Selection maintains floral color polymorphism in the scarlet paintbrush, Castilleja coccinea, reflecting combined ecological factors
Data files
Sep 08, 2025 version files 99.69 MB
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Genetics_denovo_data.zip
97.79 MB
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Habitat_data.zip
639.94 KB
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Landscape_data.zip
601.92 KB
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Morphology_data.zip
607.65 KB
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README.md
44.13 KB
Abstract
Premise: Evolutionary theory predicts polymorphism should be rare; however, variation in floral color is common, often attributed to drift, plasticity, or variable selection. Examining floral color polymorphism both within contact zones and across a species’ range can reveal mechanisms maintaining this variation. Here, we used a multistep approach to investigate spatially heterogeneous variation in floral bract color in Castilleja coccinea.
Methods: We compared frequencies of color morphs, floral morphology, fitness, and genetic structure in regional populations and a common garden. Next, we examined habitat differences, including plant communities and edaphic factors, as potential drivers of variation. Lastly, we leveraged herbarium and iNaturalist occurrence data to investigate whether patterns were consistent at the landscape scale.
Key results: Bract color in C. coccinea is genetically heritable, with yellow dominant over red, and is under selection. Populations are predominantly monomorphic, with color distance showing no correlation to genetic or geographic distance, despite significant genetic isolation-by-distance. Yellow morphs are associated with open wetlands, while red morphs occur at drier sites associated with nearby tree cover. Red morphs demonstrated lower fitness in a common garden, suggesting tradeoffs associated with pleiotropic effects of adaptation to drier soil conditions.
Conclusions: Differences in floral color between morphs are consistent with diversification associated with a shift in ecological niche. We identified variation in edaphic and habitat conditions as probable drivers of divergence in floral color. Additionally, variation in other floral traits suggests a combined role of pollinators and habitat differences acting in concert to maintain distinct floral color morphs.
Dataset DOI: 10.5061/dryad.0k6djhbb8
Description of the data and file structure
In this study, we sought to characterize and determine the drivers of floral bract color polymorphism in Castilleja coccinea, both in a contact zone of morphotypes and across the range of the species. We focus on four primary objectives: 1) establishing that this variation is the result of selection; 2) determining if the trait is genetically inherited and associated with fitness differences; 3) identifying potential abiotic or biotic agents of selection that may be driving these patterns; and 4) determining if these patterns are generalizable across the range of the species. To accomplish this, we have completed field studies of floral traits and habitat composition, a common garden experiment, an analysis of genetic structure, and a landscape-scale analysis of herbarium and community science data.
The data files are organized into four directories: 1) Landscape scale data (Landscape_data.zip), 2) Morphology (Morphology_data.zip), 3) Habitat (Habitat_data.zip), and 4) Population genomics data (Genetics_denovo_data.zip). Note: NA in this dataset indicates data that is not available.
Files and variables
Landscape scale data
All contained in the Landscape_data.zip directory
Note: GPS coordinates (latitude and longitude) of GBIF observations across the species’ range in this directory have been rounded to the nearest 0.1° to protect potentailly sensitive populations. For access to precise location data, please contact the corresponding author. The only exceptions are populations in Illinois, where Castilleja coccinea is considered secure or has no status rank.
File: caco_all_map_rounded.csv
Description: Derived datset of herbarium and iNaturalist observations used to create the rangewide map figure (Figure 1A). This file contains 6 columns and 3701 rows (obs) of data.
Variables
- ID: unique identifier for each observation, either the iNaturalist ID number, or the herbarium ID
- latitude: north–south position of a point
- longitude: east–west position of a point
- color: describes the bract color of the observation as Red or Yellow
- Record_type: describes the origin of data as either from iNaturalist, herbarium or field collected data
- name: scientific name of species (Castilleja coccinea)
File: Anna_samples_gps.csv
Description: Field sites used to create the inset map figure (Figure 1B). This file contains 7 columns and 11 rows (obs) of data.
Variables
- Site: abbreviated site name relating to geographic location of observation IB2 = Illinois Beach 2, MW = Newark Road, = Pine Station, SP = Shaw Prairie, IB1 = Illinois Beach 1, DP = Dropseed Prairie, HP = Hoosier Prairie, MC = Meissner-Corron, NR = Newark Road, SR = Sand Ridge, GM = Gensburg-Markham
- lat: north–south position of a point
- long: east–west position of a point
- color: describes the bract color of the observation as Red or Yellow
- site_code: unique alpha numerical description of site, R = red site, Y = yellow site, P = polymorphic site
File: color_complete_rounded.csv
Description: Cleaned and filtered output of the ColorSelector pipeline (Luong et al. 2023). This file contains 35 columns and 2447 rows (obs) of data.
