------------------- GENERAL INFORMATION ------------------- 1. Title: Data and R code for analysis of mercury concentration and food web differences in walleye and yellow perch from Minnesota lakes with and without invasive zebra mussels, 2019 - 2021. 2. Corresponding Author Information Principal Investigator Contact Information Name: Naomi Blinick Institution: University of Minnesota Address: 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN 55108 Email: nsblinick@gmail.com ORCID: https://orcid.org/0000-0003-0111-2891 Associate or Co-investigator Contact Information Name: Denver Link Institution: University of Minnesota Address: 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN 55108 Email: linkx168@umn.edu ORCID: https://orcid.org/0000-0001-5596-6417 Associate or Co-investigator Contact Information Name: Gretchen Hansen Institution: University of Minnesota Address: 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN 55108 Email: ghansen@umn.edu ORCID: https://orcid.org/0000-0003-0241-7048 3. Date published or finalized for release: TBD 4. Date of data collection: 2019_06_28 through 2021_10_21 5. Geographic location of data collection (where was data collected?): Lakes in Minnesota, USA, indexed by DOW number. Lake Name (DOW) Horseshoe (11035800) Koronis (73020002) Belle (47004901) Big Sand (29018500) Island (3015300) Big Sandy (1006200) Buffalo (86009000) Little Boy (11016700) Shamineau (49012700) Big Cormorant (3057600) Clearwater (86025200) Gull (11030500) Melissa (3047500) Green (34007900) Pelican (18030800) Ten Mile (56061300) Washington (47004600) Alexander (49007900) Chippewa (21014500) North Lida (56074701) Steamboat (11050400) Shapefiles of lake boundaries can be found here: https://gisdata.mn.gov/dataset/water-lake-bathymetry 6. Information about funding sources that supported the collection of the data: Data were collected by the University of Minnesota and Minnesota Department of Natural Resources. Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Minnesota Aquatic Invasive Species Research Center (MAISRC) and the Legislative-Citizen Commission on Minnesota Resources (LCCMR), the United States Geological Survey in cooperation with the National Institutes for Water Resources (Project ID 2020MN105AIS), and by the College of Food, Agricultural, and Natural Resource Sciences, through the Water Resources Center, at the University of Minnesota-Twin Cities. 7. Overview of the data (abstract): This dataset contains δ13C and δ15N stable isotope data for 3,765 biological samples (fish, littoral macroinvertebrates, and zooplankton) collected from 21 lakes between 2019 and 2021, collaboratively by the University of Minnesota and the Minnesota Department of Natural Resources. In addition, 403 samples have corresponding mercury data, based on laboratory analyses conducted by USGS (Tate et al. 2022). Files contain these data and code for Bayesian analysis of mercury, littoral reliance, and trophic position of walleye and yellow perch across 12 zebra mussel invaded and 9 uninvaded lakes. Each analysis contains a separate markdown file. Code for establishing isotope correction factors is contained in Correction_Factors_Isotope.rmd. Littoral reliance modeling uses the R package MixSIAR and contains four separate markdown files for each fish grouping (Adult Walleye, Adult Yellow Perch, Age-0 Walleye, Age-0 Yellow Perch). Littoral reliance figures are created in a separate markdown file (Isotope_Figures.rmd) using saved model output. Mercury and Trophic Position analysis use the R package brms to fit Bayesian Hierarchical models and are contained in Mercury_Analysis.rmd and Trophic_Position_Modeling.rmd respectively. Model output is saved for each analysis as an .rds file. Details for each file can be found in the readme file. -------------------------- 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: Blinick, NB, Ahrenstorff, TD, Bethke, BJ, Fleishman AB, Janssen, SE, Krabbenhoft, DP, Link, D, Nelson, JKR, Rantala, HM, Rude, CL, Hansen, GJA. Increased mercury concentrations in walleye and yellow perch in lakes invaded by zebra mussels. In preparation. 3. Recommended citation for the data: Blinick, Naomi S; Ahrenstorff, Tyler D; Bethke, Bethany J; Fleishman, Abram B; Link, Denver; Nelson, Jenna KR; Rantala, Heidi M; Rude, Claire L; Hansen, Gretchen JA. (2023). Data and R code for analysis of mercury concentration and food web differences in walleye and yellow perch from Minnesota lakes with and without invasive zebra mussels, 2019 - 2021. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/xb7g-yc85. 