Data from: Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae)
Data files
Aug 04, 2025 version files 474.76 KB
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01_FlowCytometry_Data_Gross_etal_2025.txt
136.74 KB
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02_FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt
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03_FloralMorphologySyntheticPolyploidization_Data_Gross_etal_2025.txt
15.84 KB
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04_FloralMorphologyFieldCommonGarden_Data_Gross_etal_2025.txt
27.43 KB
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05_FlowCytometryMethods_Data_Gross_etal_2025.txt
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06_TraitMeasuringComparability_Data_Gross_etal_2025.txt
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README.md
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Abstract
Polyploidization is an important driver of evolution and diversification in flowering plants. Here, we assess how repeated polyploidization may have shaped diversification of floral morphology in Lithophragma bolanderi (Saxifragaceae). This species comprises multiple cytotypes and varies geographically in its interactions with specialized pollinating moths in the genus Greya (Prodoxidae). Past studies have shown that coevolution with these moths has favored particular suites of floral characters but does not fully explain local and regional floral diversification. We combined phenotypic and genomic data from more than 1800 individuals from 40 L. bolanderi populations spread across its entire range. Flow-cytometric analyses revealed a geographic mosaic of populations comprising one to four of three dominant (diploid, tetraploid, hexaploid) and three rare (triploid, pentaploid, octoploid) cytotypes. Whole-genome resequencing of a subset of populations suggested that polyploids arose from multiple autopolyploidization events, rather than a single event and/or through hybridization, albeit with some signals consistent with low levels introgression from the congener Lithophragma glabrum. Quantification of flower traits from plants grown in a common garden showed that cytotype explained more than 15% of the variation in floral morphology, with polyploids showing more variability than diploids. Experimental induction of neopolyploids directly induced phenotypic changes but also indicated that local selection may have favored subsequent convergence in floral morphology among cytotypes in natural populations. Collectively, this comprehensive and integrative approach provides novel insights into how variability generating processes, such as polyploidization integrates with selection from species interactions to shape local floral diversification.
This dataset contains all morphological and flow cytometry data newly collected for the following article:
Karin Grossa, Homa Papoli Yazdi, Elisabeth Schlager, Jodie Lilley, Andrés Romero-Bravo, Anna Runemark, John N Thompson, and Magne Friberg. Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae). Proceedings of the National Academy of Sciences.
Details concerning the methodology and analyses of all data are described in the main text and the SI Appendix file of the article above.
This dataset consists of the following six data files (file type: tab-delimited .txt files):
- 01_FlowCytometry_Data_Gross_etal_2025.txt
- 02_FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt
- 03_FloralMorphologySyntheticPolyploidization_Data_Gross_etal_2025.txt
- 04_FloralMorphologyFieldCommonGarden_Data_Gross_etal_2025.txt
- 05_FlowCytometryMethods_Data_Gross_etal_2025.txt
- 06_TraitMeasuringComparability_Data_Gross_etal_2025.txt
Description of the data and file structure
1. 01_FlowCytometry_Data_Gross_etal_2025.txt
These data were used to assess the presence, abundance, and geographical distribution of Lithophragma bolanderi cytotypes. These data were also the source for all analyses in which ploidy level was used as a factor.
The file contains the following columns:
- FlowCytometryID: Individual ID used for flow cytometry analyses. Those starting with “UU_” were analyzed by one of the authors at Uppsala University and those starting with “PCS_” were analyzed by Plant Cytometry Service (https://www.plantcytometry.nl/).
- Population: Three-letter abbreviation of the population name.
- Latitude: Latitude in °N on the population level.
- Longitude: Longitude in °E on the population level.
- SeedFamily: Seed family (seeds collected from a single plant being half- and/or full-sibs) identity. Note that as this is not applicable to our field-collected samples, “NA” is listed for these samples.
- PlantID: Individual code for each plant. Note that for the field-collected samples (each sample is from a different individual), the “FlowCytometryID” and the “PlantID” are the same.
- Year: Year when the plants were grown and/or collected and analyzed. “2017” for the plants from the first greenhouse common-garden cohort (sowed in September/October 2016), “2018” for the plants from the second greenhouse common-garden cohort (sowed in August/September 2017), and “2019” for the samples collected in the field in spring 2019.
- Place_PlantGrowing_SampleCollection: Information whether leaf material was collected from plants grown in the greenhouse common-garden at Uppsala University (“GreenhouseCommonGarden_UU”) or from plants in the natural populations in California (“Field_CA”).
