DOI: 10.5061/dryad.f4qrfj6xk
title: Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations

description: 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.
description: There are two primary data sets here.
 <strong>Data set #1: Color morph frequences across
 treatments: </strong> 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. <strong>Data Set #2: Downwelling
 irradiance data:</strong> 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.
description: Meta-Data for Data Associated with the Article
 “<strong>Polyphenisms and polymorphisms: genetic variation in
 plasticity and color variation within and among bluefin killifish
 populations</strong>” <strong>Explanations for the data
 in the file “Killifish_plasticity.csv”.
 </strong> 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 <strong>Explanations
 for Data in attenuation_light.csv</strong>
 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.