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Phenotypic plasticity can alter traits that are crucial to population\n establishment in a new environment, before adaptation can occur. How often\n phenotypic plasticity enables subsequent adaptive evolution is unknown,\n and examples of the phenomenon are limited. We investigated the hypothesis\n of plasticity-mediated persistence as a means of colonization of\n agricultural fields in one of the world’s worst weeds, Raphanus\n raphanistrum ssp. raphanistrum. Using non-weedy native populations of the\n same species and subspecies as a comparison, we tested for\n plasticity-mediated persistence in a growth chamber reciprocal transplant\n experiment. We identified traits with genetic differentiation between the\n weedy and native ecotypes as well as phenotypic plasticity between growth\n chamber environments. We found that most traits were both plastic and\n differentiated between ecotypes, with the majority plastic and\n differentiated in the same direction. This suggests that phenotypic\n plasticity may have enabled radish populations to colonize and then adapt\n to novel agricultural environments."],"TechnicalInfo":["# Growth Chamber Reciprocal Transplant Dataset\n [https://doi.org/10.5061/dryad.4mw6m90kb](https://doi.org/10.5061/dryad.4mw6m90kb) This dataset contains the phenotypic data collected from plants grown in the growth chamber reciprocal transplant experiment, as well as the conditions in the growth chambers. ## Description of the data and file structure The dataset contains three sheets: "Chamber Conditions", "Main Data", and "Leaf Data" (although much of the information in "Leaf Data" has been incorporated into "Main data") ### Chamber Conditions This sheet contains the temperature and day length set points for each chamber each week. All temperature and day length information from the two weather stations used (LGER and KBTL) were collected from [www.wunderground.com](http://www.wunderground.com). Variables: * Granada, Spain (LGER) - the dates from which we collected temperature and day length information from the Grenada, Spain weather station (LGER) to simulate in the Winter Annual chamber * HighTempGrenada - the Winter Annual chamber's daytime set points, based on the average maximum temperature in Grenada on a given day * LowTempGrenada - the Winter Annual chamber's nighttime set points, based on the average minimum temperature in Grenada on a given day * DayLengthGrenada - the length of time the Winter Annual chamber was in its day cycle (lights on and typically higher temps), based on length of visible light in Grenada * DayStartGrenada - programed start of day time in the Winter Annual growth chamber * DayEndGrenada - programmed end of day time in the Winter Annual growth chamber * Date Set - the real-life date on which we changed the chamber conditions. * Augusta, MI (KBTL) - the dates from which we collected temperature and day length information from the Augusta, MI, USA weather station (KBTL) to simulate in the Spring Annual chamber * HighTempAugusta - the Spring Annual chamber's daytime set points, based on the average maximum temperature in Augusta on a given day * LowTempAugusta - the Spring Annual chamber's nighttime set points, based on the average minimum temperature in Augusta on a given day * DayLengthAugusta - the length of time the Spring Annual chamber was in its day cycle (lights on and typically higher temps), based on length of visible light in Augusta * DayStartAugusta - programed start of day time in the Spring Annual growth chamber * DayEndAugusta - programmed end of day time in the Spring Annual growth chamber ### Main Data This sheet contains all of the data used in our analyses, as well as descriptors for plants and growth chambers. Variables: * Chamber # - the number designation of the four growth chambers used in this study * Environment - the growing conditions in a given growth chamber, with "Winter Annual" corresponding to the "Grenada, Spain (LGER)" columns in Chamber Conditions, and "Spring Annual" corresponding to "Augusta, MI (KBTL)" * Ecotype - variety of* R. raphanistrum*, either weedy or native * Population - the six source populations used in this study identified by their location codes, with the final two letters denoting country or state (FR=France, ES=Spain, NY=New York, NC=North Carolina) and the first two letters denoting a specific location in those areas (available in Table 1 of the manuscript) * Matriline -  a line number is listed when discrete matrilines are known from field collections, but not for seeds collected in bulk (in which case the cell will be blank) * Flat - plants were arranged into four flats in each chamber, and the flats within a chamber were each assigned a number (1-4) * Position - the position of each plant within a flat was also tracked and pots were assigned a position number (1-35) * Pot# - Number assigned to each plant to give it