4. Was data derived from another source? Yes If yes, list source(s): Michael T. Tate, Sarah E. Janssen, Naomi Blinick, Denver Link, Jenna KR Nelson, Gretchen Hansen, and David P. Krabbenhoft, 2022, Walleye (Sander vitreus), Yellow Perch (Perca flavescens) and Surface Water Mercury Concentrations in Minnesota Lakes: U.S. Geological Survey data release, https://doi.org/10.5066/P9XGZD51. 5. 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 --------------------- 1. File List A. Filename: readmeV2.txt Short description: Description of data, updated 20240813 to add Revisions2024_08.zip B. Filename: Percid_ZM_HG_Data_Release.Rproj Short description: R Project file containing all data, scripts, and output C. Data.zip Filename: Isotope_Data.csv Short description: Raw stable isotope values of δ13C and δ15N with sample collection data Filename: Mercury_Data.csv Short description: Mercury concentration data for fish samples. Data sourced from accompanying USGS Data Release (Tate et al. 2022). Filename: Source_Isotope.csv Short description: Aggregated baseline invertebrate data used for MixSIAR modeling Filename: TEF_Isotope.csv Short description: Trophic enrichment factor data supplied for MixSIAR modeling Filename: Zooplankton_Correction_Data.csv Short description: Raw zooplankton stable isotope values of δ13C and δ15N used in ethanol correction Filename: Adult_WAE_Isotope.csv Short description: Baseline corrected adult walleye isotope values for MixSIAR modeling Filename: Adult_YEP_Isotope.csv Short description: Baseline corrected adult yellow perch isotope values for MixSIAR modeling Filename: Age0_WAE_Isotope.csv Short description: Baseline corrected age-0 walleye isotope values for MixSIAR modeling Filename: Age0_YEP_Isotope.csv Short description: Baseline corrected age-0 yellow perch isotope values for MixSIAR modeling Filename: Corrected_Isotope_Data.csv Short description: Isotope data corrected for zooplankton ethanol storage and fish trophic enrichment. Contains data used for MixSIAR and trophic position modeling Filename: Adult_WAE_Model_Output.rds Short description: MixSIAR model output for adult walleye (posterior distributions, model diagnostics, prior plots, etc.) for a model run with 3,000,000 iterations, 1,500,000 burn-in, thinning rate of 500, and 3 chains Filename: Adult_YEP_Model_Output.rds Short description: MixSIAR model output for adult yellow perch (posterior distributions, model diagnostics, prior plots, etc.) for a model run with 3,000,000 iterations, 1,500,000 burn-in, thinning rate of 500, and 3 chains Filename: Age0_WAE_Model_Output.rds Short description: MixSIAR model output for age-0 walleye (posterior distributions, model diagnostics, prior plots, etc.) for a model run with 3,000,000 iterations, 1,500,000 burn-in, thinning rate of 500, and 3 chains Filename: Age0_YEP_Model_Output.rds Short description: MixSIAR model output for age-0 yellow perch (posterior distributions, model diagnostics, prior plots, etc.) for a model run with 3,000,000 iterations, 1,500,000 burn-in, thinning rate of 500, and 3 chains Filename: Adult_WAE_Distributions_Isotopes.rds Short description: 18,000 posterior distribution samples for adult walleye from MixSIAR modeling used to generate plots and summary statistics of littoral reliance Filename: Adult_YEP_Distributions_Isotopes.rds Short description: 18,000 posterior distribution samples for adult yellow perch from MixSIAR modeling used to generate plots and summary statistics of littoral reliance Filename: Age0_WAE_Distributions_Isotopes.rds Short description: 18,000 posterior distribution samples for age-0 walleye from MixSIAR modeling used to generate plots and summary statistics of littoral reliance Filename: Age0_YEP_Distributions_Isotopes.rds Short description: 18,000 posterior distribution samples for age-0 yellow perch from MixSIAR modeling used to generate plots and summary statistics of littoral reliance Filename: Mercury_BRMS_Fit.rds Short description: saved model run for mercury Bayesian Hierarchical model Filename: Trophic_Position_Fit.rds Short description: saved model run for trophic position Bayesian Hierarchical model D. Scripts.zip Filename: Adult_WAE_Isotope_Modeling.Rmd Short description: Contains code for MixSIAR modeling of littoral reliance for adult walleye Filename: Adult_YEP_Isotope_Modeling.Rmd Short description: Contains code for MixSIAR modeling of littoral reliance for adult yellow perch Filename: Age0_WAE_Isotope_Modeling.Rmd Short description: Contains code for MixSIAR modeling of littoral