This readme.txt file was generated on 20240603 by Raymond Newman, a revision of 20220809 Kathyrn Gannon draft
Recommended citation for the data: Gannon, K. A., R.M. Newman and R.A. Thum. 2022. Data and R-code for ÒIntegrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessmentÓ Journal of Aquatic Plant Management 60(1):1-9.


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GENERAL INFORMATION
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1. Title of Dataset: Data and R-code for: ÒIntegrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessmentÓ Gannon et al. 2022. Journal of Aquatic Plant Management 60:1-9.


2. Author Information

Authors: 
Kathryn A. Gannon, Department of Plant Science and Plant Pathology, Montana State University, Plant Bioscience Building, P.O. Box 173150, Bozeman, MT 59717 Present address: Department of Ecology and Evolutionary Biology, Cornell University,Ithaca, NY 14853 
Email: kag326@cornell.edu 
ORCID: 

Raymond M. Newman, Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, 2003 Upper Buford Circle, St. Paul, MN 55108
Email: newma004@umn.edu
ORCID: 0000-0002-1170-3217


Ryan A. Thum, Department of Plant Science and Plant Pathology, Montana State University, Plant Bioscience Building, P.O. Box 173150, Bozeman, MT 59717
Email: ryan.thum@montana.edu
ORCID: 0000-0002-0270-1535


3. Date published or finalized for release: 20220831
4. Date of data collection (range):  
Plant management data and point intercept surveys collected from May 2018 through September 2020, genetic IDs completed in 2019-2021, data compiled in 2021.

5. Geographic location of data collection (where was data collected?):  Minnesota 
Lake 		  State County 	DOW 		Latitude 		Longitude  
Christmas 	  MN 	  Hennepin 	27013700 	44853048.479400N 	93832040.199400W 
Bald Eagle 	  MN 	  Ramsey 	62000200 	4586057.2400N 		9380059.399400W
Grays Bay 	  MN 	  Hennepin 	27013301 	44857014.039400N 	93829040.200W
Ham 		  MN 	  Anoka 	20005300 	45815025.5600N 		93813018.8400W 
Independence 	  MN 	  Hennepin 	27017600 	4581045.479400N 	93838041.999400W 
North Arm 	  MN 	  Hennepin 	27013313 	44857031.3200N 		9383701200W
Phelps Bay 	  MN 	  Hennepin 	27013301 	44854056.159400N 	93838056.400W 
Smiths Bay 	  MN 	  Hennepin 	27013302 	4485709.359400N 	9383401.919400W 

6. Information about funding sources that supported the collection of the data: 
This project was supported by the Minnesota Aquatic Invasive Species Center, with funding provided by the Minnesota Environmental and Natural Resources Trust Fund, as recommended by the Legislative-Citizen Commission on Minnesota Resources. Additional support was provided by the Montana Agricultural Experiment Station (project MONB00249), the Minnesota Agricultural Experiment Station USDA National Institute of Food and Agriculture (Hatch grant MIN-41-081), the Michigan Invasive Species Grant Program (www.michigan.gov/invasives), and the U.S. Army Engineer Research and Development Center (ERDC Cooperative Agreement W912HZ2020060).

7. Overview of the data (abstract): 
Invasive Eurasian watermilfoil (Myriophyllum spicatum L.) hybridizes with native northern watermilfoil (Myriophyllum sibiricum Komarov). Previous genetic studies have identified numerous distinct Eurasian and hybrid strains that can differ in their invasiveness (e.g., growth and potential for spread) and response to herbicides. To identify problematic or invasive strains of watermilfoil we assessed the response of different watermilfoil strains to aquatic vegetation management in eight Minnesota lakes over the course of 3 yr. Specifically, we looked for changes in strain composition of watermilfoil populations over time to identify strains of specific interest for further characterization of growth and herbicide response. Eurasian watermilfoil was collected from point intercept surveys (125 to 230 points at each waterbody) before and after herbicide treatments and generally twice per year over 3 years. Plants were idented to genotype using microsatellite markers and changes in genotype occurrence and frequency were assess for changes over time and in response to treatment. Additional details and methods are presented in Gannon et al. 2022.  


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data: Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/

2. Links to publications that cite or use the data: Gannon, K. A., R.M. Newman and R.A. Thum. 2022. Integrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessment. Journal of Aquatic Plant Management 60(1):1-9.   https://apms.org/wp-content/uploads/japm-60-01-1-full.pdf

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




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DATA & FILE OVERVIEW
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1. File List
   A. Filename: All_Lakes_KAG_020322.csv     
      Short description: Dataset containing year and season, lake, taxon (Eurasian watermilfoil, northern watermilfoil, or hybrid) and strain for each plant sample analyzed.        

   B. Filename: DRUM_All_Lakes_KAG_072324.rmd       
      Short description: Code used to pull in complete datasets, separate data by lake, print summary statistics, analyze the data using simulated Chi Squared for each lake, and create visualizations.   

