Explanation of field names for the file Alyrata1105DataF2RqtlE.csv: This was the data file for input into R/qtl, used for QTL analyses of the North Carolina field site data in Remington et al. Genetics manuscript. It was generated by extracting only the Ma-Sp F2 progeny samples from the complete data file for the North Carolina field site (i.e. excluding the samples from natural populations and the Ma-Sp F1 progeny), and adding the genetic marker data for these F2 samples. Notes: Second row indicates the linkage group and third row cM position in the linkage group for each marker. Missing data are coded as "NA". ** Denotes fields that were not used in any of the analyses in the Genetics Manuscript. Pop Population: all F2. ** FamFixed Same as Fam. These two fields are redundant in this subset of the field data. Fam Reciprocal: A = Spiterstulen cytoplasm (Sp1Ma1 x Ma2Sp2 cross), B = Mayodan cytoplasm (Ma2Sp2 x Sp1Ma1 cross). ** Seed Consecutive seedling number within each reciprocal. Rep Block (or replication) in which the plant was planted in the NC field study. ** Row Row coordinate for plant in NC field site. ** Col Column coordinate for plant in NC field site. These are A-Z,AA-AT in order. Each Block had four columns, then two columns were skipped before starting the adjacent Block. Thus, there are no plants in Col E-F, K-L, etc. ** InitDiam November 2005 rosette diameter along largest axis, measured just before field planting. ("Fall diameter" in manuscript.) MeanD1_306 The mean value of Diam1_306 for the Block in which the plant was planted. This was used as a block productivity covariate in scanone and single-locus analyses, and in structural equation models. Surv306 Recorded as 1 if plant was alive for March 2006 measurement, 0 if dead. ** BoltDate Julian date at which bolting (visible elongation of assumed reproductive shoot) was first noted on the plant. (NOTE: The apparently bolting shoots never did actually flower on some plants.) FlowerDate Julian date at which first open flower was noted on the plant. Diam1_306 Pre-reproductive rosette diameter along largest axis at March 2006 measurement, in mm. ("Spring diameter" in manuscript.) ** Diam2_306 Pre-reproductive rosette diameter along second largest axis at March 2006 measurement, in mm. ** Area_306 Rosette “area” = Diam1_306*Diam2_306; NOT the true elliptical area, which would be calculated as Area_306 * pi/4. ** ShootHt306 The height above ground of the first flower to open. ** S06TotalShoots The total number of reproductive shoots (flowering shoots, or inflorescences) produced over the main 2006 reproductive season (March to late June). This was left blank if no reproductive shoots were produced. S06TotalShootsZ Same as S06TotalShoots, except that 0 was recorded for live plants at the end of the reproductive season that produced no reproductive shoots (i.e. plants for which S06Flowered = 0). ("Reproductive shoots" in manuscript.) S06Flowered Recorded as 1 if plant flowered, and as 0 if it did not. Recorded only for plants still alive in June 2006 unless they had recently died. ** S06SampledShoots The number of representative reproductive shoots that were sampled to count siliques. ** AfterColl(1/0) Recorded as 1 if siliques were counted after the sample was collected to determine seed mass and seeds/silique, and otherwise a 0. ** S06AdjSiliques If AfterColl=1, this adjusts S06TotalSiliques to account for the expected number of siliques that were collected from the sampled shoots, and converts to an integer. Specifically, a correction S06CollSiliques*S06SampledShoots/S06TotalShoots is added to the value of S06TotalSiliques. ** S06TotalSiliques The total number of siliques counted from the sampled reproductive shoots. ** S06CollSiliques The total number of siliques collected from the plant to estimate seeds per silique and seed mass. S06SilPerShoot The estimated mean number of siliques (fruits) per shoot, calculated as S06AdjSiliques/S06SampledShoots. ("Siliques per shoot" in manuscript.) ** S06Seeds The total number of seeds counted from the collected siliques. S06SeedPerSil The estimated mean number of seeds per silique (seeds per fruit), calculated as S06Seeds/S06CollSiliques. ("Seeds per silique" in manuscript.) ** S06SeedWt The total mass of the seeds obtained from the collected siliques, in mg. ** S06WtPer100 The estimated mean mass of 100 seeds, calculated as 100*S06SeedWt/S06Seeds. ("Seed mass" in manuscript.) ** ReprodOutput The estimated total reproductive output ("total seed