reliance for age-0 walleye Filename: Age0_YEP_Isotope_Modeling.Rmd Short description: Contains code for MixSIAR modeling of littoral reliance for age-0 yellow perch Filename: Correction_Factors_Isotope.Rmd Short description: Contains code for zooplankton ethanol correction, baseline aggregation, and trophic correction for fish isotope values. Generates output used in MixSIAR and trophic position modeling Filename: Isotope_Figures.Rmd Short description: Contains code to construct plots and summary statistics of littoral reliance using aggregated MixSIAR output for adult walleye, adult yellow perch, age-0 perch, and age-0 walleye for each invasion status Filename: Mercury_Analysis.Rmd Short description: Contains code for fitting Bayesian Hierarchical model for mercury concentrations with respect to invasion status of zebra mussels. Generates figures and summary statistics for difference hypotheses, random effects, and predictive concentrations with length - an update was made 20240813 called Revised_Mercury_Analysis.Rmd and can be found in Revisions2024_08.zip Filename: Trophic_Position_Modeling.Rmd Short description: Contains code for fitting Bayesian Hierarchical model for trophic position with respect to invasion status of zebra mussels. Generates figures and summary statistics for difference hypotheses and random effects E. Revisions2024_08.zip ADDED TO DATASET 20240813 Filename: Revised_Mercury_Analysis.Rmd Short description: Updated mercury analysis script Filename:lake_characteristics.csv Short description: Data file that contains more lake information used in the new analysis 2. Relationship between files: The data contain three main analyses conducted in R: stable isotopes to determine littoral reliance (using theMixSIAR package), mercury (using the brms package), and trophic position (also using the brms package). MixSIAR modeling was split into four fish groupings (age-0 walleye, age-0 perch, adult walleye, adult yellow perch). Code for MixSIAR modeling is identical except for calling specific fish grouping data. Each MixSIAR model contains a saved model run for the given fish grouping with zooplankton corrected and uncorrected for ethanol storage (files ending in .rds). For aggregation of MixSIAR output and figure creation, a separate markdown file was created (Isotope_Figures.Rmd). Isotope correction factors and baseline aggregation (Correction_Factors_Isotope.Rmd) were completed for the littoral reliance and trophic position modeling.Correction_Factors_Isotope.Rmd contains code that creates the data inputs for MixSIAR (littoral reliance) and trophic position modeling. 3. Additional related data collected that was not included in the current data package: Numbers and lengths of other fish species, as well as δ13C and δ15N isotope data from other fish species and additional aquatic invertebrates were also collected during the course of this study and not included here. 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: All samples were collected in summer months (June-August) from 2019-2021. To supplement sample numbers, some age-0 walleye were collected as part of the Minnesota Department of Natural Resources standardized fall electrofishing surveys. Zooplankton data for the ethanol correction was collected in June 2022. Fish collection: Small littoral fish were caught by the University of Minnesota using seines, small-mesh gill nets, and electrofishing. Adult fish samples were obtained via gill net, trap net, or electrofishing as part of the Minnesota Department of Natural Resources standardized lake monitoring. When possible, doral muscle chunks were taken directly from fish and stored on ice for total mercury and stable isotope processing. When unable to immediately process fish in the field, they were flash frozen with dry ice and processed in the lab. Invertebrate collection: Invertebrates were collected using kicknets, hand collection, PONAR grabs, and zooplankton tows. Benthic invertebrates were stored in a glass vial of lake water within a cooler of ice for several hours prior to processing to ensure gut clearance. Benthic invertebrates were then sorted into taxonomic groups, placed in vials, and frozen. For larger benthic invertebrates (ex. gastropods and unionids), muscle tissue collected from the organism and frozen. Zooplankton were captured with vertical tows using an 80μm net at the deepest points of the lakes. The zooplankton samples were immediately preserved in undiluted reagent-grade 90.5% ethanol. Non-predatory zooplankton were sorted under a microscope in the