   C. Filename: DRUM_All_Lakes_KAG_072324.html       
      Short description: Html file displaying all R analysis and output.   

   D. Filename: SUPPLEMENTAL_MAPS_081422RNF.pdf
	Short description: Supplemental maps, with location of watermilfoil strains and herbicide treatments in the study lakes, referred to in publication.

2. Relationship between files: The raw data (All_Lakes_KAG_020322.csv) are read into  DRUM_All_Lakes_KAG_072324.rmd where statistical summaries are printed and saved, data is analyzed and visualizations are produced.  All code was written in R, analysis code was subsequently converted to .Rmd file then to the .html file in this repository.     



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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
See methods in Gannon KA, Newman RM, and Thum RA 2022 ÓIntegrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessmentÓ Journal of Aquatic Plant Management 60(1):1-9. Briefly, Eurasian watermilfoil was collected from point intercept surveys (125 to 230 points at each waterbody) before and after herbicide treatments and generally twice per year over 3 years. Plants were idented to genotype using microsatellite markers and changes in genotype occurrence and frequency were assess for changes over time and in response to treatment. 


2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>
Raw point-intercept survey data were compiled from each lake. For each lake and time point, raw point-intercept data were combined with genetic results based on the sample code for each plant. All time points and lakes were compiled into a single database. All other data development steps are described in Gannon, Newman & Thum 2022. 


3. Instrument- or software-specific information needed to interpret the data:
Program R (Full details of R session information including the packages used are available at the bottom of each output html file)

4. Standards and calibration information, if appropriate: NA


5. Environmental/experimental conditions: NA


6. Describe any quality-assurance procedures performed on the data: NA


7. People involved with sample collection, processing, analysis and/or submission:
Gannon KA, Newman RM, and Thum RA completed data and analysis for: Integrating DNA fingerprinting of invasive watermilfoil strains into aquatic vegetation monitoring and assessment. Jasmine Eltawely and Raymond Newman led collection of many of the samples in 2018 and 2019, and Newman and Jane Feely led collection in 2020.  Additional assistance was provided by Keegan Lund and Kylie Katoor of the Minnesota Department of Natural Rsources. Patrick Selter (Professional Lake Management) and Keegan Lund provided information on herbicide treatments.  





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DATA-SPECIFIC INFORMATION FOR: All_Lakes_KAG_020322.csv
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1. Number of variables: 6


2. Number of cases/rows: 1550



3. Missing data codes:
        None


4. Variable List
                

    A. Name: Sample_Code
       Description: Code given to each plant sample and when received by the Thum lab. Used to track individual plants through the analysis process. 


    B. Name: Lake
       Description: Lake where each plant sample was collected See Geographic location above for coordinates and Lake identifiers
                    
		Bald_Eagle = Bald Eagle Lake, MN 
		Christmas = Christmas Lake, MN 
		Grays_Bay = Grays Bay in Lake Minnetonka, MN 
		Ham = Ham Lake, MN 
		Independence = Independence Lake, MN 
		North_Arm = North Arm of Lake Minnetonka, MN 
		Phelps_Bay = Phelps Bay of Lake Minnetonka, MN 
		Smiths_Bay = Smiths Bay of Lake Minnetonka, MN 

    C. Name: Taxa
       Description: Taxonomic identification of each plant sample based on genetic analysis of micro satellite markers 
		EWM = Eurasian watermilfoil (Myriophyllum spicatum L.) 
		HWM = hybrid watermilfoil (Myriophyllum spicatum L. x Myriophyllum sibiricum Komarov) 
		NWM = northern watermilfoil (Myriophyllum sibiricum Komarov) 


    D. Name: Year
       Description: calendar year that sample was collected (2018, 2019, or 2020) 
                    
    
    E. Name: Year_TP
       Description: calendar year that sample was collected and the time during the season (early summer pre treatment or late summer post treatment) 
		2018.0 = Early summer 2018 (pre treatment if treatment was carried out)  
		2018.5 = Late summer 2018 (post treatment if treatment was carried out)
		2019.0 = Early summer 2019 (pre treatment if treatment was carried out)  
		2019.5 = Late summer 2019 (post treatment if treatment was carried out)
		2020.0 = Early summer 2020 (pre treatment if treatment was carried out)  
		2020.5 = Late summer 2020 (post treatment if treatment was carried out)


    F. Name: Strain
       Description: We refer to identified strains by a four-character code: the first two letters indicate the waterbody in which the strain was identified (or MC if found in multiple waterbodies); the middle letter indicates whether the strain is pure Eurasian watermilfoil (E), native northern watermilfoil (N), or a hybrid (H); and the final number distinguishes strains of the same taxa within the same waterbody. The abbreviation MC stands for Minnesota Clones and was used to distinguish strains that were found in multiple waterbodies included in this study.