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

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.

本元数据对应论文《表型可塑性与遗传多态性：蓝鳍鳉（bluefin killifish）种群内部及种群间的可塑性遗传变异与体色变异》的关联数据，为文件"Killifish_plasticity.csv"中数据的详细说明。

本研究对春季种群（spring population）与沼泽种群（swamp population）的雌雄个体开展了一系列杂交实验。针对每个种群，我们尝试获取代表4种主要体色模式的2尾雄性个体（详见第8列）。同时，我们尝试将每一尾雄性亲本与两尾独立的雌性亲本（通常记为雌亲a与雌亲b）进行杂交。对于每一组父本-雌亲组合，我们计划获取50枚鱼卵，并将其均分至两个养殖缸中：一个缸内为模拟春季种群生境的清水，另一个缸内为模拟沼泽种群生境的茶色水。将幼体饲养至性成熟后，对其体色进行评分。基于上述实验，我们分析了杂交组合、雄性体色模式以及水处理（即光照环境）对雄性体色表达的影响。本数据集对应的R脚本为"Killifish_plasticity_Fulleretal_script1.R"、"Killifish_plasticity_Fulleretal_script2.R"、"Killifish_plasticity_Fulleretal_script3.R"与"Killifish_plasticity_Fulleretal_script4.R"。

### 列1至列28详细说明
列1："tank"——养殖缸编号。该编号反映了父本ID（数字形式）、雌亲ID（字母形式）以及养殖水体类型（茶色水或清水）。
列2："sire"——父本的数字编码。
列3："dam"——雌亲的字母编码ID。
列4："malepop"——父本所属种群，为春季种群或沼泽种群。
列5："femalepop"——雌亲所属种群，为春季种群或沼泽种群。
列6："cross"——亲本种群来源组合，共4种杂交类型：(1) 沼泽种群雄性×沼泽种群雌性，记为"swmxswf"；(2) 沼泽种群雄性×春季种群雌性，记为"swmxspf"；(3) 春季种群雄性×沼泽种群雌性，记为"spmxswf"；(4) 沼泽种群雄性×沼泽种群雌性，记为"swmxswf"。
列7："water"——养殖水体类型，为清水或茶色水。
列8："malecolorpattern"——父本的体色模式，共4种可能的类型：(1) 背鳍后部呈红色、臀鳍为纯红色的雄性个体，记为"rr"（详见补充图1a）；(2) 背鳍后部呈黄色、臀鳍为纯红色的雄性个体，记为"yy"（详见补充图1b）；(3) 背鳍后部呈红色、臀鳍为纯蓝色的雄性个体，记为"rb"（详见补充图1e）；(4) 背鳍后部呈黄色、臀鳍为纯蓝色的雄性个体，记为"yb"（详见补充图1f）。
列9："Color_blue"——父本臀鳍是否为纯蓝色。"rb"与"yb"型个体记为"blue"；"rr"与"yy"型个体记为"not blue"。
列10："swamp_other"——杂交组合是否均由沼泽种群的父本与雌亲组成。"swmxswf"型杂交记为"swamp"；其余3种涉及春季种群父本和/或雌亲的杂交类型记为"other"。
列11："females"——该养殖缸中雌性个体的总数。
列12："totalmaleswithcolor"——该养殖缸中可记录体色模式的雄性个体总数。
列13："totalsolidred"——该养殖缸中臀鳍为纯红色的雄性个体总数。
列14："totalsolidblue"——该养殖缸中臀鳍为纯蓝色的雄性个体总数，包含补充图1中的C、D、E、F、L、M与P号雄性个体。
列15："totalsolidyellow"——该养殖缸中臀鳍为纯黄色的雄性个体总数，包含补充图1中的B与K号雄性个体。
列16："totalanyyellow"——该养殖缸中背鳍后部、臀鳍或腹鳍带有黄色的雄性个体总数，包含补充图1中的B、D、F、H、J、K与L号雄性个体。
列17："totalanyred"——该养殖缸中背鳍后部、臀鳍或腹鳍带有红色的雄性个体总数，包含补充图1中的A、C、E、G与I号雄性个体。
列18："totalanyblue"——该养殖缸中臀鳍带有蓝色的雄性个体总数，包含补充图1中的C、D、E、F、L、M、P、G、H、I、J与O号雄性个体。
列19："totalsolidorange"——该养殖缸中臀鳍为纯橙色的雄性个体总数。
列20："totalanyorange"——该养殖缸中背鳍后部、臀鳍或腹鳍带有橙色的雄性个体总数，包含补充图1中的N与O号雄性个体。
列21："totalred_blue_combo"——该养殖缸中臀鳍带有红-蓝组合色的雄性个体总数，包含补充图1中的G与I号雄性个体。
列22："totalyellow_blue_combo"——该养殖缸中臀鳍带有黄-蓝组合色的雄性个体总数，包含补充图1中的H与J号雄性个体。
列22："totalorange_blue_combo"——该养殖缸中臀鳍带有橙-蓝组合色的雄性个体总数，对应补充图1中的O号雄性个体。
列23："propanyred"——可记录体色的雄性个体中，带有任意红色斑纹个体的占比，计算公式为totalanyred / totalmaleswithcolor。
列24："propanyyellow"——可记录体色的雄性个体中，带有任意黄色斑纹个体的占比，计算公式为totalanyyellow / totalmaleswithcolor。
列25："propsolidred"——可记录体色的雄性个体中，臀鳍为纯红色个体的占比，计算公式为totalsolidred / totalmaleswithcolor。
列26："propsolidyellow"——可记录体色的雄性个体中，臀鳍为纯黄色个体的占比，计算公式为totalsolidyellow / totalmaleswithcolor。
列27："propsolidblue"——可记录体色的雄性个体中，臀鳍为纯蓝色个体的占比，计算公式为totalsolidblue / totalmaleswithcolor。
列28："propanyblue"——可记录体色的雄性个体中，臀鳍带有蓝色斑纹个体的占比，计算公式为totalanyblue / totalmaleswithcolor。

### 文件"attenuation_light.csv"数据说明
该数据为埃弗格莱兹湿地（Everglades）26 Mile Bend点位与瓦古拉河（Wakulla River）点位的下行辐照度光谱（downwelling irradiance spectrum）。光谱数据于2017年5月与6月使用Ocean Optics S2000型分光光度计采集，以氘-卤灯光源（deuterium-halogen light source）进行校准。光谱采集时，将Ocean Optics余弦校正器（cosine-corrector）连接至延长线，分别在水面上方（0 cm）、水面下方1 cm处以及38 cm深度处进行多次光谱测量。测量于晴朗天气的上午中旬开展。针对每一组深度与种群组合，将重复采集的光谱数据取平均值。本数据集对应的R脚本为"Downwellling_spectra.R"。

### 该文件列1至列4详细说明
列1："wavelength"——波长数据，以2 nm为间隔，范围为300至750 nm。
列2："photons"——光子通量数据，单位为photons/cm²/s/nm。
列3："pop"——种群编号，共两种："glades"（埃弗格莱兹湿地的沼泽种群）与"wakulla"（以泉水补给的瓦古拉河春季种群）。
列4："depth"——测量深度，单位为厘米，分别记录了水面（0 cm）、水面下方1 cm处以及38.1 cm深度处的下行辐照度。