- AnalysisPlace: Information where and by whom flow cytometry analyses were run. “UppsalaUniversity” for the samples analyzed by one of the authors at BIOVIS (Biolgical Visualisation) at Uppsala University, Sweden (https://biovis.uu.se/), and “PlantCytometryService” for the samples analyzed by Plant Cytometry Service (https://www.plantcytometry.nl/).
- IS: The species used as internal standard (IS) for the flow cytometry analyses.
- SampleISRatio: The sample:IS ratio calculated by dividing the median of the L. bolanderi peak by the median of the IS peak.
- PloidyLevel: Plant ploidy level determined based on discontinuities in the sample:IS ratios, and the information on the known ploidy levels from karyological counts by Taylor (1965) [R. L. Taylor, The genus Lithophragma (Saxifragaceae). University of California Publications in Botany 37, 1–122 (1965).]. “2x”: diploid, “3x”: triploid, “4x”: tetraploid, “5x”: pentaploid, “6x”: hexaploid, “8x”: octoploid.
2. 02_FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt
These data, or a subset thereof, were used to assess differences in floral morphology among Lithophragma bolanderi cytotypes both in univariate and multivariate analyses. For multivariate analyses, only traits with all pairwise correlations < 0.7 were included. These data were also used to estimate population means separately for diploids, tetraploids, and hexaploids using linear mixed-effect models (for details, see the main text and SI Appendix of the paper from which these data are), and these estimates, or a subset thereof, were used for additional analyses of differences among cytotypes that could only be conducted at the population level, such as the assessments of the effect of geographic distance on floral morphology differences and the relative contribution of plant ploidy level and Greya moth community on floral morphology variation. For details on how the traits were measured, see Fig. 2 and SI Appendix, Text S4, of the paper from which these data are.
The file contains the following variables:
- Population: Three-letter abbreviation of the population name.
- SeedFamily: Seed family (seeds collected from a single plant being half- and/or full-sibs) identity.
- PlantID: Individual code for each plant.
- Latitude: Latitude in °N on the population level.
- Longitude: Longitude in °E on the population level.
- Year: Year when the plants were grown and/or collected and analyzed. “Year1” for the plants from the first greenhouse common-garden cohort (sowed in September/October 2016), “Year2” for the plants from the second greenhouse common-garden cohort (sowed in August/September 2017).
- PloidyLevel: Plant ploidy level. “2x”: diploid, “4x”: tetraploid, “6x”: hexaploid.
- PloidyLevelMethod: Information whether relative ploidy level was measured using flow cytometry (“measured”), or whether it was set to be the same as the relative ploidy level measured using flow cytometry on another plant from the same seed family in populations where all analyzed samples had the same ploidy level (“inferred”).
- PloidyPop: A factor combining the information on plant ploidy level from column “PloidyLevel” and the population identity from column “Population”. This factor was used to estimate population means separately for diploids, tetraploids, and hexaploids using linear mixed-effect models (for details, see the main text and SI Appendix of the paper from which these data are) for further analyses.
- FlDi: Flower diameter in mm.
- CorOpDi: Corolla-opening diameter in mm.
- PetLen: Petal length in mm.
- PetWid: Petal width in mm.
- CorGap: Corolla gap in mm.
- FlLen: Overall flower length in mm.
- IntFlLen: Internal floral length in mm.
- OvDep: Ovary depth in mm.
- FlFlair: Floral flair in mm.
- LgAng: Long floral angle in mm.
- FlWid: Floral width in mm.
- NectLen: Nectary disc length in mm.
- LobeDi: Diameter of the largest stigmatic lobe in mm.
- LobeC: Stigma circumference in mm.
- StyleHt: Pistil height above the nectary disk in mm.
- FrillCode: Binary trait for the shape of the petal edge with “1” representing a lobed petal edge and “0” a whole petal edge. “NA” indicates that the assessment of the shape of the petal edge was unfortunately not possible.
- PC1: Score of the principal component 1 of a principal component analysis including the nine traits (“CorOpDi”, “PetLen”, “PetWid”, “CorGap”, “IntFlLen”, “OvDep”, “FlWid”, “LobeDi”, “StyleHt”) that had all pairwise correlations < 0.7.
- PC2: Score of the principal component 2 of a principal component analysis described in the description of the column “PC1”.