Variables
- iNatID: unique identifier of observation derived from ihttps://www.inaturalist.org/
- species: species name
- long: east–west position of a point
- lat: north–south position of a point
- year: year of observation
- month: month of observation
- day: month of observation
- Nsamples: number of pixels sampled for one observation using the ColorSelector R shiny applicaiton
- Rmean: mean red value of sampled pixels in obeservation
- Rmedian: median of red value of sampled pixels in obeservation
- Rmax: maximum of red value for sampled pixels
- Rmin: minimum of red value for sampled pixels
- Rvariance: variance of red values for samples pixels
- Rstdev: standard deviation of red values for sampled pixels
- Gmean: mean green value of sampled pixels in obeservation
- Gmedian: median of green value of sampled pixels in observation
- Gmax: maximum of green value for sampled pixels
- Gmin: minimum of green value for sampled pixels
- Gvariance: variance of green values for samples pixels
- Gstdev: standard deviation of green values for sampled pixels
- Bmean: mean blue value of sampled pixels in observation
- Bmedian: median of blue value of sampled pixels in observation
- Bmax: maximum of blue value for sampled pixels
- Bmin: minimum of blue value for sampled pixels
- Bvariance: variance of blue values for sample pixels
- Bstdev: standard blue of green values for sampled pixels
- poly: if the observation represents a polymorphic population. values "Y" = yes, "N" = No
- RGB_vector: Bract color RGB values were transformed into a single vector value by treating each color as a point in n-dimensional space and determining the Euclidean distance of each point from the origin.
- Hue: hue value of observation (from HSV spectrum)
- Saturation: saturation value of observation (from HSV spectrum)
- Value: value of observation (from HSV spectrum)
- Category: bract color category. values "Red" or "Yellow" or "Orange"
- Category_binary: binary bract color category "Red" or "Yellow"
- Fill: hex code of hue value
- Adjusted_hue: hue value adjusted from a
File: anna_confirmed_final_rounded.csv
Description: Confirmed and filtered herbarium specimen information. This file contains 23 columns and 1322 rows (obs) of data.
Variables
- ID: Unique identifier for each herbarium record
- Accession.ID: Accession or catalog identifier for the sample
- Anna.Data: Reference to data associated with Anna
- Duplicate: Indicates duplicate samples
- Herbarium.ID: Herbarium specieman
- lat: GPS coordinates (latitude)
- long: GPS coordinates (longitude)
- Accuracy: Accuracy of the GPS coordinates (character)
- County: County where the sample is located
- State: State where the sample is located
- Collection.Month: Month of sample collection
- Collection.Day: Day of the month for sample collection
- Collection.Yr: Year of sample collection
- Day.Month: Date in day/month format
- Julian.Days: Day of the year of collection (Julian date)
- Accuracy.of.date: Precision of collection date (character)
- Yellow: Indicates presence of yellow color or label description (TRUE or FALSE)
- Confirmed: Indicates confirmation status of bract color (TRUE or FALSE)
- Color.Notes: Additional notes on color from herbarium label
- Location: Location information for the sample
- Habitat: Habitat type where the sample was collected
- Incomplete: Indicates incomplete data on label
- color: Color classification of the sample (factor; yellow or red)
File: COMPLETE_Herbarium_rounded.csv
Description: Herbarium specimen data file - unfiltered. This file contains 31 columns and 2883 rows (obs) of data.
Variables
- ID: Unique identifier for each herbarium record
- Accession.ID: Accession or catalog identifier for the sample
- Anna.Data: Reference to data associated with Anna (TRUE or FALSE)
- Duplicate: Indicates duplicate herbarium collections
- Herbarium.ID: Herbarium name
- GPS.North: GPS coordinates (latitude)
- GPS.West: GPS coordinates (longitude)
- Accuracy: Accuracy of the GPS coordinates (character)
- County: County where the sample is located
- State: State where the sample is located
- Collection.Month: Month of sample collection
- Collection.Day: Day of the month for sample collection
- Collection.Yr: Year of sample collection
- Day.Month: Date in day/month format
- Julian.Days: Day of the year (Julian date)
- Accuracy.of.date: Precision of collection date
- Yellow: Indicates presence of yellow color or label description (TRUE or FALSE)
- Confirmed: Indicates confirmation status of bract color (TRUE or FALSE)
- Color.Notes: Additional notes on color from herbarium label
- Location: Location information for the sample
- Habitat: Habitat type where the sample was collected
- PLSS.data: Public Land Survey System (PLSS) data
- TSR: Township, section, and range (PLSS data)
- Incomplete: Indicates incomplete data on label
- PLSS.notes: Additional notes related to PLSS data
- Notes: General notes about the sample
- GPS.North.original: Original GPS latitude before adjustments
- GPS.West.original: Original GPS longitude before adjustments
- GPS.PLSS: GPS coordinates converted to PLSS format
- GPS.Google.Earth: GPS coordinates from Google Earth
- Acc.to.Sect: Accession to section reference
File: CACO_colors_rounded.csv
Description: Output of the ColorSelector pipeline averaged by observation - unfiltered. This file contains 19 columns and 2525 rows (obs) of data.
Variables
- iNatID: Unique identifier of observation derived from ihttps://www.inaturalist.org/
- species: species name
- long: east–west position of a point
- lat: north–south position of a point
- year: year of observation
- month: month of observation
- day: month of observation
- Nsamples: number of pixels sampled for one observation using the ColorSelector R Shiny application
- R.mean: Mean red intensity value in the RGB color model
- R.median: Median red intensity value in the RGB color model
- R.max: Maximum red intensity value in the RGB color model
- R.min: Minimum red intensity value in the RGB color model
- R.variance: Variance of red intensity values in the RGB color model
- R.stdev: Standard deviation of red intensity values in the RGB model
- G.mean: Mean green intensity value in the RGB color model
- G.median: Median green intensity value in the RGB color model
- G.max: Maximum green intensity value in the RGB color model
- G.min: Minimum green intensity value in the RGB color model
- G.variance: Variance of green intensity values in the RGB color model
- G.stdev: Standard deviation of green intensity values in the RGB model
- B.mean: Mean blue intensity value in the RGB color model
- B.median: Median blue intensity value in the RGB color model
- B.max: Maximum blue intensity value in the RGB color model
- B.min: Minimum blue intensity value in the RGB color model
- B.variance: Variance of blue intensity values in the RGB color model
- B.stdev: Standard deviation of blue intensity values in the RGB model
- poly: Polymorphic site, if site had more than one floral morph visible in iNat image
Morphology data
All files contained in the Morphology_data.zip directory.
File: CACO_ccHSV_field_20250506.csv
Description: Bract color, bract measurements, floral measurements, RGB, HSV values for individual plants, and proportion of color by site This file contains 36 columns and 448 rows (obs) of data.
Variables
- Site Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- Plan ID: unique numerical ID for each individual plant with decimal indicating the flower measured on each plant
- Bract.Color: alpha numeric Royal Horticulture Society code for color
- ID: unique numerical ID for each flower
- Plant ID: unique numerical ID for each individual plant
- Tag No: unique numerical ID for each individual plant
- Bract.Length: length of bract from bact base to lobe tips (mm)
- Bract.Base: length of bract base to lobe base (mm)
- Bract.Width: width of bract at widest point (mm)
- Bract.Lobe: count of number of bract lobes
- Calyx.Outer: length of outer calyx segment (mm)
- Calyx.Inner: length of inner calyx segment (mm)
- Corolla.Tube.Length: length of corrolla tube (mm)
- Corolla.Galea.Length: length of corrolla galea (mm)
- Corolla.Tube.Width: width of corrolla tube (mm)
- Stamen.Length: stamen length (mm)
- Style.Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length)
- R: red value in RGB color space
- G: green value in RGB color space
- B: blue value in RGB color space
- hex: hexcode from RGB color vector
- Hue: hue value in HSV colorspace
- Saturation: saturation value in HSV colorspace
- Value: value in HSV color space
- Category: bract color category. values "Red" or "Yellow" or "Orange"
- Fill: hexcode from hue value
- Adjusted_Hue: hue value corrected for circularity
- observation: value of 1
- Category2: bract color category values "Red" or "Yellow"
- SitePropRed: proportion of plants that were red
- SitePropYellow: proportion of plants that were yellow
- Site.Color: dominant site color as "Red" or "Yellow"
- Site.ColorFine: dominant site color as "Red" or "Yellow" or "Yellow_mixed"
- morphSite: individual plant color with sites color (eg. Red - Yellow)
- pch_ind: shape values as 21 (circle) or 22 (square)
File: CACO_cgHSV_cg_20250506.csv
Description: Bract color, bract measurements, floral measurements, RGB, HSV values for individual plants, and proportion of color by (maternal) site This file contains 37 columns and 841 rows (obs) of data.
Variables
- Site Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- Plant ID: unique numerical ID for each individual plant with decimal indicating the flower measured on each plant
- Maternal Bract Color: alpha numeric Royal Horticulture Society code for maternal bract color
- Common garden ID: umerical ID for common garden
- RHS.Code: alpha numeric Royal Horticulture Society code for plant color
- ID1: unique numerical ID for each individual plant
- CGID: umerical ID for common garden
- BractLength: length of bract from bact base to lobe tips
- BractBase: length of bract base to lobe base
- BractWidth: width of bract at widest pointt
- Bract.Lobe: count of number of bract lobes
- Calyx.Outer: length of outer calyx segment (mm)
- Calyx.Inner: length of inner calyx segment (mm)
- Corolla.Tube.Length: length of corrolla tube (mm)
- Corolla.Galea.Length: length of corrolla galea (mm)
- Corolla.Tube.Width: width of corrolla tube (mm)
- Stamen.Length: stamen length (mm)
- Style.Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length))
- R: red value in RGB color space
- G: green value in RGB color space
- B: blue value in RGB color space
- hex: hexcode from RGB color vector
- Hue: hue value in HSV colorspace
- Saturation: saturation value in HSV colorspace
- Value: value in HSV color space
- Adjusted_Hue: hue value corrected for circularity
- Category: bract color category. values "Red" or "Yellow" or "Orange"
- Fill: hexcode from hue value
- Category2: bract color category values "Red" or "Yellow"
- observation: observation
- SitePropYellow: proportion of plants that were yellow
- Site.Color: dominant site color as "Red" or "Yellow"
- Site.ColorFine: dominant site color as "Red" or "Yellow" or "Yellow_mixed"
- pch_ind: shape values as 21 (circle) or 22 (square)
- nmds1m: nmds axis 1 position
- nmds2m: nmds axis 2 position
File: CACO_CGcolorOffspring_collapsed_20241115.csv
Description: Offspring of controlled cross experiment. This file contains 48 columns and 24 rows (obs) of data.
Variables
- Site.Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- MaternalBractColor: alpha numeric Royal Horticulture Society code for maternal bract color
- MaternalColCatBroad: bract color category values "Red" or "Yellow"
- count: count of offsping
- os_2D: Offspring RHS Color: 2D
- os_3A: Offspring RHS Color: 3A
- os_3B: Offspring RHS Color: 3B
- os_3C: Offspring RHS Color: 3C
- os_4A: Offspring RHS Color: 4A
- os_4B: Offspring RHS Color: 4B
- os_4C: Offspring RHS Color: 4C
- os_5A: Offspring RHS Color: 5A
- os_5B: Offspring RHS Color: 5B
- os_6A: Offspring RHS Color: 6A
- os_7A: Offspring RHS Color: 7A
- os_7B: Offspring RHS Color: 7B
- os_8A: Offspring RHS Color: 8A
- os_9A: Offspring RHS Color: 9A
- os_9B: Offspring RHS Color: 9B
- os_10A: Offspring RHS Color: 10A
- os_12A: Offspring RHS Color: 12A
- os_12B: Offspring RHS Color: 12B
- os_13A: Offspring RHS Color: 13A
- os_13B: Offspring RHS Color: 13B
- os_21A: Offspring RHS Color: 21A
- os_22A: Offspring RHS Color: 22A
- os_22B: Offspring RHS Color: 22B
- os_23A: Offspring RHS Color: 23A
- os_25A: Offspring RHS Color: 25A
- os_25B: Offspring RHS Color: 25B
- os_N25A: Offspring RHS Color: N25A
- os_N25B: Offspring RHS Color: N25B
- os_26A: Offspring RHS Color: 26A
- os_28A: Offspring RHS Color: 28A
- os_30A: Offspring RHS Color: 30A
- os_30B: Offspring RHS Color: 30B
- os_N30A: Offspring RHS Color: N30A
- os_N30B: Offspring RHS Color: N30B
- os_N30C: Offspring RHS Color: N30C
- os_31A: Offspring RHS Color: 31A
- os_32A: Offspring RHS Color: 32A
- os_33A: Offspring RHS Color: 33A
- os_33B: Offspring RHS Color: 33B
- os_35A: Offspring RHS Color: 35A
- os_39B: Offspring RHS Color: 39B
- os_N39B: Offspring RHS Color: N39B
- os_yellow: offspring yellow
- os_red: offsping red
File: CG_bract_only.csv
Description: Bract measurements (length, width, number etc) of individual plants in the common garden. This file contains 13 columns and 442 rows (obs) of data.
Variables
- Site.Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant site color as "Yellow" or "Orange"
- MplantID: maternal plant unique numerical ID
- ColorM.RHS.: alpha numeric Royal Horticulture Society code for maternal bract color
- ColorM: maternal plant color as "Yellow" or "Orange"
- CGID: unique plant ID number in common garden
- ColorP: color of the individual plant as "Yellow" or "Orange"
- ColorP..RHS.: alpha numeric Royal Horticulture Society code for individual bract color
- Bract.Length: length of bract from bact base to lobe tips
- Bract.Base: length of bract base to lobe base
- Bract.Width: width of bract at widest pointt
- BractNo: count of number of bract lobes
- ColorSP: color of the site (S) with color of the individual plant (P)
File: CG_floral.csv
Description: Floral measurements (Calyx, corolla, stamen, style etc) of individual plants in the common garden. This file contains columns 17 columns and 431 rows (obs) of data.
Variables
- Site.Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant site color as "Yellow" or "Orange"
- MPlant.ID: maternal plant unique numerical ID
- ColorM..RHS.: alpha numeric Royal Horticulture Society code for maternal bract color
- ColorM: maternal plant color as "Yellow" or "Orange"
- CGID: unique plant ID number in common garden
- ColorP: color of the individual plant as "Yellow" or "Orange"
- ColorP..RHS.: alpha numeric Royal Horticulture Society code for individual bract color
- Calyx.Outer: length of outer calyx segment (mm)
- Calyx.Inner: length of inner calyx segment (mm)
- Corolla.Tube.Length: length of corrolla tube (mm)
- Corolla.Galea.Length: length of corrolla galea (mm)
- Corolla.Tube.Width: width of corrolla tube (mm)
- Stamen.Length: stamen length (mm)
- Style.Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length))
- ColorSP: color of the site (S) with color of the individual plant (P)
File: Field_bract_only.csv
Description: Bract measurements (length, width, number etc) of individual plants in the field. This file contains 10 columns and 336 rows (obs) of data.
Variables
- site name: site name (Text); geographic location of observation Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site grouped into two categories (Yellow or Orange)
- PlantID: unique numerical ID for each individual plant
- ColorID: alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- Bract length : length of floral bract measured from base to tip (mm)
- Bract Base: width of floral bract base (mm)
- Bract Width: width of floral bract at its widest point (mm)
- BractNo: number of bracts (integer)
- ColorSP: combination of site color (ColorS = dominant bract color of site grouped into two categories (Yellow or Orange)) and plant color (ColorP = individual plant bract color grouped into two categories (Yellow or Orange))
File: Field_floral.csv
Description: Floral measurements (calyx, corolla, stamen, style etc) of individual plants in the field. This file contains 14 columns and 478 rows (obs) of data.
Variables
- site name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site grouped into two categories (Yellow or Orange)
- Plant ID: unique numerical ID for each individual plant
- Color (RHS): alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- Calyx Outer: length of outer calyx segment (mm)
- Calyx Inner: length of inner calyx segment (mm)
- Corrolla Tube: length of corrolla tube (mm)
- BractNo: number of bracts (integer)
- Corolla Galea Length: length of corrolla galea (mm)
- Corolla Tube Width: width of corrolla tube (mm)
- Stamen Length: stamen length (mm)
- Style Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length))
- ColorSP: combination of site color (ColorS = dominant bract color of site grouped into two categories (Yellow or Orange)) and plant color (ColorPwith individual plant bract color grouped into two categories (Yellow or Orange))
File: Fruit_flower_CG.csv
Description: Fitness estimates (height, number of stems, flowers, fruits, fruit to flower ratio, herbivory, seed viability) of individual plants in common garden. This file contains 19 columns and 367 rows (obs) of data.
Variables
- SiteID: site name; geographic location of maternal plant accession (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site of maternal plant acession grouped into two categories (Yellow or Orange)
- PlantID: maternal plant unique numerical ID
- Treatment: type of observation, (text) recorded as either Morphology or Fitness
- ColorM(RHS): color of materal plant, alpha numeric Royal Horticulture Society code for color
- ColorM: color of maternal plant, plant bract color grouped into two categories (Yellow or Orange)
- CommGDID: individual plant in common garden unique numerical ID
- ColorP(RHS): color of plant, alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- Height: height of plant (cm)
- Stems: number of stems (integer)
- Flowers: number of flowers (integer)
- Fruit: number of fruits (integer)
- Herbivory: categorical estiamte of herbivory, values = TRUE, FALSE
- Failures: number of flowers that failed to set fruit
- Ratio: ratio of fruits to flowers
- ColorSM: variables Color S and ColorM combined
- ColorSP: vairables ColorS and ColorP combined
- ColorSMP: variables ColorS, ColorM and ColorP combined
File: Fruit_flower_Field_Herbivory.csv
Description: Herbivory estimates of individual plants at field sites. This file contains 13 columns and 152 rows (obs) of data.
Variables
- Site: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site grouped into two categories (Yellow or Orange)
- PlantID: unique numerical ID for each individual plant
- Treatment: type of observation, (text) recorded as either Morphology, Fitness or Herbivory
- Color(RHS): alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- LeavesNo: number of leaves (integer)
- DamageL: number of leaves damaged by herbivory (integer)
- FlowersNo: number of flowers (integer)
- DamageFl: number of flowers damaged by herbivory (integer)
- ColorSP: combination of Site color (ColorS = dominant bract color of site grouped into two categories (Yellow or Orange)) and plant color (ColorPwith individual plant bract color grouped into two categories (Yellow or Orange))
- PropLeaves: proportion of damaged leaves to total leaves (ratio)
- PropFlowers: proportion of damaged flowers to total flowers (ratio)
File: Fruit_flower_Field_Seed.csv
Description: Seed counts (capsule fill) estimates of individual plants at field sites. This file contains 11 columns and 176 rows (obs) of data.
Variables
- Population: site name (Text); geographic location of observation Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site grouped into two categories (Yellow or Orange)
- Plant ID #: unique numerical ID for each individual plant
- Treatment: type of observation, (text) recorded as either Morphology or Fitness
- Bract Color: alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- Total: total number of seed capsules
- AvgOfFilled (>50%): average number of seed capsules that were more than 50% filled
- AvgOfEmpty (<50%): average number of seed capsules that were less than 50% filled
- ratio: ratio of filled to total seed capsules
- ColorSP: combination of site color (ColorS = dominant bract color of site grouped into two categories (Yellow or Orange)) and plant color (ColorP = individual plant bract color grouped into two categories (Yellow or Orange))
File: CACO_JF_Colorofplants_20241111.csv
Description: Index of data collection for morphology, fitness, or herbivory by individual plant ID and site. This file contains 7 columns and 541 rows (obs) of data.
Variables
- Plant ID: unique numerical ID for each individual plant
- SiteID : site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- Year: year of data collection
- Date: date of data collection
- Treatment: type of observation, (text) recorded as either Morphology or Fitness or Herbivory
- Broad Color ROY: plant bract color grouped into three categories (Red or Orange or Yellow)
- Bract Color: alpha numeric Royal Horticulture Society code for color
File: CACO_JFdata_NMDScg_20241023.csv
Description: Floral morphology data for common garden plants (input for NMDS). This file contains 19 columns and 841 rows of data.
Variables
- Site Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- Plant ID: unique numerical ID for maternal plant
- Maternal Bract Color: alpha numeric Royal Horticulture Society code for maternal bract color
- Common Garden ID: umerical ID for common garden
- RHS Code: alpha numeric Royal Horticulture Society code for color
- ID1: unique numerical ID for each individual plant
- CGID: umerical ID for common garden
- Bract Length: length of bract from bact base to lobe tips
- Bract Base: length of bract base to lobe base
- Bract Width: width of bract at widest pointt
- Bract Lobe: count of number of bract lobes
- Calyx Outer: length of outer calyx segment (mm)
- Calyx Inner: length of inner calyx segment (mm)
- Corolla Tube Length: length of corrolla tube (mm)
- Corolla Galea Length: length of corrolla galea (mm)
- Corolla Tube Width: width of corrolla tube (mm)
- Stamen Length: stamen length (mm)
- Style Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length))
File: CACO_JFdata_NMDSfield_20241023.csv
Description: Floral morphology data for field plants (input for NMDS). This file contains 18 columns and 532 rows (obs) of data.
Variables
- Site Name: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- Plant ID: unique numerical ID for each individual plant with decimal indicating the flower measured on each plant
- Bract Color: alpha numeric Royal Horticulture Society code for color
- ID: unique numerical ID for each individual plant
- Plant ID: unique numerical ID for each individual plant
- Tag No: unique numerical ID for each individual plant
- Bract Length: length of bract from bact base to lobe tips
- Bract Base: length of bract base to lobe base
- Bract Width: Witch of bract at widest pointt
- Bract Lobe: count of number of bract lobes
- Calyx Outer: length of outer calyx segment (mm)
- Calyx Inner: length of inner calyx segment (mm)
- Corolla Tube Length: length of corrolla tube (mm)
- Corolla Galea Length: length of corrolla galea (mm)
- Corolla Tube Width: width of corrolla tube (mm)
- Stamen Length: stamen length (mm)
- Style Length: style length (mm)
- Herkogamy: separation of anthers and stigma (stamen length - stigma length))
File: Fruit_flower_Field.csv
Description: Fruit-to-flower ratio of individual plants at field sites This file contains description 12 columns and 178 rows of data.
Variables
- rows (obs): 178
- SiteID: site name; geographic location of observation (Text) Illinois Beach 2, Newark Road, Pine Station, Shaw Prairie, llinois Beach 1, Dropseed Prairie, Hoosier Prairie, Meissner-Corron, Newark Road, Sand Ridge, Gensburg-Markham
- ColorS: dominant bract color of site grouped into two categories (Yellow or Orange)
- PlantID: unique numerical ID for each individual plant
- Treatment: type of observation, (text) recorded as either Morphology or Fitness
- ColorP(RHS): alpha numeric Royal Horticulture Society code for color
- ColorP: plant bract color grouped into two categories (Yellow or Orange)
- Height: height of flowering stem (cm)
- Flowers: number of flowers (integer)
- Fruit: number of fruits (integer)
- Failures: number of flowers that failed to set fruit (integer)
- Ratio: ratio of number of fruits to number of flowers for each plant
- ColorSP: combination of Site color (ColorS = dominant bract color of site grouped into two categories (Yellow or Orange)) and plant color (ColorPwith individual plant bract color grouped into two categories (Yellow or Orange))
File: ColorChart.csv
Description: Color conversion chart for RGB, HSV. CIE, hex codes and UCL colors of individual plants in the field. This file contains 23 columns and 236 rows (obs) of data.
Variables
- ColorID : Unique identification number for each observation
- RHS.: Royal Horticultural Society (RHS) color page number and letter
- RHS.page.: Royal Horticultural Society (RHS) color page number
- RHS.Hue: Royal Horticultural Society (RHS) letter
- Color.Vector.distance: Bract color RGB values were transformed into a single vector value by treating each color as a point in n-dimensional space and determining the Euclidean distance of each point from the origin (zero). This was calculated by summing the squares of the three individual RGB values and calculating the square root of the total.
- Field1: Field assesment of color, categorical as Orange, Red or Yellow
- Color : Field assesment of color, categorical as Yellow, Greenish Yellow, Orangish Yellow, Yellowish pink, Orange, Yellowish Green, Reddish Orange, Yellowish Pink, Pink, Red, Purplish Red, Purplish Pink
- UCL.: Universal Color Language
- UCL.name: Universal Color Language name
- R: Red (RGB) colorspace
- G: Green (RGB) colorspace
- B : Blue (RGB) colorspace
- hex.RGB: Hexcode from RGB colorspace
- R..sRGB : sRGB (standard RGB) colorspace R value (red value)
- G..sRGB: sRGB (standard RGB) colorspace G value (green value)
- B.sRGB: sRGB (standard RGB) colorspace B value (blue value)
- L...CIE.Lab: CIELAB color space L value or lightness value
- a...CIE.Lab: CIELAB color space a value or green value
- b...CIE.Lab: CIELAB color space b value or blue value
- L....CIE.LCh: CIE LCh Colour Space L value or lightness value
- C....CIE.LCh : CIE LCh Colour Space C value
- h....CIE.LCh: CIE LCh Colour Space h value
File: KimDiss_CACOcross20250114b.csv
Description: Results from controlled crosses in the common garden. This file contains 8 columns and 17 rows (obs) of data.
Variables
- MaternalColCatBroad maternal plant color as as "Red" or Yellow
- MaternalColCatFine maternal plant color "Scarlet" or "Orange" or "Yellow"
- Pollen_donor pollen donor color as "Red" or Yellow
- Pollen_donor_fine pollon donor color "Scarlet" or "Orange" or "Yellow"
- OffspringColor offspring color as "Red" or Yellow
- OffspringColorFine offspring color as "Scarlet" or "Orange" or "Yellow"
- count count of offspring
- n_crosses count of crosses
Habitat Data
All files contained in the Habitat_data.zip directory
File: Soil.csv
Description: Herbarium soil and habitat properties. This file contains 18 columns and 427 rows (obs) rows of data.
Variables
- ID: Unique identifier for each plant
- GPS.North: GPS coordinates (latitude)
- GPS.West: GPS coordinates (longitude)
- County: County where the sample is located (character)
- State: State where the sample is located (character)
- Confirmed: Confirmation status of bract color (TRUE or FALSE)
- ColorS: Dominant bract color of site of maternal plant acession grouped into two categories (Yellow or Orange)
- Texture_short: Simplified soil texture classification (factor; loam, sandy clay, silt loam, sandy loam, silt clay loam)
- Eco.I: EPA Eco-reigon 1 classification (integer; 5, 8 or 9)
- Saturation: Soil saturation level (integer)
- Field_Capacity: Field capacity of the soil (integer)
- Available_water: Amount of water available in the soil (integer)
- Texture_broad: Broad soil texture classification (factor; clay loam muck, sand, other)
- Wet.Area: Indicates if the area is is described as wet or wetland on herabrium label (TRUE or FALSE)
- DRY: Indicates if the area is is described as dry on herabrium label (TRUE or FALSE)
- Combined: Combined classification of soil (TRUE or FALSE)
- Forested: Indicates if the area is described as forested on herabrium label (TRUE or FALSE)
- Prairie: Indicates if the area is is described as prairie on herabrium label (TRUE or FALSE)
File: Popaverages.csv
Description: Field site characteristics (soil moisture, texture, cover class and plant communities). This file contains columns and rows (obs) of data.
Variables
- Site: site name
- Code: abreviated site name relating to geographic location of observation IB2 = Illinois Beach 2, MW = Newark Road, = Pine Station, SP = Shaw Prairie, IB1 = Illinois Beach 1, DP = Dropseed Prairie, HP = Hoosier Prairie, MC = Meissner-Corron, NR = Newark Road, SR = Sand Ridge, GM = Gensburg-Markham
- Site#: unique numerical identifier of site
- GPS North : north–south position of a point
- GPS West: east–west position of a point
- Color S: dominant bract color grouped into two major categories Red or Yellow
- Color Sx: dominant bract color grouped into three categories Red or Yellow or Polymorphic
- County: describes geographic location of observation
- State: describes geographic location of observation
- Percent Yellow: percent of individuals recorded as yellow
- Yellow: number of individuals recorded as having yellow bracts
- Red: number of individuals recorded as having yellow bracts
- BareSoil: proportion of ground in quadrat that was classfied as having no vegetation
- FineDebris: proportion of ground in quadrat that was classfied as having fine debris
- Dry (UPL or FACU): proportion of plants identified in community surveys as being obligate or facultatice upland plants
- Wet (OBL or FACW): proportion of plants identified in community surveys as being obligate or facultative wetland plants
- NRCS Soil: soil category as defined by National Resource Conservation Service
- Soil Moisture Content: percent soil volumetric water content (VWC)
- % Sand: percent of sand in soil
- % Silt: percent of silt in soil
- % Clay: percent of clay in soil
File: Phenology.csv
Description: Phenology of herbarium observations. This file contains 8 columns and 2854 rows (obs) of data.
Variables
- ID: Unique identifier for each observation
- Accession.ID: Accession or catalog identifier for the sample
- GPS.North: GPS coordinates (latitude)
- GPS.West: GPS coordinates (longitude)
- State: State of collection (character)
- Julian.Days: Day of the year (Julian date)
- ColorS: Dominant bract color of site of maternal plant acession grouped into two categories (Yellow or Orange)
- Confirmed: Confirmation status of bract color (TRUE or FALSE)
File: HabitatII.csv
Description: Site characteristics from herbarium labels and EPA Ecoregions This file contains 14 columns and 1343 rows (obs) of data.