lab and processed for isotope analysis. Profundal invertebrate specimens were collected using PONAR grabs from approximately 12m depth (or the deepest point if the lake was shallower than 12m) . Isotopic processing: All samples were subjected to standard stable isotope lab processing. They were dried at 60 degrees celsius for 24-48 hours, homogenized, and precisely weighed to 1mg (+/- 0.2mg). Natural abundance of δ13C and δ15N analysis was performed at the University of California Davis Stable Isotope Facility. Mercury processing: Details on mercury sample processing can be found in the accompanying USGS data release at: https://doi.org/10.5066/P9XGZD51 2. Methods for processing the data: All analyses were performed using analysis specific packages (MixSIAR, tidyverse, R2jags) in R. Analyses were performed using R version 4.2.2. Code is provided for replication of all analyses. 3. Instrument- or software-specific information needed to interpret the data: Program R with analysis specific packages is required to run the analysis. 4. Standards and calibration information, if appropriate: Delta values for stable isotopes are expressed relative to international standards VPDB (Vienna Pee Dee Belemnite) and atmospheric N2 (air) for carbon and nitrogen, respectively. Calibration data for stable isotope analysis: During analysis, samples are interspersed with several replicates of at least four different laboratory reference materials. These reference materials have been previously calibrated against international reference materials, including: IAEA-600, USGS-40, USGS-41, USGS-42, USGS-43, USGS-61, USGS-64, and USGS-65) reference materials. A sample’s provisional isotope ratio is measured relative to a reference gas peak analyzed with each sample. These provisional values are finalized by correcting the values for the entire batch based on the known values of the included laboratory reference materials. The long term standard deviation is 0.2 ‰ for 13C and 0.3 ‰ for 15N. (https://stableisotopefacility.ucdavis.edu/carbon-and-nitrogen-solids) 5 . People involved with sample collection, processing, analysis and/or submission: Naomi S. Blinick, Tyler D. Ahrenstorff, Bethany J. Bethke, Abram B. Fleishman, Denver Link, Jenna K.R. Nelson, Heidi M. Rantala, Claire L. Rude, Gretchen J. A. Hansen, numerous MN DNR staff. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Isotope_Data.csv ----------------------------------------- 1. Number of variables: 17 2. Number of cases/rows: 3765 3. Missing data codes: Code/symbol NA Definition: Not applicable or data not available 4. Variable List 1. Name: Project_ID 1. Description: unique identifier assigned to every fish and invertebrate collected. The two letter suffix corresponds to the lake where the samples was collected: AL = Alexander, BL= Belle, BC = Big Cormorant, BS = Big Sand, BY = Big Sandy, BU = Buffalo, CH = Chippewa, CW = Clearwater, GR = Green, GU = Gull, HS = Horseshoe, IS = Island, KO = Koronis, LB = Little Boy, ME = Melissa, NL = = North Lida, PE = Pelican, SH = Shamineau, ST = Steamboat, TM = Tenmile, WA = Washington. The three digit numeric code is arbitrary. 2. Name: Year 1. Description: year sample was collected 3. Name: Lake 1. Description: lake name from which the sample was collected 4. Name: Group 1. Description: Major taxa identification: fish, invertebrate, zooplankton 5. Name: Habitat 1. Description: Major habitat classification where each organism was collected. -Offshore: fish were collected in MNDNR gillnetting surveys, invertebrates were collected via PONAR grabs, and zooplankton were collected with vertical tows. -Littoral: fish in this habitat were collected with beach seines, experimental gillnets, and electrofishing. Invertebrates were collected via kicknets and native unionid mussels were collected via snorkeling in some locations (with appropriate permits from MNDNR). 6. Name: Date1 1. Description: The date the sample was collected. 7. Name: Taxa_general 1. Description: Fish are classified in this column to genus. Macroinvertebrates are classified to class or family. Zooplankton are classified as either Copepods & Cladocerans (herbivorous primary consumers), or Predatory Zooplankton (genera Leptodora and Chaoborus), which were not included as baseline consumers. 8. Name: Taxa_specific1 1. Description: Fish are classified to species in this column. Macroinvertebrates are classified to the next specific taxonomic tier, either family or genus. 