This readme.txt file was generated on <2022-12-30> by Emily Dittmar ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Temporal variation in selection influences microgeographic local adaptation 2. Author Information Principal Investigator Contact Information Name: Emily Dittmar Institution: University of Georgia Address: 2502 Miller Plant Sciences, Athens, GA 30602-7271 Email: dittmare@gmail.com ORCID: 0000-0002-3085-6796 Associate or Co-investigator Contact Information Name: Doug Schemske Institution: Michigan State University Email: schem@msu.edu 3. Date of data collection (single date, range, approximate date) 2012-2016 4. Geographic location of data collection: Jasper Ridge Biological Preserve, San Mateo county California Greenhouse data collected from Michigan State University, East Lansing Michigan 5. Information about funding sources that supported the collection of the data: National Science Foundation, Doctoral Dissertation Improvement Grant, DEB-1407149 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: ReciprocalTransplant.csv Fitness data of source populations in both soil types across the four years of study B. Filename: SeedPlots.csv Fitness data of source populations in both soil types from plants started from seeds instead of seedlings C. Filename: Greenhouse.csv Fitness data of source populations in both soil types grown in the greenhouse under two watering treatments D. Filename: Hydroponic.csv Fitness data of source populations grown in different nutrient solutions with varying amounts of MgSO4 E. Filename: JRPrecipitationData.csv Precipitation data collected from Jasper Ridge and Woodside, California weather station and provided by Nona Chiariello on 9/10/2015 (Note: the raw file was provided in .xls format. See 'Precipitation_analyses.R' script for code used to create formatted version uploaded here 2. Relationship between files: The sandstone or serpentine source populations & soils are consistent across datasets/experiments. 3. Additional related data collected that was not included in the current data package: Flowering time data of parental populations from the same field and greenhouse experiments, as well as fitness data from F5 advanced-generation hybrids from the same field experiment can be found at: https://doi.org/10.5061/dryad.t1778 The rainfall data discussed in the manuscript was provided by Jasper Ridge Biological Preserve -------------------------- METHODOLOGICAL INFORMATION -------------------------- ReciprocalTransplant.csv: Reciprocal transplant experiments were conducted at Jasper Ridge Biological Preserve (JRBP) in San Mateo county California during four spring growing seasons between 2012-2015 with populations of Leptosiphon parviflorus. These populations grow on serpentine soil and sandstone soil in close proximity (~100 m.) at JRBP. Plants were transplanted at the seedling stage. Source seeds were collected from maternal plants grown in common greenhouse conditions that descended from plants collected from both populations at the study locations. After germination, seedlings were first transplanted into plug trays containing either serpentine or sandstone soil collected from the study site, and then transplanted into the field. During the first 1-2 weeks of growth all plants were watered, after which supplemental watering ceased. Any seedlings that died before establishment (defined as 10 days after field transplant) were excluded from the dataset. Study plants were censused periodically to count the number of flowers and fruits produced and whenever possible fruits were collected to count the number of seeds per fruit. SeedPlots.csv: Seeds from each population were collected from maternal plants grown in a common greenhouse environment, and in mid-December, roughly the time period that plants naturally germinate in the field, five seeds from each source population were placed in 100 cells in randomized order across an 11 x 24 grid. The remaining cells were kept empty to ensure that natural germinants were not being counted. In March, (approximately 3 months after sowing), plants in each grid position were thinned to leave only one focal seedling to follow for remaining fitness estimates. Greenhouse.csv: Greenhouse experiments were performed at [redacted] using soil collected from JRBP at both field locations. Seeds were germinated using the same methods as described for the field experiment, except after two weeks in an incubator, seedlings were transplanted to cone-tainers filled with a mixture of sieved field soil (serpentine or sandstone) and perlite in a 4:1 ratio. Seedlings were top watered for 3 days after transplanting, and then exclusively bottom watered. After one month of growth, plants were randomly assigned to one of two treatments: an unlimited water treatment where plants were continuously bottom watered throughout the duration of the experiment, or a drought treatment, where watering was ceased when the first plant began flowering, which occurred approximately one month after transplanting. Hydroponic.csv: Hydroponic experiments were performed at Michigan State University. Seeds from each parental population were sown in randomized order directly into rockwool sheets of 1” x 1” cubes (©Grodan) saturated with deionized water. These were placed in the dark at 4°C for ten days while periodically spraying with nutrient solution. They were then transferred to a growth chamber set at 22°C, 12-hour days and the rockwool was kept moist using 1⁄2 strength Hoagland’s solution and supplemental spraying of deionized water. After five days in the growth chamber, seedling germination and survival were censused. Seedlings were allowed to grow in half-strength Hoagland’s solution for an additional