a unique identifier -- for plants with individual matrilines tracked, pot # only went up to 2, while plants with unknown matrilines had pot numbers up to 40 to ensure individuals could be tracked * Plant Date - the date seeds were sown into each pot * Germ[1-5] - the date that each one of 5 seeds planted emerged as a germinant -- blank cells indicate that a germinant did not emerge * Plant Kept - the emergence date of the single plant that remained in the pot after excess germinants were thinned; missing values mean no germinants emerged or did not survive past the seedling stage * Days to Emergence - calculated as the day of emergence minus the planting date; missing values mean no germinants emerged or did not survive past the seedling stage * Rosette Photo Date - the date on which overhead and side photos of plants were taken, also the day the plants first showed signs of bolting (buds visible); missing values mean the plant did not survive to bolting * \\# Rosette Leaves - the number of leaves in the basal rosette, counted on the day of bolting; missing values mean the plant did not survive to bolting * Rosette Height - the vertical height of the tallest free-standing basal rosette leaf, measured from the height of the soil (cm); missing values mean the plant did not survive to bolting * 1st flower date - the date on which the first flower on a plant opened; missing values mean the plant did not survive to flowering * Days to First Flower - calculated as 1st flower date minus emergence date; missing values mean the plant did not survive to flowering * 1st Flower Height - measured on the first flower date, it is the vertical distance from the soil to the point at which the first open flower's pedicel connects to the main stalk (cm); missing values mean the plant did not survive to flowering * Ovule # - collected from typically the third flower to open, it is the number of ovules in one flower of a given plant; missing values mean the plant did not survive to flowering or ovules were not clearly visible * Notes - any additional information on a plant that we tracked * Blossom Photo Date - the date on which we took top and side photographs of at least the third flower to open, taken at the same time that ovule number was counted; missing values mean the plant did not survive to flowering  * PetalLength - measured using a top-view photo in Image J, the distance from the tip of the petal to where it meets the floral tube in the center of the floral display (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * PetalWidth - measured using a top-view photo in Image J, the distance from the widest part of the petal, perpendicular to the line measured for petal length (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * Tube - measured using a side-view photo in Image J, the length of the most clearly visible petal from where it meets the pedicel to the apex of its curve outward (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * LAnther - measured using a side-view photo in Image J, the length of the anther of the long stamen from where it meets its filament to its tip (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * LFilament - measured using a side-view photo in Image J, the length of the frontmost (closest to the camera) long filament from where it meets the pedicel to where it meets its anther (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * SAnther - measured using a side-view photo in Image J, the length of the anther of the short stamen from where it meets its filament to its tip (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * SFilament - measured using a side-view photo in Image J, the length of the frontmost (closest to the camera) short filament from where it meets the pedicel to where it meets its anther (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * Pistil - measured using a side-view photo in Image J, the length of the pistil made by drawing a line down the center of the pistil from the top of the stigma to where it meets the pedicel (mm); missing values mean the plant did not survive to flowering or the view in the photo was obscured so the measurement could not be taken * AntherExsertion - calculated as long filament length minus the tube length (mm); missing values mean the plant did not survive to flowering or that either one of the values needed for the measurement was missing * AntherSeparation - calculated as long filament length minus the short filament length (mm); missing values mean the plant did not survive to flowering or one or that either one of the values needed for the measurement was missing * FlowerSize - the geometric mean of all floral traits (excluding anther exsertion and anther separation; mm); missing values mean the plant did not survive to flowering or one or more flower trait was missing * LeafWidth - measured using either a top-view or side-view photo in Image J, the distance between each edge of the leaf measured at its widest point, with the line being perpendicular to the central leaf vein on the largest fully visible leaf (more information in the Leaf Data sheet; cm); missing values mean the plant did not survive to bolting or a picture was not taken * LeafLength -  measured using either a top-view or side-view photo in Image J using the segmented line tool, follow the central vein of the largest visible leaf from the center of the rosette to the tip of the leaf (more information in the Leaf Data sheet; cm); missing values mean the plant did not survive to bolting or a picture was not taken ### Leaf Data This sheet includes some additional information about Leaf Length and Leaf Width measurements. Side image was only used when leaf was not flat or clearly visible in the top image. Variables: * Top Photo Image - image ID of the top view photo of the plant being measured * Ecotype - the ecotype of the plant (more information in Main Data) * Population - the population that the plant belongs to (more information in Main Data) * Plant Label - the label visible in the image -- includes population, matriline (when available), and pot # * Leaf Width (cm) - measured using the top-view photo in Image J, the distance between each edge of the leaf measured at its widest point, with the line being perpendicular to the central leaf vein on the largest fully visible leaf; missing values mean that a picture was not taken or the leaf was obscured in the top view photo * Leaf Length 1 (cm) - measured using the top-view photo in Image J using the segmented line tool, follow the central vein of the largest visible leaf from the center of the rosette to the tip of the leaf; missing values mean that a picture was not taken or the leaf was obscured in the top view photo * Side Photo Image - Image ID of the side view photo of the plant being measured; side image was only used when leaf was not flat or clearly visible in the top image, so missing values indicate that the length and width of the leaf could be reliably measured using the top view photo * Leaf Length 2 (cm) - measured using the side-view photo in Image J using the segmented line tool, follow the central vein of the largest visible leaf from the center of the rosette to the tip of the leaf; missing values mean that a picture was not taken or that the length of the leaf could be reliably measured using the top view photo * Leaf Width 2 (cm) - measured using the side-view photo in Image J, the distance between each edge of the leaf measured at its widest point, with the line being perpendicular to the central leaf vein on the largest fully visible leaf; missing values mean that a picture was not taken or that the width of the leaf could be reliably measured using the top view photo * Notes - any additional information about the the measurement of a particular plants' leaf length or width"]} 

Abstract Traits that have lost function sometimes persist through evolutionary time. Persistence may occur if there is not enough standing genetic variation for the trait to allow a response to selection, if selection against the trait is weak relative to drift, or if the trait has a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in northeast Spain. A. thaliana is highly self-pollinating and prior work suggests short stamens do not contribute to self-pollination. We found a cline in short stamen number from retention of short stamens in high-elevation populations to incomplete loss in low-elevation populations. We did not find evidence that limited genetic variation constrains short stamen loss at high elevations, nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in northeast Spain that are different from loci associated with variation in short stamens across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms contributing to an elevational cline in short stamen number so further research is clearly warranted. 

{"Abstract":["Traits that have lost function sometimes persist through evolutionary\n time. Persistence may occur if there is not enough standing genetic\n variation for the trait to allow a response to selection, if selection\n against the trait is weak relative to drift, or if the trait has a\n residual function. To determine the evolutionary processes shaping whether\n nonfunctional traits are retained or lost, we investigated short stamens\n in 16 populations of Arabidopsis thaliana along an elevational cline in\n northeast Spain. A. thaliana is highly self-pollinating and prior work\n suggests short stamens do not contribute to self-pollination. We found a\n cline in short stamen number from retention of short stamens in high\n elevation populations to incomplete loss in low elevation populations. We\n did not find evidence that limited genetic variation constrains short\n stamen loss at high elevations, nor evidence for divergent selection on\n short stamens between high and low elevations. Finally, we identified