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Experimental Observations on the decay of Environmental DNA from Bighead and Silver Carp-Data
Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore eDNA decay in waste materials and reproductive cells obtained from captive stocks of the invasive bigheaded carps, Hypophthalmichthys nobilis and H. molitrix, as well as the influence of differing levels of water turbulence, temperature, microbial load, and pH on rates of eDNA decay. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in decay half-life as much as 5.5X more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5X. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25X, despite relatively little apparent increase in the overall microbial load, indicating the microbial sources, not only loads, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6X reduction in eDNA half-life. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay conditions and a slow decay conditions, and tracked eDNA decay over 91 days, we observed a 5.0X greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1X and 3.3X, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate, and thus the interpretation of eDNA survey results.
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Envrionmental DNA data for Refinement of eDNA as an early monitoring tool at the landscape-level: Data
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These environmental DNA data and corresponding water quality data were collected and analyzed by the Fish and Wildlife Service in 2017. The samples were collected from 4 sites in pools 17 and 18 in the Upper Mississippi River on 3 sampling trips. The data was used to study occupancy modeling of eDNA data and determine optimal sampling effort required for reliable detection of invasive Bighead Carp and Silver Carp in streams with similar attributes at the Mississippi River.
Illinois River basin silver carp and bighead carp eDNA gradient study from 2015
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This data was collected by the US Fish and Wildlife Service to see if environmental DNA (eDNA) varied across pools and within pools in the Illinois River basin. The data was collected in 2015 from three different habitat types: shoreline, main channel, and bays. The resulting data were then analyzed using an occupancy model.
Illinois River basin silver carp and bighead carp eDNA gradient study from 2015
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This data was collected by the US Fish and Wildlife Service to see if environmental DNA (eDNA) varied across pools and within pools in the Illinois River basin. The data was collected in 2015 from three different habitat types: shoreline, main channel, and bays. The resulting data were then analyzed using an occupancy model.
USFWS Midwest and Northeast Regions Bighead and Silver Carp environmental DNA (eDNA) Database
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The invasive carp environmental DNA (eDNA) sample data was collected and processed by the U.S. Fish and Wildlife Service (USFWS) and is used for the early detection and monitoring of invasive carp. The reportable eDNA detection summary data along with static maps are shared with the public along with a public facing ArcGIS Online Feature layer, Web Map, and Dashboard. For further information on data collection and processing please refer to the Quality Assurance Project Plan eDNA Monitoring of Bighead and Silver Carps (see files and links). Additional information on the Invasive carp eDNA program for the U.S. Fish and Wildlife Service can be found on the Whitney Genetics Lab Facility web page (see files and links). A positive eDNA detection result means there was invasive carp eDNA in the water body, which can be from live or dead fish, but it could have also been transported via boat, bird, or water current. A positive eDNA detection does not necessarily mean there were invasive carp present at the time samples were taken. For more information or questions, please contact the eDNA Program Coordinator, Nick Frohnauer at (nicholas_frohnauer@fws.gov). Complete ISO 19115 FGDC metadata can be found under the hosted view feature layer on the FWS AGOL platform.
USFWS Midwest and Northeast Regions Bighead and Silver Carp environmental DNA (eDNA) Database
공공데이터포털
The invasive carp environmental DNA (eDNA) sample data was collected and processed by the U.S. Fish and Wildlife Service (USFWS) and is used for the early detection and monitoring of invasive carp. The reportable eDNA detection summary data along with static maps are shared with the public along with a public facing ArcGIS Online Feature layer, Web Map, and Dashboard. For further information on data collection and processing please refer to the Quality Assurance Project Plan eDNA Monitoring of Bighead and Silver Carps (see files and links). Additional information on the Invasive carp eDNA program for the U.S. Fish and Wildlife Service can be found on the Whitney Genetics Lab Facility web page (see files and links). A positive eDNA detection result means there was invasive carp eDNA in the water body, which can be from live or dead fish, but it could have also been transported via boat, bird, or water current. A positive eDNA detection does not necessarily mean there were invasive carp present at the time samples were taken. For more information or questions, please contact the eDNA Program Coordinator, Nick Frohnauer at (nicholas_frohnauer@fws.gov). Complete ISO 19115 FGDC metadata can be found under the hosted view feature layer on the FWS AGOL platform.
Laboratory estimates of eDNA degradation rates for Actinionais ligamentina eDNA
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Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the mucket (Actinonias ligamentina) from water samples collected in the laboratory. Samples were collected from experiments performed from November 01, 2019 to November 15, 2019 at the USGS Columbia Environmental Research Center, Missouri
Laboratory estimates of eDNA degradation rates for Actinionais ligamentina eDNA
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Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the mucket (Actinonias ligamentina) from water samples collected in the laboratory. Samples were collected from experiments performed from November 01, 2019 to November 15, 2019 at the USGS Columbia Environmental Research Center, Missouri
Taxonomic composition of environmental DNA acquired by filtration from the St. Regis River, New York
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Environmental DNA (eDNA) surveys have become important tools for monitoring aquatic biodiversity. Barcode sequencing of eDNA generates community profiles that, while potentially biased in both capture and amplification, can nonetheless yield high information content per unit cost. While factors affecting eDNA capture and amplification have been heavily studied, watershed-scale assessments of fish communities and our confidence in such have been less frequent. We performed an initial watershed-scale characterization of fish eDNA using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our bioinformatic approach included 1) direct estimation of sequencing error from unambiguous mappings (alignments) and simulation of error in taxonomic assignment under various mapping criteria; 2) binning of species based on inferred assignment error rather than by taxonomic rank; and 3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented for the St. Regis River, New York, United States, which supports a valuable recreational fishery and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. We found that 300 mL drawn through 25-mm filters yielded greater than 5 ng/µL DNA at most sites in August and September, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state-level checklist into 85 single-species bins and seven multispecies bins. Of 48 taxonomic bins actually observed in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants post-collection. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence.
Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka)
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qPCR detection results for Topeka Shiner eDNA surveys in MN and IA Oxbows. This data was used to determine the optimal eDNA sampling methods for this species in oxbow habitats. The methods used to collect this data and the summary and interpretation of the results can be found in our final report entitled: Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka).
Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka)
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qPCR detection results for Topeka Shiner eDNA surveys in MN and IA Oxbows. This data was used to determine the optimal eDNA sampling methods for this species in oxbow habitats. The methods used to collect this data and the summary and interpretation of the results can be found in our final report entitled: Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka).
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