five days before being randomly assigned to one of four treatments with two replicate blocks per treatment. Block location in the growth chamber was randomized twice per week. The nutrient solution (1⁄2-strength Hoagland’s) was provided by the MSU growth chamber facility and contained calcium nitrate (3.6 mmole l-1), potassium nitrate (2.5 mmol l-1), potassium phosphate (400 μM l-1), boric acid (24 μM l-1), manganous sulphate (5 μM l-1), zinc sulphate (700 nmol l-1), copper sulphate (263 nmol l-1), and sequestrene iron chelate (38 mg l-1) dissolved in deionized water. The control solution (also used in the initial growth stages of all plants) contained 1 mmol l-1 MgSO4. The treatments consisted of a control treatment (half-strength Hoagland’s containing 1 mmol l-1 MgSO4), and three treatments with increasing amounts of magnesium sulfate (50 mM, 100 mM, 150 mM) added to the nutrient solution. Solutions were replaced two times per week, which allowed the rock wool to stay moist throughout the experiment. Plants were censused twice a week for flowering and survival and at the end of the experiment the total lifetime production of flowers was counted for each individual. A leak in one of the flats caused plants in one of the control blocks to dry and senesce prematurely, therefore these plants were excluded from analyses of fecundity and total fitness. JRdailyprecip1983-2015.csv Data collected from weather station data at Jasper Ridge Biological Preserve. Data also available from Woodside Fire Station from NOAA (used to fill in gaps when precipitation data were missing from JRBP) Data were formatted to make machine-readable (see Precipitation_analyes.R) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ReciprocalTransplant.csv ----------------------------------------- 1. Number of variables: 12 2. Number of cases/rows: 1599 Each row corresponds to data from an individual plant. Plants were planted in randomized order in each soil type (PlotRow and PlotColumn correspond to the grid position of the plant in a study plot) 3. Missing data codes: NA Data was not collected 4. Variable List A. Name: Year The year which the reciprocal transplant experiment was conducted 2012-2015 B. Name: SoilType Description: The soil environment where the plant was grown Sand or Serp C. Name: Population Description: The source population SandPop or SerpPop D. Name: PlotRow Description: The row position of the individual in the plot E. Name: PlotColumn Description: The column position of the individual in the plot F. Name: Edge Description: Whether or not the position was on the edge of the plot Edge or Non-edge G. Name: Plot_Rep Description: The plot replicate in each soil type In 2014 and 2015 replicate plots were used in each soil type, in 2012-2013 there was only 1 plot per soil type H. Name: Surv_flr Description: Whether of not the plant survived to flower 0 = died before flowering 1 = survived to flower I. Name: Num_flrs Description: The total number of flowers the plant produced in its lifetime NA means that data was not obtained J. Name: Num_frts Description: The total number of fruits the plant produced in its lifetime NA means that data was not obtained K. Name: Numfruits_collected Description: The total number of fruits collected from each plant for counting seeds NA means no fruits were collected L. Name: Num_seeds Description: The total number of seeds counted out of the total number of fruits collected ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: SeedPlots.csv ----------------------------------------- 1. Number of variables: 19 2. Number of cases/rows: 528 Five seeds were sown at each grid position listed. Some cells were kept empty to ensure that natural germinants were not being counted. After 3 months, seedlings were thinned to leave 1 individual for lifetime fitness censuses. See methodological information for more details 3. Missing data codes: NA Data was not collected blank Cells where no seeds were sown 4. Variable List A. Name: SoilType Description: The soil environment where the plant was grown Sand or Serp B. Name: Population Description: The source population SandPop or SerpPop (blank means that no seeds were sown at this position) C. Name: SeedBatch Description: The time period over which seeds were collected from maternal plants in the greenhouse D. Name: PlotRow Description: The row position in the plot E. Name: PlotColumn Description: The column position in the plot F. Name: Edge Description: Whether or not the plant position was on the edge of the plot Edge or Non-edge G. Name: NumGerm_Jan Description: The number of seedlings counted at the first census in January H. Name: AveSize_Jan Description: The average size of the seedlings that germinated in January 1 = small 2 = medium 3 = large I. Name: Total_germ Description: The total number of seedlings that germinated based on three censuses conducted (January, February, March). J. Name: TotalSurv_March Description: The total number of seedlings that survived until March (3 months after sowing) K. Name: GERM_FOCAL Description: Whether or not a seedling germinated 0 = No seedlings germinated 1 = At least 1 seedling germinated L. Name: SEEDLING_SURV_FOCAL Description: Whether or not a seedling survived for the first 3 months 0 = No seedlings survived 1 = At least 1 seedling survived this time period M. Name: SIZE_FOCAL Description: The size of the focal seedling left after thinning in March 1 = small 2 = medium 3 = large N. Name: SURV_FLR Description: Whether or not the focal seedling survived to flower 0 = Died before flowering 1 = Survived to flower O. Name: DATE_FF Description: The date that the focal plant began flowering P. Name: NUM_FLRS Description: The total number of flowers the focal plant produced in its lifetime Q. Name: NUM_FRTS Description: The total number of fruits the focal plant produced in its lifetime R. Name: NUMFRUITS_COLLECTED Description: The total number of fruits collected from the focal plant for counting seeds NA means no fruits were collected S. Name: NUMSEEDS Description: The total number of seeds counted out of the total number of fruits collected from the focal plant ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Greenhouse.csv ----------------------------------------- 1. Number of variables: 8 2. Number of cases/rows: 454 3. Missing data codes: NA Data not collected 4. Variable List A. Name: Plant Description: A unique number for each plant on each flat B. Name: SoilType Description: The soil type used Sand or Serp C. Name: Population Description: The source population SandPop or SerpPop D. Name: Treatment Description: The watering treatment applied Control = Plants were bottom-watered continuously throughout experiment Dry = Watering ceased when the first plant began flowering E. Name: Initial_flat Description: The flat (i.e. block) the plant was growing in before being assigned to a treatment F. Name: treatment_flat Description: The flat replicate (two flats nested within each treatment level) a plant was grown in after being assigned to a treatment G. Name: Surv_flr Description: Whether or not the plant survived to flower 0 = died before flowering 1 = survived to flower H. Name: Num_flrs Description: The total number of flowers the plant produced in its lifetime ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Hydroponic.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 400 3. Missing data codes: NA 4. Variable List A. Name: Plant_Num Description: The unique plant identifier B. Name: Tray Description: The tray (block) a plant was grown in (8 in total- 2 per treatment) C. Name: Tray_Row Description: The row position a plant was germinated on in the tray D. Name: Tray_Column Description: The column position a plant was germinated on in the tray E. Name: MgSO4_mM Description: The treatment imposed- corresponds to the amount (mM) of MgSO4 added to the solution F. Name: Population Description: The source population SandPop or SerpPop G. Name: Germinated Description: Whether or not a seed germinated at that position. Plants with a "N" (did not germinate) were excluded from analyses H. Name: Date_FF Description: The date a plant first flowered I. Name: Date_Harvested Description: The date a plant was harvested after being fully senesced J. Name: SURV_FLR Description: Whether the plant survived to flower (1=yes, 0=no) K. Name: NUM_FLR Description: The total number of flowers a plant produced L. Name: BIOMASS Description: The dry biomass weight of each plant (mg) M. Name: Notes Description: Whether there was anything to note about the data in that row ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: JRPrecipitationData.csv ----------------------------------------- 1. Number of variables: 12 2. Number of cases/rows: 12045 3. Missing data codes: NA 4. Variable List A. Name: Day_of_Year Description: The day of the year in numeric format (1=Jan 1) B. Name: Year Description: The year of observation (1983-2015) C. Name: JRBP Description: The amount of precipitation (in mm) recorded on that day at Jasper Ridge Biological Preserve D. Name: Wdside Description: The amount of precipitation (in mm) recorded on that day at Woodside Fire Station F. Name: location Description: Whether the record is from JR (Jasper Ridge Biological Preserve) or Woodside (Woodside Fire Station) G. Name: rainfall Description: The precipitation datapoint used for plotting (used data from JRBP unless not available on that day) H. Name: Day Description: The day of the year in numeric format (1=Jan 1), as in 'Day_of_Year' (A.) I. Name: fYear Description: The year of observation (same as B.), treated as a factor for graphing J. Name: date1 Description: Day of year expressed as date in Year-Month-Day format, with arbitrary year (here is 2014 for all) K. Name: date2 Description: The date in Day/Month format (date1 with arbitrary year removed) L. Name: month Description: The calendar month M. Name: date3 Description: The calendar date with the correct year expressed as Year-Month-Day -------------------------------------- INCLUDED SCRIPTS: Local_Adaptation.zip -------------------------------------- Scripts included here were cloned from Github repository: https://github.com/EDitt/Local_Adaptation on 4/26/23 See ASTER_summary.md for summary of ASTER models ReciprocalTransplant.R This file includes the code used to test significance of model covariates in the creation of table 1 Predict_Figure.R This files includes the code used to estimate predicted total seed counts for each population in each soil type for figure 2 Functions.R This file includes a function called on in Predict_Figure.R Precipitation_analyses.R The code used to wrangle the raw precipitation data (wrangled dataset provided in Dryad as "JRPrecipitationData.csv") and to analyze rainfall patterns across years ------------ SESSION INFO ------------ R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aster_1.1-2 dplyr_1.0.10 ggplot2_3.3.6 lubridate_1.8.0 stringr_1.4.1 tidyr_1.2.1 readxl_1.4.1 loaded via a namespace (and not attached): [1] rstudioapi_0.14 magrittr_2.0.3 munsell_0.5.0 tidyselect_1.1.2 colorspace_2.0-3 R6_2.5.1 [7] rlang_1.0.5 fansi_1.0.3 tools_3.6.3 grid_3.6.3 gtable_0.3.1 utf8_1.2.2 [13] cli_3.4.0 DBI_1.1.3 withr_2.5.0 ellipsis_0.3.2 assertthat_0.2.1 tibble_3.1.8 [19] lifecycle_1.0.2 purrr_0.3.4 vctrs_0.4.1 trust_0.1-8 glue_1.6.2 stringi_1.7.8 [25] compiler_3.6.3 pillar_1.8.1 cellranger_1.1.0 scales_1.2.1 generics_0.1.3 pkgconfig_2.0.3