production") of the plant, calculated as S06TotalShoots*S06SilPerShoot*S06SeedPerSil. This was recorded as NA if any of the terms were missing. ReprodOutputZ Same as ReprodOutput, except that 0 was recorded for live plants at the end of the reproductive season that produced no reproductive shoots (i.e. plants for which S06Flowered = 0). ** CollDate The Julian date on which the data on the number of reproductive shoots, the number of siliques per shoot, and June rosette diameter were collected. Surv606 Recorded as 1 if the plant was alive on CollDate, and 0 otherwise. ** Shoots606 Recorded as 1 if the plant had newly-developing reproductive shoots (not included in S06TotalShoots) on CollDate, and 0 otherwise. ** Flowering606 Recorded as 1 if the plant was flowering as of CollDate, and 0 otherwise. Diam1_606 Post-reproductive rosette diameter along largest axis at June 2006 measurement, in mm. ("Post-reproductive diameter" in manuscript.) ** Diam2_606 Post-reproductive rosette diameter along second largest axis at June 2006 measurement, in mm. ** Area_606 Rosette “area” = Diam1_606*Diam2_606; NOT the true elliptical area, which would be calculated as Area_606 * pi/4. dDiam1 Net reproductive season change (in mm) in rosette diameter along largest axis, calculated as Diam1_606-Diam1_306. ("Net reproductive season diameter growth" in manuscript.) ** dDiam2 Net reproductive season change in rosette diameter along second largest axis, calculated as Diam2_606-Diam2_306. ** dArea Net reproductive season change in rosette area, calculated as Area_606-Area_306; NOT the change in true elliptical area, which would be calculated as dArea * pi/4 Surv1106 Recorded as 1 if the plant could be identified and was alive as of late November/early December 2006, and 0 otherwise. ** Diam1_1206 Late November/early December2006 rosette diameter along largest axis on live plants, in mm. ** Diam2_1206 Late November/early December2006 rosette diameter along second largest axis on live plants, in mm. Final A unique consecutive number to identify each plant. PC1 – PC6 First through sixth principal components, based on principal components analysis of the following six traits: Diam1_306, S06TotalShootsZ, S06SilPerShoot, S06SeedPerSil, S06WtPer100, and dDiam1. These had previously been calculated from the F2 field data using prcomp in R, with Alyrata1105Data090808CombR.txt as the data file. ** Cross SNx = F2 with Spiterstulen cytoplasm, NSx = F2 with Mayodan cytoplasm. (Redundant with Fam in this subset of the field data, but with different coding.) Genot Recorded as 1 if plant was genotyped for genetic markers, and 0 if it was not genotyped (e.g. plant died before tissue for DNA isolation could be collected or DNA was unavailable). F20D22 – FRO1 Genotyped markers. Second row is the chromosome (linkage group) number, and third row is the marker location along the linkage group in cM (Kosambi map function, from previously-constructed linkage maps). Coding is as follows: Fully-informative markers: 1 = Ma1/Ma2 homozygote, 2 = Sp1/Ma2 heterozygote, 3 = Ma1/Sp2 heterozygote, 4 = Sp1/Sp2 heterozygote. F2 configuration markers: 1 = Ma homozygote, 10 = heterozygote, 4 = Sp homozygote. Partially-informative markers, polymorphic only in Ma1/Sp1 F1: 5 = Ma1/--, 6 = Sp1/--. Partially-informative markers, polymorphic only in Sp2/Ma2 F1: 7 = Ma2/--, 8 = Sp2/--. Details of genotype data and marker info can be found in Supplementary table 1 in Leppälä and Savolainen 2011 (Evolution 65:2959-2972) ------------------------------------------------------------------------- Explanation for file FieldDataNCCombined.csv: This is the data file for input into R for population-level analyses of North Carolina field site data in Remington et al. Genetics manuscript. Notes: Missing data are coded as "NA". ** Denotes fields that were not used in any of the analyses in the Genetics Manuscript. Pop Population: F1 = F1 progeny from Sp1 x Ma1 and Ma2 x Sp2 cross, F2 = F2 progeny from Sp1Ma1 x Ma2Sp2 cross, I = Ithaca, N = North Carolina (i.e. Mayodan), P = Plech, S = Spiterstulen ** FamFixed Same as Fam for F1 and F2 populations; same as Pop otherwise. Fam Family: For F2, this is the reciprocal: A = Spiterstulen cytoplasm (Sp1Ma1 x Ma2Sp2 cross), B = Mayodan cytoplasm (Ma2Sp2 x Sp1Ma1 cross). For F1: NS = Ma2 x Sp2 cross, SN = Sp1 x Ma1 cross. For populations I, N, P, and S: Identifies the full-sib family within each population. ** Seed Consecutive seedling number within each reciprocal. Rep Block (or