Data Package Metadata View Summary

Application of eDNA as a tool for assessing fish population abundance, Northern Wisconsin, US, 2017 - 2018

General Information

Data Package:
Local Identifier:	knb-lter-ntl.383.1
Title:	Application of eDNA as a tool for assessing fish population abundance, Northern Wisconsin, US, 2017 - 2018
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	Environmental DNA concentrations, WDNR/GLIFWC mark-recapture population estimates, and abiotic lake data on 24 lakes in Wisconsin's Ceded Territory used to evaluate the relationship between walleye abundance and environmental DNA density and its application as a fisheries management tool.
Publication Date:	2020-02-03

Time Period

Begin:

2017-07-01

End:

2018-08-31

People and Organizations
Contact:	Spear, Michael J (University of Wisconsin-Madison, Center for Limnology) [ email ]
Contact:	Vander Zanden, Jake M (University of Wisconsin-Madison, Center for Limnology) [ email ]
Creator:	Spear, Michael J (University of Wisconsin-Madison, Center for Limnology)
Creator:	Embke, Holly S (University of Wisconsin-Madison, Center for Limnology)
Creator:	Krysan, Patrick J (University of Wisconsin-Madison, Department of Horticulture)
Creator:	Vander Zanden, Jake M (University of Wisconsin-Madison, Center for Limnology)

Data Entities
Data Table Name:	LakeInformation.csv
Description:	Mark-recapture walleye population estimate data, qPCR summary statistics, and other lake information
Data Table Name:	Raw_eDNA_StartingQuantities.csv
Description:	Individual starting quantity values for each qPCR replicate.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-ntl/383/1/9f402c55691a018b3308dcb41801a15c
Name:	LakeInformation.csv
Description:	Mark-recapture walleye population estimate data, qPCR summary statistics, and other lake information
Number of Records:	24
Number of Columns:	21

Table Structure

Object Name:

LakeInformation.csv

Size:

3363 bytes

Authentication:

f3dd1f628341726f9a10172ae55875f9 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

LakeName

LakeCode

WisconsinWaterBodyIdentificationCode

YearSampled

MarkRecaptureAgency

LakeArea

Longitude

Latitude

MarkRecaptureAdultWalleyePopulationEstimate

MarkRecaptureAdultWalleyeBiomassEstimate

MarkRecaptureCoefficientofVariation

MeaneDNAStartingQuantity

qPCRStandardEfficiency

qPCRStandardRsquared

MaximumDepth

WaterClaritySecchi Depth

Age0WalleyeCPUE

MeanWalleyeSize

WalleyeDensity

WalleyeBiomass

Definition:

Name of Lake

Code used in data to describe lake in other data, code, or manuscripts

State of Wisconsin ID number for waterbodies

When mark-recapture and eDNA data was collected

State management agency that collected mark-recapture data

Surface area of lakes in hectares

Longitude of middle of lake

Latitude of middle of lake

Estimate of adult walleyes in that lake that year

Modeled biomass of adult walleye in that lake that year

Coefficient of variation describing adult walleye population estimate

Starting quantity of walleye eDNA copies at the beginning of each qPCR reaction, averaged across four qPCR replicates and nine lake samples

Standard efficiency of qPCR reactions, averaged across qPCR replicates and nine lake samples

R squared of qPCR reactions, averaged across qPCR replicates and nine lake samples

Maximum depth of lake

Water clarity of lake

pH of lake water

Estimate of age-0 walleye from that lake in that year

Average size of an individual walleye, calculated by dividing walleye biomass by walleye density

Number of walleye per acre

Modeled biomass of walleye per acre

Storage Type:

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

Name of Lake

Definition

Code used in data to describe lake in other data, code, or manuscripts

Definition

State of Wisconsin ID number for waterbodies

Unit	nominalYear
Type	natural
Min	2017
Max	2018

Definition

State management agency that collected mark-recapture data

Unit	hectare
Type	real
Min	33.99
Max	654.37

Unit	degree
Type	real
Min	-90.16
Max	-88.85

Unit	degree
Type	real
Min	45.53
Max	46.24

Unit	number
Type	real
Min	49.98
Max	8481

Unit	kilogram
Type	real
Min	38.92
Max	16510.18

Unit	dimensionless
Type	real
Min	0.08
Max	0.29

Unit	number
Type	real
Min	0
Max	330

Unit	dimensionless
Type	real
Min	80.8
Max	103.1

Unit	dimensionless
Type	real
Min	0.98
Max	1

Unit	meter
Type	real
Min	4.5
Max	28.5

Unit	meter
Type	real
Min	1.2
Max	6.9

Unit	dimensionless
Type	real
Min	6.49
Max	7.79

Unit	numberPerKilometerShoreline
Type	real
Min	0
Max	41.32

Unit	kilogram
Type	real
Min	0.19
Max	4.01

Unit	numberPerHectare
Type	real
Min	0.8
Max	52.39

Unit	kilogramsPerHectare
Type	real
Min	0.6
Max	46.79

Missing Value Code:

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-ntl/383/1/feb6d0fcad55986c126cd2dc93977967
Name:	Raw_eDNA_StartingQuantities.csv
Description:	Individual starting quantity values for each qPCR replicate.
Number of Records:	1180
Number of Columns:	5

Table Structure

Object Name:

Raw_eDNA_StartingQuantities.csv

Size:

18257 bytes

Authentication:

5e3bfeb442e2fb2f15b63a64d1ef0c31 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

YearSampled

LakeCode

WithinLakeSiteNumber

WithinSiteqPCRReplicateNumber

StartingQuantity

Definition:

Year in which eDNA data was collected

Code for lake name; see Lake Information data file for bridge from code to lake name.