3. 03_FloralMorphologySyntheticPolyploidization_Data_Gross_etal_2025.txt
These data were used to assess the direct effects of polyploidization on floral morphology by comparing synthetically generated neopolyploids with established diploids and established tetraploids and colchicine-treated plants that remained diploid. With these data univariate and multivariate analyses were conducted. For multivariate analyses, the same raits as for the data of the Lithophragma bolanderi plants from the multi-population greenhouse common-garden were included. For details on how the traits were measured, see Fig. 2 and SI Appendix, Text S5.5, of the paper from which these data are.
The file contains the following variables:
- Population: Three-letter abbreviation of the population name.
- SeedFamily: Seed family (seeds from a single cross) identity.
- IndividualID: Individual code for each plant within a seed family.
- Donor_Seed_Family: Seed family identity of the pollen donor of the cross.
- Donor_ID: Individual identity of the pollen donor of the cross.
- Receiver_Seed_Family: Seed family identity of the pollen receiver of the cross.
- Receiver_ID: Individual identity of the pollen receiver of the cross.
- ParentalSeedFamily_Donor_Receiver: Factor combining the information of the column “Donor_Seed_Family” (number in front of “”) and the column “Receiver_Seed_Family” (number after “”).
- Year: Year when the plants were collected and analyzed. “2021” for the plants from the first cohort (sowed in March 2021), “2022” for the plants from the second cohort (sowed in December 2021).
- FlowCytometryID: Individual ID used for flow cytometry analyses. “NA”: no flow cytometry analyses was conducted for this control plant.
- SampleISRatio: The sample:internal-standard (IS) ratio calculated by dividing the median of the L. bolanderi peak by the median of the IS peak. “NA”: no flow cytometry analyses was conducted for this control plant.
- PloidyLevel: Plant ploidy level determined based the sample:IS ratios and the ploidy level information previously determined (see “1. FlowCytometry_Data_Gross_etal_2025.txt”). “2x”: diploid, “3x”: triploid, “4x”: tetraploid.
- Treatment: Information whether the parental plants were treated with colchicine (“treatment”) or not “control”).
- Treatment_Ploidy: Factor combining the information from column “Treatment” and “PloidyLevel”.
- FlDi: Flower diameter in mm.
- CorOpDi: Corolla-opening diameter in mm.
- PetLen: Petal length in mm.
- PetWid: Petal width in mm.
- CorGap: Corolla gap in mm.
- IntFlLen: Internal floral length in mm.
- FlFlair: Floral flair in mm.
- LgAng: Long floral angle in mm.
- FlLen: Overall flower length in mm.
- OvDep: Ovary depth in mm.
- FlWid: Floral width in mm.
- NectLen: Nectary disc length in mm.
- LobeDi: Diameter of the largest stigmatic lobe in mm.
- LobeC: Stigma circumference in mm.
- StyleHt: Pistil height above the nectary disk in mm.
- PC1: Score of the principal component 1 of a principal component analysis including the nine traits (“CorOpDi”, “PetLen”, “PetWid”, “CorGap”, “IntFlLen”, “OvDep”, “FlWid”, “LobeDi”, “StyleHt”) also included in principal component analysis run on the traits in the data file “2. FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt”.
- PC2: Score of the principal component 2 of a principal component analysis described in the description of the column “PC1”.
4. 04_FloralMorphologyFieldCommonGarden_Data_Gross_etal_2025.txt
These data were used to compare the floral morphology between plants growing in natural populations and plants grown in the multi-population greenhouse common-garden from seeds collected in these natural populations for a subset of the populations included in the data file “2. FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt”.
The file contains the following variables:
- Population: Three-letter abbreviation of the population name.
- PlantID: Individual code for each plant. Note that the numerical part of the “PlantID” for the greenhouse-grown plants is the seed family (seeds collected from a single plant being half- and/or full-sibs) identity and the letter code part of the “PlantID” for plants in the natural population is the three-letter abbreviation of the name of the population.
- Latitude: Latitude in °N on the population level.
- Longitude: Longitude in °E on the population level.
- Origin: Information whether the measurements were taken from plants in the natural populations (“Field”) or from plants grown in the greenhouse common-garden (“Greenhouse”).
- FlDi: Flower diameter in mm.
- CorOpDi: Corolla-opening diameter in mm.
5. 05_FlowCytometryMethods_Data_Gross_etal_2025.txt
These data were used to assess the comparability of the flow-cytometry protocol by Plant Cytometry Service (https://www.plantcytometry.nl/) with the one used by the authors at BIOVIS (Biolgical Visualisation) at Uppsala University, Sweden (https://biovis.uu.se/).
The file contains the following variables:
- FlowCytometryID: Individual ID used for the flow cytometry analyses of the samples analyzed by Plant Cytometry Service.