9. Name: Taxa_specific2 1. Description: Macroinvertebrates are classified to the next specific taxonomic tier, either genus or species. Fish and zooplankton do not receive further classification in this column. 10. Name: Taxa_specific3 1. Description: Macroinvertebrates are classified to the next specific taxonomic tier (species) when possible. Fish and zooplankton do not receive further classification in this column. 11. Name: FFG 1. Description: Functional feel group (1): CG = collector gatherer, FF = filter feeder, Omn = omnivore, Pred = predator, SC = scraper, SH = shredder 12. Name: Length 1. Description: Fish total length in mm. NA for invertebrates and zooplankton. 13. Name: YOY 1. Description: Designation for young-of-the-year (age-0) fish. NA for invertebrates and zooplankton. 14. Name: ZM_Status 1. Description: zebra mussel invasion status of the lake where the sample was collected. Uninvaded = lakes without confirmed zebra mussel presence. ZM = lakes that are confirmed invaded by zebra mussels by MNDNR. 15. Name: d.13.C 1. δ13C of animal tissue expressed relative to international standard, VPDB (Vienna Pee Dee Belemnite) 16. Name: d.15.N 1. δ15N of animal tissue, expressed relative to international standard: atmospheric N2 (air). 17. Name: Baseline.Flag 1. Description: Y = samples used to calculate the littoral or pelagic baseline. NA = samples not used for baseline calculation. Work Cited: 1. R. W. Merritt, K. W. Cummins, An Introduction to the Aquatic Insects of North America (Kendall Hunt, 1996). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: TEF_Isotope.csv ----------------------------------------- 1. Number of variables: 4 2. Number of cases/rows: 2 3. Missing data codes: None used in these data. 4. Variable List 1. Name: Meand13C 1. Description: Trophic enrichment for carbon isotope, set to 0 as trophic enrichment was corrected before modeling 2. Name: SDd13C 1. Description: Variation in trophic enrichment for carbon isotope, set to 0 as trophic enrichment was corrected before modeling 3. Name: Meand15N 1. Description: Trophic enrichment for nitrogen isotope, set to 0 as trophic enrichment was corrected before modeling 4. Name: SDd15N 1. Description: Variation in trophic enrichment for nitrogen isotope, set to 0 as trophic enrichment was corrected before modeling ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Corrected_Isotope_Data.csv ----------------------------------------- This file is a direct output from the Correction_Factor_Isotope.Rmd, details on the creation / mutation of columns can be found in that .Rmd file. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Source_Isotope.csv ----------------------------------------- This file is a direct output from the Correction_Factor_Isotope.Rmd, details on the creation / mutation of columns can be found in that .Rmd file. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Mercury_Data.csv ----------------------------------------- Details on mercury data can be found in the accompanying USGS data release at: https://doi.org/10.5066/P9XGZD51 ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: lake_characteristics.csv ----------------------------------------- 1. Number of variables: 8 2. Number of cases/rows: 21 3. Missing data codes: None used in these data. 4. Variable List A. Lake Description: Name of lake where sample was taken B. centroid_lon Description: Longitude of the centroid of the lake where the sample was taken. Observations derived from USGS water column temperature predictions data from doi:10.5066/P9EQQER7 C. centroid_lat Description: Latitude of the centroid of the lake where the sample was taken. Observations derived from USGS water column temperature predictions data from doi:10.5066/P9EQQER7 D. hydrologic_class Description: hydrological classification of each lake obtained through the LAGOSNE package in R with the citation: Soranno P, Bacon L, Beauchene M, Bednar K, Bissell E, et. a (2017). “LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.” Gigascience, 6(12) E. Percent_Wetland Description: percentage of wetland area within the catchment area of the lake. Observations derived from MNDNR lakeshed project from http://www.mngeo.state.mn.us/committee/standards/mgmg/metadata.htm F. WS_Lake_Ratio Description: lakeshed to lake area ratio. Observations derived from MNDNR lakeshed project from http://www.mngeo.state.mn.us/committee/standards/mgmg/metadata.htm G. area Description: area of the lake in acres Observations derived from MNDNR lakeshed project from http://www.mngeo.state.mn.us/committee/standards/mgmg/metadata.htm H. Invasion Description:zebra mussel invasion status Y or N