This readme.txt file was generated on 27Dec2023 by Michael R Verhoeven Recommended citation for the data: Larkin, Daniel J; Verhoeven, Michael R; Bacon, Jonah A. (2023). Complete Data and Analysis for: Effects of seed traits and dormancy break treatments on germination of four aquatic plant species. Retrieved from the Data Repository for the University of Minnesota. https://conservancy.umn.edu/handle/11299/254884. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Complete Data and Analysis for: Effects of seed traits and dormancy break treatments on germination of four aquatic plant species 2. Author Information Principal Investigator Contact Information Name: Michael R Verhoeven Institution: University of Minnesota Address: 135 Skok Hall; 2003 Upper Buford Circle; St Paul MN 55108 Email: michael.verhoeven.mrv@gmail.com ORCID: https://orcid.org/0000-0002-6340-9490 Associate or Co-investigator Contact Information Name: Jonah A Bacon Institution: University of Alaska – Fairbanks Address: 2150 Koyukuk Drive, Fairbanks, AK 99775 Email: jabacon@alaska.edu ORCID: https://orcid.org/0000-0002-5594-5576 Associate or Co-investigator Contact Information Name: Daniel J Larkin Institution: University of Minnesota Address: 135 Skok Hall; 2003 Upper Buford Circle; St Paul MN 55108 Email: djlarkin@umn.edu ORCID: https://orcid.org/0000-0001-6378-0495 3. Date published or finalized for release: 29Jun2023 4. Date of data collection (single date, range, approximate date): 14Oct2019 to 31Aug2020 5. Geographic location of data collection (where was data collected?): Seeds were collected from aquatic plants in Norris Lake (Anoka County, MN, USA; 45.378521, -93.390226). Experiments were conducted at the Minnesota Aquatic Invasive Species Research Center's Containment labs at the University of Minnesota, Saint Paul MN. 6. Information about funding sources that supported the collection of the data: This research was supported by: the Minnesota Environmental and Natural Resources Trust Fund as recommended by the Minnesota Aquatic Invasive Species Research Center and the Legislative-Citizen Commission on Minnesota Resources (M.V., D.L.); the Undergraduate Research Opportunities Program at the University of Minnesota (J.B.); the National Science Foundation (M.V., Graduate Research Fellowship Program [Grant No. CON-75851, project 00074041]); and the USDA National Institute of Food and Agriculture through the Minnesota Agricultural Experiment Station (D.L.). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. 7. Overview of the data (abstract): This repository contains the raw data and code necessary to conduct the analyses in the companion paper. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (http://creativecommons.org/publicdomain/zero/1.0/) 2. Links to publications that cite or use the data: Michael R. Verhoeven, Jonah A. Bacon and Daniel J. Larkin. (2023). Effects of seed traits and dormancy break treatments on germination of four aquatic plant species. Aquatic Botany. doi:https://doi.org/10.1016/j.aquabot.2023.103746 3. Was data derived from another source? No If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- File List Filename: Readme_Seeds_Verhoeven_2023.txt Short description: Readme for repository describing repo contents, resationships, and usage for companion paper Filename: Seeds_germination.csv Short description: Germination trial data Filename: Seeds_viability.csv Short description: Viability trial data Filename: Seedgerm_stats_figs_manuscript.R Short description: R script for analysis Filename: Seedgerm_stats_figs_manuscript.html Short description: HTML analysis report (produced from R script) Filename: Seed_photos.zip Short description: Photos referenced in datasets for seed traits and TZ viability Filename: Seedtraits_FIJI_Macro.txt Short description: Macro for processing seed images to extract trait data (size, shape, color) Filename: Seeds_Chamberconditions.csv Short description: Germination trial data from chamber (germinating environment) checks. 2. Relationship between files: Experiments conducted and described in companion manuscript produced germination and viability data found in the two data files (Seeds_viability.csv, Seeds_germination.csv). The file Seeds_Chamberconditions.csv describes growth chamber conditions recorded over the course of the experiment. Next, the file Seedtraits_FIJI_Macro.txt was used to process images in Seed_photos.zip to extract seed trait data, which were added to the two data files (Seeds_viability.csv, Seeds_germination.csv). These two data files were then used to conduct the analyses described in the companion paper in program R using Seedgerm_stats_figs_manuscript.R (this anlaysis is also presented as a more readable report format in Seedgerm_stats_figs_manuscript.html). -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See companion paper for detail. 