- SeedFamily: Seed family (seeds from a single cross) identity.
- PlantID: Individual code for each plant.
- Population: Three-letter abbreviation of the population name.
- DonorID: Individual identity of the pollen donor of the cross. Note that the three letters at the beginning of the code are the three-letter abbreviation of the population name, and the numerical part is the seed family (seeds collected from a single plant being half- and/or full-sibs) identity.
- ReceiverID: Individual identity of the pollen receiver of the cross. Note that the three letters at the beginning of the code are the three-letter abbreviation of the population name, and the numerical part is the seed family (seeds collected from a single plant being half- and/or full-sibs) identity.
- PloidyLevel: Plant ploidy level. “2x”: diploid, “4x”: tetraploid, “6x”: hexaploid.
- Donor_SampleBnRatio_UU: The sample:internal-standard (IS) ratio of the pollen-donor plant calculated by dividing the median of the Lithophragma bolanderi peak by the median of the IS peak (Brassica napus was used as IS). The flow cytometry analyses to quantify these sample:IS rations were conducted by one of the authors at Uppsala University. For the plant with the “DonorID” “MIN11450A” flow cytometry analysis was unfortunately not possible and the “Donor_SampleBnRatio_UU” was calculated as the mean sample:IS ratio of the other individuals of that plant’s seed family for which quantification of the sample:IS ratio was possible (these sample:IS ratios were 0.83423624 for MIN11450H, 0.82111261 for MIN11450I, 0.83191792 for MIN11450J, 0.83046457 for MIN11450K, and 0.83886178 for MIN11450L).
- Receiver_SampleBnRatio_UU: The sample:IS ratio of the pollen-donor plant calculated by dividing the median of the L. bolanderi peak by the median of the IS peak (B. napus was used as IS). The flow cytometry analyses to quantify these sample:IS rations were done by one of the authors at Uppsala University.
- SampleIBnRatio_UU: The sample:IS ratio quantified based on the flow cytometry analyses conducted by one of the authors at Uppsala University and calculated as the mean of “Donor_SampleBnRatio_UU” and “Receiver_SampleBnRatio_UU”.
- SampleBnRatio_PCS: The sample:IS ratio quantified by Plant Cytometry service using B. napus as IS in the flow cytometry analyses.
- SampleAsRatio_PCS: The sample:IS ratio quantified by Plant Cytometry service using Allium schoenoprasum as IS in the flow cytometry analyses.
6. 06_TraitMeasuringComparability_Data_Gross_etal_2025.txt
These data were used to ensure that the measuring of the floral morphological traits were repeatable, because the flowers were apportioned among three persons to conduct the measurements. In particular, these data were used to compute the correlation of one person remeasuring a subset of the flowers measured by the two other persons. Note that the measures of the flowers in this data file might slightly differ from the measures for the flowers with the same plant ID in the file “2. FloralMorphology27PopulationCommonGarden_Data_Gross_etal_2025.txt”, because this one person remeasured some traits for all flowers and took some additional measures to ensure the accuracy of the measures (such as visually checking for “outliers” separately for each population and cytotype, double-checking these measures, and remeasuring them if necessary) after the assessment of the correlation of measurements between two different persons. For details on how the traits were measured, see Fig. 2 and SI Appendix, Text S4, of the paper from which these data are.
The file contains the following variables:
- Person: Person who measured the floral morphological traits based on the photos taken of the flowers. “P1”: person 1, “P2”: person 2, “P3”: person 3, who was the person remeasuring a subset of the flowers measured by P1 and P2.
- Measuring: Information whether the measurements were initial measurements conducted by P1 or P2 (“1stMeasuring”) or remeasurements conducted by P3 (“Remeasuring”).
- Population: Three-letter abbreviation of the population name.
- PlantID: Individual code for each plant. The numerical part of the “PlantID” is the seed family (seeds collected from a single plant being half- and/or full-sibs) identity.
- PetLen1: Length of the first randomly selected petal in mm.
- PetWid1: Width of the first randomly selected petal in mm.
- PetLen2: Length of the second randomly selected, non-adjacent petal in mm.
- PetWid2: Width of the second randomly selected, non-adjacent petal in mm.
- CorGap: Corolla gap in mm.
- FlLen: Overall flower length in mm.
- IntFlLen: Internal floral length in mm.
- FlFlair: Floral flair in mm.
- LgAng1: Long floral angle measured in the first direction in mm.
- LgAng2: Long floral angle measured in the second direction in mm.
- FlWid: Floral width in mm.
