[{"schema":{"name":"mdJson","version":"2.8.1"},"contact":[{"contactId":"CID001","isOrganization":false,"name":"Patrick DeHaan","memberOfOrganization":["CID002"],"phone":[{"service":["mobile"],"phoneNumber":"608-518-6133"}],"electronicMailAddress":["patrick_dehaan@fws.gov"],"onlineResource":[{"name":"Whitney Genetics Lab Website","uri":"https://www.fws.gov/office/whitney-genetics-laboratory"}],"positionName":"Project Leader","contactType":"federal"},{"contactId":"CID002","isOrganization":true,"name":"Whitney Genetics Lab","address":[{"addressType":["mailing","physical"],"deliveryPoint":["555 Lester Ave"],"city":"Onalaska","administrativeArea":"WI","postalCode":"54650","country":"USA"}],"onlineResource":[{"name":"Lab Website","uri":"https://www.fws.gov/office/whitney-genetics-laboratory"}],"contactType":"federal"},{"contactId":"7f2ac40b-a3c6-47d8-861c-71f296211f45","isOrganization":true,"name":"La Crosse Fish and Wildlife Conservation Office (FWCO)","address":[{"addressType":["mailing","physical"],"deliveryPoint":["555 Lester Ave"],"city":"Onalaska","administrativeArea":"WI","postalCode":"54650","country":"USA"}],"onlineResource":[{"uri":"https://www.fws.gov/office/la-crosse-fish-and-wildlife-conservation","name":"Office Website"}],"contactType":"federal"}],"metadata":{"metadataInfo":{"metadataIdentifier":{"identifier":"6d3958a7-1da1-443b-a7a8-d2b73b84789f","namespace":"urn:uuid"},"metadataContact":[{"party":[{"contactId":"CID001"}],"role":"author"}],"defaultMetadataLocale":{"language":"eng","characterSet":"UTF-8","country":"USA"},"metadataDate":[{"date":"2024-10-31T05:00:00.685Z","dateType":"distribution"}],"metadataOnlineResource":[{"name":"USFWS ServCat","uri":"https://ecos.fws.gov/ServCat/","protocol":"Web browser","description":"The tabular dataset and associated metadata for this project have been archived in the USFWS ServCat data repository","function":"download"}],"metadataStatus":"final"},"resourceInfo":{"resourceType":[{"type":"tabularDataset","name":"TopekaData_ServCat.csv"}],"citation":{"title":"Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka)","date":[{"date":"2024-10-31T05:00:00.679Z","dateType":"released","description":"Date the dataset was released online"}],"responsibleParty":[{"party":[{"contactId":"CID002"}],"role":"custodian"}],"alternateTitle":["October 2024 Topeka Shiner qPCR Dataset"]},"pointOfContact":[{"party":[{"contactId":"CID001"}],"role":"author"},{"party":[{"contactId":"7f2ac40b-a3c6-47d8-861c-71f296211f45"}],"role":"collaborator"},{"party":[{"contactId":"CID002"}],"role":"distributor"}],"abstract":"This dataset was generated by the Whitney Genetics Lab and the La Crosse Fish and Wildlife Conservation Office to determine the optimal methods to conduct eDNA sampling for Topeka Shiners in oxbow habitats. The dataset represents detection results from a qPCR assay. An abstract from the final report for this project follows:\n\nTopeka Shiner (Notropis topeka) is an endangered fish species that inhabits oxbows, floodplains, and small headwater streams throughout the central United States. Habitat loss and alterations represent the main threats to this species and conservation actions have included restoring oxbows that were historically occupied. Information on species occupancy is critical for evaluating the success of habitat restoration efforts, however, collection efforts can be difficult. Traditionally, sampling for Topeka Shiners has relied on seining. The effectiveness of seine surveys depends largely on habitat characteristics including oxbow size, depth, and substrate. Environmental DNA surveys have emerged as a method to effectively survey across broad landscapes and collect data on species occupancy. In this study our objectives were to: 1) Refine eDNA laboratory methods for Topeka Shiner (specifically increase the sensitivity of existing methods); and 2) Evaluate multiple eDNA field collection methods in order to make recommendations for future Topeka Shiner monitoring efforts. We modified an existing eDNA assay by adding a hydrolysis probe, which resulted in a highly sensitive tool for Topeka Shiner eDNA detection. From 2021 to 2022, we compared three different eDNA collection methods to evaluate their effectiveness: surface water grabs with centrifugation, surface water grabs with vacuum manifold filtration, and on-site surface water filtration using Smith Root filter packs. eDNA sampling at oxbows was followed by seine surveys to confirm species presence/absence. At each site where Topeka Shiners were collected in seine surveys, we also detected Topeka Shiner eDNA. Control sites where Topeka Shiners were presumed absent and no individuals were collected in seine surveys, had no eDNA detections. At one site with unknown Topeka Shiner status, no individuals were collected via seine surveys, but we did detect eDNA. At all sites where Topeka Shiners were presumed present, we detected Topeka Shiner eDNA and collected shiners in sein surveys. Logistic regression showed that sampling method (i.e., centrifuge, vacuum filtration, Smith Root filtration) was a significant factor predicting detection rate, with centrifugation and Smith Root filtration having higher overall detection rates compared to vacuum filtration. We used linear regression to evaluate which sampling method collected the greatest amount of eDNA. Once again, collection method did have a significant effect on the number of copies per liter collected. At sites sampled in 2021, centrifugation had much higher copies detected than vacuum filtration. In 2022, there was much greater variability in the number of copies detected, and the comparison between vacuum filtration and Smith Root filtration was much more site dependent. For future sampling events, we suggest using Smith Root filters as the most efficient and economical means for collecting eDNA samples for Topeka Shiners.","status":["final"],"defaultResourceLocale":{"language":"eng","characterSet":"UTF-8","country":"USA"},"timePeriod":{"timeInterval":{"units":"year","interval":3},"startDateTime":"2021-01-01T06:00:00.000Z","endDateTime":"2024-10-31T05:00:00.566Z","description":"The project was conducted during this time period. 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SCIENCE > BIOSPHERE > ECOSYSTEMS > FRESHWATER ECOSYSTEMS","path":["Science Keywords","EARTH SCIENCE","BIOSPHERE","ECOSYSTEMS","FRESHWATER ECOSYSTEMS"]}],"keywordType":"theme","thesaurus":{"date":[{"date":"2018-12-12","dateType":"revision"}],"description":"GCMD Science Keywords Example Description","title":"Global Change Master Directory (GCMD) Science Keywords","edition":"Version 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topeka","commonName":["Topeka Shiner"],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"isITIS":true}],"taxonomicSystem":[{"citation":{"title":"Integrated Taxonomic Information System (ITIS)","date":[{"date":"2024-10-31","dateType":"transmitted","description":"Taxa imported from ITIS"}],"presentationForm":["webService","webSite"],"otherCitationDetails":["Retrieved from the Integrated Taxonomic Information System on-line database, https://www.itis.gov."],"onlineResource":[{"uri":"https://www.itis.gov","name":"ITIS website","protocol":"HTTPS","function":"information","description":"ITIS contains taxonomic information on plants, animals, fungi, and microbes of North America and the 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","generalScope":"This project focused on the use of environmental DNA (eDNA) to detect Topeka Shiners."}]},"dataQuality":[{"scope":{"scopeCode":"tabularDataset"},"systemIdentifier":{"uid":"65591df6-0561-4e21-a714-084225379f21"}}]},"metadataRepository":[{"citation":{"title":"Tabular dataset and associated .JSON metadata file"},"repository":"data.gov"}],"dataDictionary":[{"citation":{"title":"Topeka Shiner eDNA Data Dictionary","date":[{"date":"2024-10-31T18:49:06.741Z","dateType":"creation"}]},"subject":["tabularDataset"],"responsibleParty":{"party":[{"contactId":"CID001"}],"role":"author"},"entity":[{"entityId":"4a55b54d-d7cd-41c0-91f5-e139f5aab435","attribute":[{"allowNull":false,"codeName":"Sample_ID","dataType":"character varying","definition":"The unique ID for each sample"},{"allowNull":false,"codeName":"Collection_Site","dataType":"character varying","definition":"Name of the site where the sample was collected"},{"allowNull":false,"codeName":"Collection_Date","dataType":"character varying","definition":"Date of sample collection"},{"allowNull":false,"codeName":"Collection_ Method","dataType":"character varying","definition":"Method for eDNA collection"},{"allowNull":false,"codeName":"Sample_Type","dataType":"character varying","definition":"Environmental Sample or blank"},{"allowNull":false,"codeName":"Cq_Value","dataType":"integer","definition":"The value the qPCR detection curve crosses the threshold detection line"},{"allowNull":false,"codeName":"Starting_Quantity","dataType":"integer","definition":"The starting quantity of DNA in the reaction. Determined by the BioRad software based on standard curve data."},{"allowNull":false,"codeName":"Water_Volume_Processed(L)","dataType":"integer","definition":"The amount of water collected for the sample"},{"allowNull":false,"codeName":"Elution_Volume","dataType":"integer","definition":"Final DNA extraction elution for the sample"}],"codeName":"TopekaData_ServCat","definition":"Topeka Shiner eDNA Detection Data","commonName":"Topeka eDNA results"}]}],"mdDictionary":["bc0b5544-a589-4385-b730-ede601b2a4cd"]}]