replication) in which the plant was planted in the NC field study. ** Row Row coordinate for plant in NC field site. ** Col Column coordinate for plant in NC field site. These are A-Z,AA-AT in order. Each Block had four columns, then two columns were skipped before starting the adjacent Block. Thus, there are no plants in Col E-F, K-L, etc. InitDiam Pre-reproductive rosette diameter along largest axis at time of transplanting to field site, in mm. ("Fall diameter" in manuscript.) Surv306 Recorded as 1 if plant was alive for March 2006 measurement, 0 if dead. ** BoltDate Julian date at which bolting (visible elongation of assumed reproductive shoot) was first noted on the plant. (NOTE: The apparently bolting shoots never did actually flower on some plants.) FlowerDate Julian date at which first open flower was noted on the plant. Diam1_306 Pre-reproductive rosette diameter along largest axis at March 2006 measurement, in mm. ("Spring diameter" in manuscript.) ** Diam2_306 Pre-reproductive rosette diameter along second largest axis at March 2006 measurement, in mm. ** Area_306 Rosette “area” = Diam1_306*Diam2_306; NOT the true elliptical area, which would be calculated as Area_306 * pi/4. ** ShootHt306 The height above ground of the first flower to open. S06TotalShoots The total number of reproductive shoots (flowering shoots, or inflorescences) produced over the main 2006 reproductive season (March to late June). This was left blank if no reproductive shoots were produced. S06TotalShootsZ Same as S06TotalShoots, except that 0 was recorded for live plants at the end of the reproductive season that produced no reproductive shoots (i.e. plants for which S06Flowered = 0). ("Reproductive shoots" in manuscript.) S06Flowered Recorded as 1 if plant flowered, and as 0 if it did not. Recorded only for plants still alive in June 2006 unless they had recently died. ** S06SampledShoots The number of representative reproductive shoots that were sampled to count siliques. ** AfterColl(1/0) Recorded as 1 if siliques were counted after the sample was collected to determine seed mass and seeds/silique, and otherwise a 0. ** S06AdjSiliques If AfterColl=1, this adjusts S06TotalSiliques to account for the expected number of siliques that were collected from the sampled shoots, and converts to an integer. Specifically, a correction S06CollSiliques*S06SampledShoots/S06TotalShoots is added to the value of S06TotalSiliques. ** S06TotalSiliques The total number of siliques counted from the sampled reproductive shoots. ** S06CollSiliques The total number of siliques collected from the plant to estimate seeds per silique and seed mass. S06SilPerShoot The estimated mean number of siliques (fruits) per shoot, calculated as S06AdjSiliques/S06SampledShoots. ("Siliques per shoot" in manuscript.) ** S06Seeds The total number of seeds counted from the collected siliques. S06SeedPerSil The estimated mean number of seeds per silique (seeds per fruit), calculated as S06Seeds/S06CollSiliques. ("Seeds per silique" in manuscript.) ** S06SeedWt The total mass of the seeds obtained from the collected siliques, in mg. ** S06WtPer100 The estimated mean mass of 100 seeds, calculated as 100*S06SeedWt/S06Seeds. ("Seed mass" in manuscript.) ** ReprodOutput The estimated total reproductive output ("total seed production") of the plant, calculated as S06TotalShoots*S06SilPerShoot*S06SeedPerSil. This was recorded as NA if any of the terms were missing. ReprodOutputZ Same as ReprodOutput, except that 0 was recorded for live plants at the end of the reproductive season that produced no reproductive shoots (i.e. plants for which S06Flowered = 0). ** CollDate The Julian date on which the data on the number of reproductive shoots, the number of siliques per shoot, and June rosette diameter were collected. Surv606 Recorded as 1 if the plant was alive on CollDate, and 0 otherwise. ** Shoots606 Recorded as 1 if the plant had newly-developing reproductive shoots (not included in S06TotalShoots) on CollDate, and 0 otherwise. ** Flowering606 Recorded as 1 if the plant was flowering as of CollDate, and 0 otherwise. Diam1_606 Post-reproductive rosette diameter along largest axis at June 2006 measurement, in mm. ("Post-reproductive diameter" in manuscript.) ** Diam2_606 Post-reproductive rosette diameter along second largest axis at June 2006 measurement, in mm. ** Area_606 Rosette “area” = Diam1_606*Diam2_606; NOT the true elliptical area, which would be calculated as Area_606 * pi/4. dDiam1 Net reproductive season