- NectLen: Nectary disc length in mm.
- LobeDi: Diameter of the largest stigmatic lobe in mm.
- LobeC1: Outer distance between stigmatic lobe 1 and 2 in mm.
- LobeC2: Outer distance between stigmatic lobe 2 and 3 in mm. “NA”: this measurement was not possible for this flower because it had only two stigmatic lobes.
- LobeC3: Outer distance between stigmatic lobe 3 and 1 in mm or between stigmatic lobe 3 and 4 for flowers that had 4 stigmatic lobes. “NA”: this measurement was not possible (see explanation to “LobeC2”).
- LobeC4: Outer distance between stigmatic lobe 4 and 1 in mm in case there were four stigmatic lobes. “NA”: this measure was not possible, because there were only two or three (this is the case by far the most flowers) stigmatic lobes in the flower.
- StyleHt: Pistil height above the nectary disk in mm.
Sharing/Access information
These data are not accessible at another location.
These are original data and not derived from another source.
In 29 natural populations of the plant Lithophragma bolanderi in the Sierra Nevada, California, USA, seeds were collected. A subset of these seeds was grown in a greenhouse common-garden. When the plants were well established, leaf material was collected and analyzed using flow cytometry (conducted by one of the authors with Brassica napus as internal standard) to assess plant ploidy level, flower diameter and corolla-opening diameter were measured of fresh flowers using digital calipers, and flowers were collected, stored in 70% ethanol, dissected, and photographed to quantify additional floral morphological traits based on the photos and to assess the shape of the petal edge. As the flowers were apportioned among three persons to conduct the measurements, one of these persons remeasured a subset of the flowers measured by the other two persons. In cases where the measurements were not highly correlated, this one person remeasured these traits for all samples. This one person also visually checked for “outliers” separately for each population and cytotype, double-checked these measures, and remeasured them if necessary. The morphological floral traits with all pairwise correlations < 0.7 were included in a principal coordinate analysis (PCA) and the principal components (PCs) used for further analyses were also included in the dataset.
In a subset of the natural populations of the plant L. bolanderi, in which seeds were collected, flower diameter and corolla-opening diameter were measured of fresh flowers using digital calipers and compared to the flower diameter and corolla-opening diameter measured on a randomly selected subset of the plants from the same populations grown in the greenhouse common-garden (see above).
In an addition 11 natural populations of the plant L. bolanderi, leaf material was collected and analyzed using flow cytometry (conducted by Plant Cytometry Service [https://www.plantcytometry.nl/] with Allium schoenoprasum as internal standard) to assess plant ploidy level.
Some L. bolanderi plants were grown from seeds (derived from crosses between individuals of the same cytotype and from the same population but from different seed families of plants grown from root bulbils of the greenhouse common-garden plants) in a greenhouse common-garden. When the plants were well established, leaf material was collected and analyzed using flow cytometry (conducted by Plant Cytomerty Service once with B. napus and once with A. schoenoprasum as internal standard). The sample to internal standard rations were compared between the two internal standards and with those of the parental seed families quantified by one of the authors with B. napus as internal standard.
An additional subset of the seeds collected in one natural L. bolanderi population, in which both diploids and tetraploids grow, was grown in a greenhouse common-garden. A subset of the diploid seedlings was treated with colchicine to induce polyploidization. When plants were well established, leaf material was collected and analyzed using flow cytometry to verify plant ploidy level. When these plants were flowering, hand-pollination crossings were conducted among colchicine treated plants that were at least partially polyploid, among diploid control plants, and among tetraploid control plants. These crosses were done to mitigate side effects of colchicine. The seeds resulting from these crossings were used to grow F1 plants. When the F1 plants were well established, leaf material of all colchicine-treated plants and a subset of the diploid and tetraploid control plants was collected and analyzed using flow cytometry (conducted by Plant Cytomerty Service with A. schoenoprasum as internal standard) to verify plant ploidy level, flower diameter and corolla-opening diameter were measured of fresh flowers using digital calipers, and flowers were collected, stored in 70% ethanol, dissected, and photographed to quantify the additional floral morphological traits based on the photos (see above). The same morphological floral traits as for the data of the L. bolanderi plants from the multi-population greenhouse common-garden were included in a PCA and the PCs used for further analyses were also included in the dataset.
For details, see:
Karin Grossa, Homa Papoli Yazdi, Elisabeth Schlager, Jodie Lilley, Andrés Romero-Bravo, Anna Runemark, John N Thompson, and Magne Friberg. Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae). Proceedings of the National Academy of Sciences.