of males with a combination of yellow and blue on their anal fins.       This includes males H and J from supplemental figure 1.

Column 22: “totalorange_blue_combo” – The total number of males with combination orange and blue on their anal fins. See male O from supplemental figure 1.

Column 23: “propanyred” – the proportion of males with any red given the total number of males with coloration.  totalanyred/totalmaleswithcolor

Column 24: “propanyyellow” - the proportion of males with any yellow given the total number of males with coloration.  totalanyyellow/totalmaleswithcolor         

Column 25: “propsolidred” – the proportion of males with solid red anal fins given the total number of males with coloration. totalsolidred/totalmaleswithcolor

Column 26: “propsolidyellow” - the proportion of males with solid yellow anal fins given the total number of males with coloration. totalsolidyellow/totalmaleswithcolor

Column 27: “propsolidblue” - the proportion of males with solid blue anal fins given the total number of males with coloration. totalsolidblue/totalmaleswithcolor

Column 28: “propanyblue” – the proportionof males with any blue on their anal fins given the total number of males with coloration. totalanyblue/totalmaleswithcolor


Explanations for Data in attenuation_light.csv

Downwelling irradiance spectrum from the Everglades site (26 Mile Bend) and the Wakulla River.  Spectra were collected in May and June 2017 with an Ocean Optics S2000 spectrophotometer.  The spectrophotometer was calibrated with a deuterium-halogen light source. Spectra were taken with an Ocean Optics cosine-corrector attached to a patch cord. Multiple spectra were taken slightly above the water surface (0 cm), slightly below the water surface (1 cm) and at 38 cm depth.  Measurements were taken at sunny conditions in the mid-morning. Replicate spectra were averaged at for each combination of depth and population.

The R script ‘Downwellling_spectra.R’ refers to these data.

Column 1: “wavelength” – data are given in 2 nm intervals from 300 to 750 nm.

Column 2: “photons” – photons are given in units of photons/cm2/s/nm.

Column 3: “pop” – this stands for population.  The two populations are ‘glades’ and ‘wakulla’. ‘Glades’ refers to our swamp population in the Everglades.  ‘Wakulla’ refers to our spring site on the spring-fed Wakulla river.

Column 4: “depth” – depth is given in centimeters. We recorded the downwelling irradiance at the surface (0 cm), slight below the surface (1cm), and at a depth of 38.1 cm. 

Funding

National Science Foundation, Award: IOB-0445127