change (in mm) in rosette diameter along largest axis, calculated as Diam1_606-Diam1_306. ("Net reproductive season diameter growth" in manuscript.) ** dDiam2 Net reproductive season change in rosette diameter along second largest axis, calculated as Diam2_606-Diam2_306. ** dArea Net reproductive season change in rosette area, calculated as Area_606-Area_306; NOT the change in true elliptical area, which would be calculated as dArea * pi/4 Surv1106 Recorded as 1 if the plant could be identified and was alive as of late November/early December 2006, and 0 otherwise. ** Diam1_1206 Late November/early December2006 rosette diameter along largest axis on live plants, in mm. ** Diam2_1206 Late November/early December2006 rosette diameter along second largest axis on live plants, in mm. Final A unique consecutive number to identify each plant. ------------------------------------------------------------------------- Explanation for file SpMaNorwayDec2010G.csv: This was the data file for input into R/qtl, used for QTL analyses of the Norway field site data in Remington et al. Genetics manuscript. Notes: Missing data are coded as "NA" Year 1 refers to the growing season after first winter, not the planting year "Summer" refers to a time period from the beginning of June until August and "Winter" time from August until May Second row indicates the linkage group and third row cM position in the linkage group for each marker. Data collected by the plant genetics group, university of Oulu - Finland Note that almost all of the phenotypic data are included in doi:10.5061/dryad.8657 Id: individual ID of the plants in the field based on their randomized position Block: indicates in which of the eight planting blocks each plant was in Cytop: indicates the cytoplasmic origin for each plant (0=Sp;1=Ma) SurvWin1: survival status of each plant after the first winter (0=dead; 1=alive) Flow1: flowering status of each plant during the first summer (0=vegetative; 1=flowered) TotFl1: total number of flowers produced in the first summer TotSh1: total number of inflorescence shoots on each plant at the end of first summer ("Reproductive shoots" in the manuscript.) TotFr1: total number of fruits on each plant at the end of the first summer FrSh1: average number of fruits per (reproductively mature) inflorescence shoot on each plant at the end of the first summer ("Siliques per shoot" in the manuscript.) SeFrG1: average number of good-looking (not flat) seeds per fruit on each plant at the end of the first summer SeedSetGsqrt1: square root of seed set at the end of the first summer, calculated as sqrt(SeedSetG1) SeedSetG1: estimated number of good-looking seeds per plant at the end of the first summer (calculated as TotFr1 * SeFrG1) SurvWin2: survival status of each plant after the second winter (0=dead; 1=alive) Flow2: flowering status of each plant during the second summer (0=vegetative; 1=flowered) TotSh2: total number of inflorescence shoots on each plant at the end of second summer TotFr2: total number of fruits on each plant at the end of the second summer FrSh2: average number of fruits per (reproductively mature) inflorescence shoot on each plant at the end of the second summer SeFrG2: average number of good-looking (not flat) seeds per fruit on each plant at the end of the second summer SeedSetGsqrt2: square root of seed set at the end of the second summer, calculated as sqrt(SeedSetG2) SeedSetG2: estimated number of good-looking seeds per plant at the end of the second summer (calculated as TotFr2 * SeFrG2) SurvWin3: survival status of each plant after the third winter (0=dead; 1=alive) SurvWin3o: survival status of each plant after the third winter for plants alive after the second winter (0=dead; 1=alive; NA=dead prior to second winter) Flow3: flowering status of each plant during the third summer (0=vegetative; 1=flowered) TotSh3 total number of inflorescence shoots on each plant at the end of third summer TotFr3: total number of fruits on each plant at the end of the third summer FrSh3: average number of fruits per (reproductively mature) inflorescence shoot on each plant at the end of the third summer SeFrG3: average number of good-looking (not flat) seeds per fruit on each plant at the end of the third summer SeedSetGsqrt3: square root of seed set at the end of the third summer, calculated as sqrt(SeedSetG2) SeedSetG3: estimated number of good-looking seeds per plant at the end of the third summer (calculated as TotFr2 * SeFrG2) SurvWin4: survival status of each plant after the fourth winter (0=dead; 1=alive) SurvWin4o: survival status of each plant after the fourth winter for plants alive after the third winter (0=dead; 1=alive; NA=dead prior to third winter) Flow4: flowering status of each plant during the fourth summer (0=vegetative; 1=flowered) TotFr4: total number of fruits on each plant at the end of fourth summer SurvWin5: survival status of each plant after the fifth winter (0=dead; 1=alive) SurvWin5o: survival status of each plant after the fifth winter for plants alive after the fourth winter (0=dead; 1=alive; NA=dead prior to fourth winter) Flow5: flowering status of each plant during the fifth summer (0=vegetative; 1=flowered) TotFr5: total number of fruits on each plant at the end of fifth summer FlStart1: flowering start date in the first summer (Julian days from the first of January each year calculated in Excel) FlStart2: flowering start date in the second summer (Julian days from the first of January each year calculated in Excel) FlStart3: flowering start date in the third summer (Julian days from the first of January each year calculated in Excel) FlStartsqrt1: square root of the flowering start date in the first summer, relative to date of earliest observed flowering (day 149). FlStartsqrt2: square root of the flowering start date in the second summer, relative to date of earliest observed flowering (day 151). FlStartsqrt3: square root of the flowering start date in the third summer, relative to date of earliest observed flowering (day 153). AreaPla: ellipse area of rosette (in cm^2, calculated as pi*longest diameter*perpendicular diameter/4) at time of planting AreaB1W: ellipse area of rosette before first winter AreaB1W: ellipse area of rosette before first winter AreaB1Sc: ellipse area of rosette before first summer, adjusted for percentage of ellipse covered by leaves Area1Fc: ellipse area of rosette at the start of flowering the first summer, adjusted for percentage of ellipse covered by leaves AreaB2Wc: ellipse area of rosette before the second winter, adjusted for percentage of ellipse covered by leaves AreaB2Sc: ellipse area of rosette before second summer, adjusted for percentage of ellipse covered by leaves Area2Fc: ellipse area of rosette at the start of flowering the second summer, adjusted for percentage of ellipse covered by leaves AreaB3Wc: ellipse area of rosette before the third winter, adjusted for percentage of ellipse covered by leaves AreaB3Sc: ellipse area of rosette before third summer, adjusted for percentage of ellipse covered by leaves AreaB4Wc: ellipse area of rosette before the fourth winter, adjusted for percentage of ellipse covered by leaves RDiam1Pla: rosette diameter along the longest axis (mm) at the time of planting ("Planting diameter" in the manuscript) RDiam1B1W: rosette diameter along the longest axis (mm) before the first winter RDiamB1S: rosette diameter along the longest axis (mm) before the first summer ("Spring diameter" in the manuscript) RDiamF1: rosette diameter along the longest axis (mm) at the start of flowering in the first summer RDiamB2W: rosette diameter along the longest axis (mm) before the second winter RDiamB2S: rosette diameter along the longest axis (mm) before the second summer RDiamF2: rosette diameter along the longest axis (mm) at the start of flowering in the second summer RDiamB3W: rosette diameter along the longest axis (mm) before the third winter RDiamB3S: rosette diameter along the longest axis (mm) before the third summer RDiaB4W: rosette diameter along the longest axis (mm) before the fourth winter F20D22 - FRO1: Genotyped markers. Second row is the chromosome (linkage group) number, and third row is the marker location along the linkage group in cM (Kosambi map function, from previously-constructed linkage maps). Coding is as follows: Fully-informative markers: 1 = Sp1/Sp2 homozygote, 2 = Sp2/Ma1 heterozygote, 3 = Ma2/Sp1 heterozygote, 4 = Ma1/Ma2 homozygote. F2 configuration markers: 1 = Sp homozygote, 10 = heterozygote, 4 = Ma homozygote. Partially-informative markers, polymorphic only in Ma1/Sp1 F1: 5 = Sp2/--, 6 = Ma1/--. Partially-informative markers, polymorphic only in Ma2/Sp2 F1: 7 = Sp1/--, 8 = Ma2/--. Note that these codings are switched from those used in the North Carolina field data. Details of genotype data and marker info can be found in Supplementary table 1 in Leppälä and Savolainen 2011 (Evolution 65:2959-2972) For questions or further information, contact David Remington (dlreming@uncg.edu).