2. Methods for processing the data: See companion paper methods section. 3. Instrument- or software-specific information needed to interpret the data: NA 4. Standards and calibration information, if appropriate: See companion paper for description. Color and scale calibration photos are included in the Seed_photos.zip file. 5. Environmental/experimental conditions: See companion paper and Seed_Chamberconditions.csv 6. Describe any quality-assurance procedures performed on the data: See methods section of companion paper. 7. People involved with sample collection, processing, analysis and/or submission: See acknowledgements section of companion paper. ---------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Seeds_germination.csv ---------------------------------------------------------------- rows: 641 cols: 31 A. Name: Seed_ID Description: Unique identifier assigned to each seed B. Name: Photo_ID(SeedID_###.CR2) Description: Name of photo used for trait measurements (other than Mass_g) of the seed (e.g., 001 corresponds to photo named SeedID_001.CR2) C. Name: Species Description: Abbreviated species name as first three letters of genus, first three letters of species (Nuphar variegata = Nup_var, Potamogeton amplifolius* = Pot_amp*, Brasenia schreberi = Bra_sch, Potamogeton natans = Pot_nat). *Note that the Potamogeton amplifolius identificaton was change to Potamogeton illinoensis after growing out the plants from germinated seeds. This species ID chnage is described and executed in the file cleanup at the beginning of the analysis file (Seedgerm_stats_figs_manuscript.R) D. Name: Treatment Description: Dormancy break treatment applied to the seed (SC = Scarify, GA = Giberrellic Acid, SC+GA = Scarified then Giberrellic acid treated) E. Name: Date_GA3 Description: Date of GA treatment start (ddMonYYYY). NA if not GA treated F. Name: Time_GA3 Description: Time of GA treatment start (24h time). NA if not GA treated G. Name: Date_chamber Description: Date of seed placed in growth chamber for start of germinaion trial (ddMonYYYY). H. Name: Time_chamber Description: Time of seed placed in growth chamber for start of germinaion trial (24h time). I. Name: Tray Description: Right of Left tray of experiment (corresponds to treatment--all Right tray seeds were treated with Giberrellic acid). J. Name: Group Description: Letter designating the tray location (paired with number) where seed was germinated in germ assays. K. Name: Number Description: Number designating the tray location (paired with letter) where seed was germinated in germ assays. L. Name: Date_germinated Description: Date of germination observed, if germinated (ddMonYYYY). Blank("") if ungerminated M. Name: Germ_Photo_ID(Germ_###.CR2) Description: Name of photos of germinated seed, separated by commas (e.g., 001,009 corresponds to photos named Germ_001.CR2 and Germ_009.CR2) N. Name: Date_planted Description: If germinated, date germination was observed (ddMonYYYY). Blank("") if ungerminated O. Name: Plant_Photo_ID(Plant_###.CR2) Description: Name of photos of plant grown from seed, separated by commas (e.g., 032,033, 034 corresponds to photos named Plant_032.CR2, Plant_033.CR2 and Plant_034.CR2) P. Name: Jar_col Description: Letter designating the jar location (paired with Jar_row) where germinants were grown out to verify ID. Q. Name: Jar_row Description: Number designating the jar location (paired with Jar_col) where germinants were grown out to verify ID. R. Name: Mass_grams Description: Seed mass in Grams. Mass measured on Sartorius ENTRIS623I-1S; Sartorius Lab Instruments GmbH & Co. KG; Goettingen, Germany. S. Name: Area Description: Area of seed shape in profile view in image (micrometers^2). T. Name: Major_axis Description: Length of long axis of seed from image (micrometers). U. Name: Minor_axis Description: Length of short axis of seed from image (micrometers). V. Name: Blue_mean Description: Mean of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (https://imagej.net/plugins/auto-threshold). Huang, L.-K., & Wang, M.