Variables
- ID: Unique identifier for each observation
- GPS.North: GPS coordinates (latitude)
- GPS.West: GPS coordinates (longitude)
- County: County where the sample is located
- State: State where the sample is located
- Eco.I: EPA Eco-reigon 1 classification (integer; 5, 8 or 9)
- ColorS: Dominant bract color of site grouped into two categories (Yellow or Orange)
- Confirmed: Indicates confirmation status of bract color (TRUE or FALSE)
- Wet.Area: Indicates if the area is is described as wet or wetland on herabrium label (TRUE or FALSE)
- DRY: Indicates if the area is is described as dry on herabrium label (TRUE or FALSE)
- Combined: Combined classification of soil (TRUE or FALSE)
- Forested: Indicates if the area is described as forested on herabrium label (TRUE or FALSE)
- Prairie: Indicates if the area is is described as prairie on herabrium label (TRUE or FALSE)
- Label.info: Additional information about the sample or label
File: Nutrients.csv
Description: Soil nutrient supply rates measured using Plant Root Simulator (PRS®) probes at multiple Castilleja coccinea field sites.
This file contains 17 columns and 12 rows (observations) of data.
Variables
- Site: Site code abbreviation where the PRS® probes were deployed
- Color: Predominant bract color morph at the site (Red or Yellow)
- NO3-N: Nitrate nitrogen (µg per 10 cm² per burial length)
- NH4-N: Ammonium nitrogen (µg per 10 cm² per burial length)
- Ca: Calcium (µg per 10 cm² per burial length)
- Mg: Magnesium (µg per 10 cm² per burial length)
- K: Potassium (µg per 10 cm² per burial length)
- P: Phosphorus (µg per 10 cm² per burial length)
- Fe: Iron (µg per 10 cm² per burial length)
- Mn: Manganese (µg per 10 cm² per burial length)
- Cu: Copper (µg per 10 cm² per burial length)
- Zn: Zinc (µg per 10 cm² per burial length)
- B: Boron (µg per 10 cm² per burial length)
- S: Sulfur (µg per 10 cm² per burial length)
- Pb: Lead (µg per 10 cm² per burial length)
- Al: Aluminum (µg per 10 cm² per burial length)
- Cd: Cadmium (µg per 10 cm² per burial length)
Notes
- Units represent nutrient supply rates as accumulated on PRS® probes during the burial period.
- Zeros indicate values below detection limits for the assay.
- Site codes (e.g., DP, GM, IB1) uniquely identify sampling locations.
- Bract color (Red or Yellow) refers to the predominant floral morph observed at each site.
Population genomics data
All files contained in the Genetics_denovo_data.zip directory
File: populations.snps_denovo_ustacks_R80_all.vcf
Description: Unfiltered VCF file from STACKS de_novo run with r = 80
File: populations.snps_R80_ustacks_filt_filt_85miss.vcf.gz
Description: Filtered VCF file contain SNPS for 37 individuals across 10 populations filtered based on these parameters: r = 80 (STACKS populations), Min depth of 5, Min genotype quality of 20, Allele balance between 0.25 and 0.75, Max depth of 50, Missing by sample cutoff 90%, Missing by SNP 85%, Min MAC 3
File: admixture_input_051525.fam
Description: Input for ADMIXTURE program run. Filtered for linkage disequilibrium with PLINK2.
File: CACO_admix_K2_rep20_thin.Q
Description: Output of ADMIXTURE program run for K = 2.
File: mapmixture_gps_EM.csv
Description: GPS coordinates of sites used to create admixture map (Figure 2) This file contains 3 columns and 10 rows rows of data.
Variables
- Site: abbreviated site name relating to geographic location of observation IB2 = Illinois Beach 2, MW = Newark Road, = Pine Station, SP = Shaw Prairie, IB1 = Illinois Beach 1, DP = Dropseed Prairie, HP = Hoosier Prairie, MC = Meissner-Corron, NR = Newark Road, SR = Sand Ridge, GM = Gensburg-Markham
- lat: Latitude of the site
- long: Longitude of the site
File: mapmixture.csv
Description: Genetic cluster assignments from the CACO_admix_K2_rep20_thin.Q file in the mapmixture format. This file contains 37 columns and 4 rows of data.
Variables
- Site: population assignment
- Individual: unique alphanumeric code for each individual in a population
- Pop1: proportion of ancestry assignment in cluster 1
- Pop2: proportion of ancestry assignment in cluster 2
Access information
Data was derived from the following sources:
- Raw sequenced data from the ddRADseq study are archived at the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA1216984 (http://www.ncbi.nlm.nih.gov/bioproject/1216984).
- iNaturalist observation data downloaded via Global Biodiversity Information Facility (GBIF):
- Research grade iNaturalist observations of Castilleja coccinea (n = 2757; iNaturalist contributors, 2024) were downloaded from the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/) in February of 2024 (doi.org/10.15468/dl.bnunfa) for processing with the ColorSelector pipeline (Luong et al., 2023).
References
GBIF.org. 2024. Global Biodiversity Information Facility Occurrence Download. Available at https://doi.org/10.15468/dl.bnunfa [accessed 08 February 2024].
iNaturalist contributors, iNaturalist (2024). iNaturalist Research-grade Observations. iNaturalist.org. Occurrence dataset https://doi.org/10.15468/ab3s5x accessed via GBIF.org on 2024-02-08.
Luong, Y., A. Gasca-Herrera, T. M. Misiewicz, and B. E. Carter. 2023. A pipeline for the rapid collection of color data from photographs. Applications in Plant Sciences 11: e11546