loci\n associated with short stamens in northeast Spain that are different from\n loci associated with variation in short stamens across latitudes from a\n previous study. Overall, we did not identify the evolutionary mechanisms\n contributing to an elevational cline in short stamen number so further\n research is clearly warranted. This dryad dataset includes the GWAS output\n results. See the github for phenotypic data and SRA for genotypic data."],"TechnicalInfo":["# Evaluating the roles of drift and selection in trait loss along an\n elevational gradient Dataset DOI:\n [10.5061/dryad.8sf7m0d0z](10.5061/dryad.8sf7m0d0z) ## Description of the\n data and file structure These files are the relatedness matrices and GWAS\n output files for a GWAS on short stamen number in *A.\n thaliana* from an elevation gradient across the Pyrenees. The\n associated paper is "Evaluating the Roles of Drift and Selection in\n Trait Loss along an Elevational Gradient" by Buysse et al. The code\n used to generate the files can be found on\n github: [https://github.com/sfbuysse/A_thaliana_StamenLoss_2025](https://github.com/sfbuysse/A_thaliana_StamenLoss_2025).  The input data is SNP information for 61 genotypes from 16 native populations of *A. thaliana*. ### Files and variables #### File: RelatednessMatrices.zip **Description:** **RelatednessMatrices.zip** contains centered Relatedness Matrices made with GEMMA v0.98.4. Relatedness matrices are *.cXX.txt and *.log.txt show the code and run log information. allSNPs.PlinkFiltering_Asin, allSNPs.PlinkFiltering_Binary, allSNPs.PlinkFiltering_raw : identical relatedness matrices made using all SNPs in the dataset after filtering with Plink. Names were changed to match the phenotype files to run the GWAS.  allSNPs.PlinkFiltering*_*raw_subset : centered relatedness matrix made with all SNPs after plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2). NoCent.PlinkFiltering_Asin, NoCent.PlinkFiltering_Binary, NoCent.PlinkFiltering_raw  : identical relatedness matrices made after excluding the centromere region and filtering with Plink. Names were changed to match the phenotype files to run the GWAS.  NoCent.PlinkFiltering_raw_subset. : centered relatedness matrix made after excluding the centromere and plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2). #### File: GWAS.zip **Description:** **GWAS.zip** contains GWAS output files. The GWAS output files are  *.assoc.txt and the code information is  *.log.txt. GWAS were run in GEMMA v0.98.4. Within each .assoc.txt file the columns are as follows: * chr = chromosome * rs = snp id (chromosome:base pair position) * ps = base pair position * n_miss = number of genotypes missing genetic information at that SNP * allele1 = minor allele * allele2 = major allele * af = minor allele frequency * beta = affect size * se = standard error for beta * log_lH1 = log liklihood of alternative hypothesis that beta does not equal 0 (H0 is that beta =0) * l_remle = restricted maximum liklihood estimates for lambda * l_mle = maximum liklihood estimates for lambda * p_wald = p value from the Wald test * p_lrt = p value from liiklihood ratio test * p_score = p value from score test allSNPs.PlinkFiltering_Asin.c : include allSNPs after filtering with plink. phenotypes were arcsine transformed before GWAS. Centered relatedness matrix used. allSNPs.PlinkFiltering_Binary.c : include allSNPs after filtering with plink. phenotypes were transformed to a binary trait before GWAS - no short stamen loss = 0, any short stamen loss = 1. Centered relatedness matrix used. allSNPs.PlinkFiltering_raw.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS. Centered relatedness matrix used. allSNPs.PlinkFiltering*_*raw_subset.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS but the individuals used were subset down to only those that had some short stamen loss (mean short stamen number < 2). Centered relatedness matrix used. NoCent.PlinkFiltering_Asin.c : Centromere excluded. Plink Filtering as before. Arcsine transformed phenotypes. Centered relatedness matrix. NoCent.PlinkFiltering_Binary.c : Centromere excluded. Plink Filtering as before. Phenotypes converted to a binary trait. Centered relatedness matrix. NoCent.PlinkFiltering_raw.c : Centromere excluded. Plink Filtering as before. Phenotypes not transformed. Centered relatedness matrix. NoCent.PlinkFiltering_raw_subset.c : Centromere excluded. Plink Filtering as before. Individuals subset to only those that had some short stamen loss. Centered relatedness matrix. ## Code/software We used GEMMA v0.98.4 to create the files. ## Access information Other publicly accessible locations of the data: * [https://github.com/sfbuysse/A_thaliana_StamenLoss_2025](https://github.com/sfbuysse/A_thaliana_StamenLoss_2025) : scripts and information for creation of input files and use of output files after generation. * Genotypic data used is submitted to NCBI SRA as accession PRJNA1246133."]}