-J. J. (1995). Image thresholding by minimizing the measures of fuzziness. Pattern Recognition, 28(1), 41–51. doi:10.1016/0031-3203(94)e0043-k W. Name: Blue_StdDev Description: Standard deviation of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail). X. Name: Blue_Mode Description: Mode of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) Y. Name: Green_mean Description: Mean of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) Z. Name: Green_StdDev Description: Standard deviation of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) AA. Name: Green_Mode Description: Mode of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) AB. Name: Red_mean Description: Mean of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) AC. Name: Red_StdDev Description: Standard deviation of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) AD. Name: Red_Mode Description: Mode of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) AE. Name: Notes Description: Notes pertaining to the seed in this row (notes made/collected during the germination trials). ---------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Seeds_viability.csv ---------------------------------------------------------------- rows: 168 cols: 22 A. Name: Seed_ID Description: Unique identifier assigned to each seed B. Name: PreTZ_Photo_ID(Viability_###.CR2) Description: Name of photo used for trait measurements (other than Mass_g) of the seed (e.g., 001 corresponds to photo named Vibility_001.CR2). Note that only 63/168 seed's traits were measure with ImageJ. C. Name: PostTZ_Photo_ID(TZ_###.CR2) Description: Name of photo captured during tetrazolium (TZ) staining assesment (other than Mass_g) of the seed (e.g., 001 corresponds to photo named Vibility_001.CR2) D. Name: Species Description: Abbreviated species name as first three letters of genus, first three letters of species (Nuphar variegata = Nup_var, Potamogeton amplifolius* = Pot_amp*, Brasenia schreberi = Bra_sch, Potamogeton natans = Pot_nat). *Note that the Potamogeton amplifolius identificaton was change to Potamogeton illinoensis after growing out the plants from germinated seeds. This species ID chnage is described and executed in the file cleanup at the beginning of the analysis file (Seedgerm_stats_figs_manuscript.R) E. Name: Tray Description: Tray for TZ incubation--used to track indiv seeds thorugh TZ assay. F. Name: Row Description: Row letter from TZ incubation tray. G. Name: Column Description: Column number from TZ incubation tray. H. Name: Embryo_stained Description: Numeric or NA describing staining of embryo relative to controls (see companion paper for detail on TZ assay). From controls, we determined that any staining > 6 was considered viable. NA = No embryo 1 = 100% of embryo colored red/pink 2 = 75-100% 3 = 50-75% 4 = 25-50% 5 = 0-25% 6 = 0% I. Name: Mass_grams Description: Seed mass in Grams. Mass measured on Sartorius ENTRIS623I-1S; Sartorius Lab Instruments GmbH & Co. KG; Goettingen, Germany. J. Name: Area Description: Area of seed shape in profile view in image (micrometers^2). K. Name: Major_axis Description: Length of long axis of seed from image (micrometers). L. Name: Minor_axis Description: Length of short axis of seed from image (micrometers). M. Name: Blue_mean Description: Mean of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (https://imagej.net/plugins/auto-threshold). Huang, L.-K., & Wang, M.-J. J. (1995). Image thresholding by minimizing the measures of fuzziness. Pattern Recognition, 28(1), 41–51. doi:10.1016/0031-3203(94)e0043-k N. Name: Blue_StdDev Description: Standard deviation of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail). O. Name: Blue_Mode Description: Mode of blue channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) P. Name: Green_mean Description: Mean of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) Q. Name: Green_StdDev Description: Standard deviation of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) R. Name: Green_Mode Description: Mode of green channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) S. Name: Red_mean Description: Mean of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) T. Name: Red_StdDev Description: Standard deviation of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) U. Name: Red_Mode Description: Mode of red channel threshold from ImageJ threshold function based on Huang's fuzzy thresholding method (seed Blue_mean field desc. for detail) V. Name: Notes Description: Notes pertaining to the chamber condition observation. ---------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Seeds_chamberconditions.csv ---------------------------------------------------------------- rows: 13 cols: 6 A. Name: Date Description: Date of growth chamber condition observations (dd-MMM-YYYY) B. Name: Time Description: Time of growth chamber condition observations (24h time) C. Name: Temperature_C Description: Temperature of griwth chamber in degrees Celsius D. Name: Relative_humidity Description: Proportion of total saturation at temperature observed in the growth chamber. E. Name: Light_umol Description: Light level at germination tray surface V. Name: Notes Description: Notes pertaining to this chamber check.