Site number within each lake where eDNA was sampled. Most lakes hold nine sites, as well as a field, filter, extraction, and qPCR no template control blank

qPCR replicate number. Each within-lake site sample was run through qPCR in four replicates

Starting quantity of walleye eDNA copies at the beginning of each qPCR reaction

Storage Type:

float

string

float

Measurement Type:

ratio

nominal

ratio

Measurement Values Domain:

Unit	nominalYear
Type	natural
Min	17
Max	18

Definition

Code for lake name; see Lake Information data file for bridge from code to lake name.

Definition

Site number within each lake where eDNA was sampled. Most lakes hold nine sites, as well as a field, filter, extraction, and qPCR no template control blank

Unit	dimensionless
Type	natural
Min	1
Max	4

Unit	number
Type	real
Min	0
Max	23.25

Missing Value Code:

Code	NA
Expl	not available

Code	NA
Expl	not available

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)	Walleye, eDNA, population estimate, Vander Zanden Lab, Hasler Lab

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package

Description:

Each lake was sampled in nine locations. Each sample received four qPCR replicates. Each lake was accompanied by a field (FLD), filter (FIL), and qPCR no template control (NTC) blank. Lakes with eDNA samples extracted together in a batch share the extraction (EXT) blank. Lakes listed without extraction blanks take the previous lake's extraction blank in the order listed in the data.

eDNA data generated as follows: We performed Real-Time quantitative polymerase chain reaction (qPCR) on extracted DNA using a BIO-RAD C1000 Thermal Cycler equipped with a CFX96 Real-Time System (Bio-Rad, Hercules, CA). Reactions used Ex Taq DNA Polymerase Hot-Start Version (TaKaRa Bio, Mountain View, CA) and a PCR primer pair and minor groove binding probe (Integrated DNA Technologies, Coralville, IA) specific for Sander vitreus (F: 5'-CTATTATACTATTTACCCTCGGGCTCG-3'; R: 5'-GTCGATTGAACAATGAAGTATTTTGC-3'; Probe: 5'-FAM-TAATTGCCTGAATGGGTC-MGBNFQ-3'; amplicon length: 175 bp) targeting the mitochondrial NADH dehydrogenase subunit 2 (ND2) region. The following PCR profile was used: 55 cycles, Td: 15 s at 95degC, Ta: 30 s at 60degC, Te: 30 s 60degC. Each reaction was 20 uL and contained 600 nM of each primer, 250 nM of probe, 7.5 uL of Ex Taq DNA Polymerase Hot-Start, 2.75 uL of Nanopure water, and 4 uL of template DNA. Primers, probe, and protocols were developed by Dysthe et al. (2017).

Mark-recapture population estimate data was collected by WDNR and GLIFWC)

People and Organizations

Creators:

Individual:

Michael J Spear

Organization:

University of Wisconsin-Madison, Center for Limnology

Email Address:

Spear.michael.j@gmail.com

Id:

https://orcid.org/0000-0002-1365-3583

Individual:

Holly S Embke

Organization:

University of Wisconsin-Madison, Center for Limnology

Email Address:

hembke@wisc.edu

Id:

https://orcid.org/0000-0002-9897-7068

Individual:

Patrick J Krysan

Organization:

University of Wisconsin-Madison, Department of Horticulture

Email Address:

pjkrysan@wisc.edu

Individual:

Jake M Vander Zanden

Organization:

University of Wisconsin-Madison, Center for Limnology

Email Address:

Mjvanderzand@wisc.edu

Id:

https://orcid.org/0000-0002-8122-1416

Contacts:

Individual:

Michael J Spear

Organization:

University of Wisconsin-Madison, Center for Limnology

Email Address:

Spear.michael.j@gmail.com

Id:

https://orcid.org/0000-0002-1365-3583

Individual:

Jake M Vander Zanden

Organization:

University of Wisconsin-Madison, Center for Limnology

Email Address:

Mjvanderzand@wisc.edu

Id:

https://orcid.org/0000-0002-8122-1416

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period

Begin:

2017-07-01

End:

2018-08-31

Geographic Region:

Description:

Ceded Territory of Northern Wisconsin, USA

Bounding Coordinates:

Northern:	46.23985	Southern:	45.52847
Western:	-90.16065	Eastern:	-88.84606

Project

Parent Project Information:

Title:

National Climate Adaptation Science Centers Program

Personnel:

Individual:	M Jake Vander Zanden
Id:	https://orcid.org/0000-0002-8122-1416
Role:	Principal Investigator

Funding:

United States Geological Survey: G16AC00222

Related Project:

Title:

North Temperate Lakes Long Term Ecological Research Program

Personnel:

Individual:	Emily H Stanley
Id:	https://orcid.org/0000-0003-4922-8121
Role:	Principal Investigator

Funding:

National Science Foundation: DEB?1440297

Maintenance

Maintenance:

Description:	completed
Frequency:

Other Metadata

Additional Metadata

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        |     |___element 'unitList'
        |     |     |___text '\n        '
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Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

Application of eDNA as a tool for assessing fish population abundance, Northern Wisconsin, US, 2017 - 2018

Data Entities

Data Table

Data Table

Data Package Usage Rights

Keywords

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Application of eDNA as a tool for assessing fish population abundance, Northern Wisconsin, US, 2017 - 2018

+/- Data Entities

Data Table

Data Table

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata