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Diatom and environmental data
These raw data associated with this research were collected as part of the United States Environmental Protection Agency's 2018-2019 National Rivers and Streams Assessment (NRSA). The worksheet "Water chemistry data" includes environmental variables examined in this study including total phosphorus (TP), total nitrogen (TN), conductivity, pH, and ecoregion. The worksheet "Diatom ASVs" includes relative abundances of gene sequence reads for each amplicon sequence variant (ASV), which are referred to as taxa. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, C. Nietch, L. Gains-Germain, C. Carpenter, J. Darling, L. Yuan, R. Mitchell, and A. Pollard. Using DNA metabarcoding to characterize national scale diatom-environment relationships and to develop indicators in streams and rivers of the United States. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 939: 173502, (2024).
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연관 데이터
Diatom and Environmental Data
공공데이터포털
Raw data associated with this research. This dataset is associated with the following publication: Yuan, L., R. Mitchell, E. Pilgrim, and N. Smucker. Inferences based on diatom compositions improve estimates of nutrient concentrations in streams. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 952: 176032, (2024).
EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study
공공데이터포털
Raw data associated with EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study. This dataset is associated with the following publication: Yuan, L., R. Mitchell, A. Pollard, C. Nietch, E. Pilgrim, and N. Smucker. Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon–environment relationships. FRESHWATER BIOLOGY. Blackwell Publishing, Malden, MA, USA, 68(3): 473-486, (2023).
EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study
공공데이터포털
Raw data associated with EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study. This dataset is associated with the following publication: Yuan, L., R. Mitchell, A. Pollard, C. Nietch, E. Pilgrim, and N. Smucker. Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon–environment relationships. FRESHWATER BIOLOGY. Blackwell Publishing, Malden, MA, USA, 68(3): 473-486, (2023).
LMR spatial temporal analysis data
공공데이터포털
This file includes the following data for 25 stream sites in the Little Miami River watershed: diatom operational taxonomic units with their numbers and relative abundances of rbcL gene sequence reads, watershed land cover, and nutrient concentration and conductivity data. This dataset is associated with the following publication: Yuan, L., N. Smucker, C. Nietch, and E. Pilgrim. Quantifying spatial and temporal relationships between diatoms and nutrients in streams strengthens evidence of nutrient effects from monitoring data. Freshwater Science. The Society for Freshwater Science, Springfield, IL, 41(1): 100-112, (2022).
LMR spatial temporal analysis data
공공데이터포털
This file includes the following data for 25 stream sites in the Little Miami River watershed: diatom operational taxonomic units with their numbers and relative abundances of rbcL gene sequence reads, watershed land cover, and nutrient concentration and conductivity data. This dataset is associated with the following publication: Yuan, L., N. Smucker, C. Nietch, and E. Pilgrim. Quantifying spatial and temporal relationships between diatoms and nutrients in streams strengthens evidence of nutrient effects from monitoring data. Freshwater Science. The Society for Freshwater Science, Springfield, IL, 41(1): 100-112, (2022).
Supplementary material for Lee et al. 2019 Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets
공공데이터포털
Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides) species complex, and elevated Nitzschia, Diploneis, and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora, Mayamaea, and Psammodictyon, indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables. This dataset is associated with the following publication: Lee, S., I. Bishop, S. Spaulding, R. Mitchell, and L. Yuan. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets.. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 102: 166-174, (2019).
Supplementary material for Lee et al. 2019 Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets
공공데이터포털
Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides) species complex, and elevated Nitzschia, Diploneis, and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora, Mayamaea, and Psammodictyon, indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables. This dataset is associated with the following publication: Lee, S., I. Bishop, S. Spaulding, R. Mitchell, and L. Yuan. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets.. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 102: 166-174, (2019).
LMR watershed temporal DNA metabarcoding 2016 study
공공데이터포털
LMR watershed temporal DNA metabarcoding 2016 study. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, H. Wu, C. Nietch, J. Darling, M. Molina, B. Johnson, and L. Yuan. Characterizing temporal variability in streams supports nutrient indicator development using diatom and bacterial DNA metabarcoding. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 831: 154960, (2022).
LMR watershed temporal DNA metabarcoding 2016 study
공공데이터포털
LMR watershed temporal DNA metabarcoding 2016 study. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, H. Wu, C. Nietch, J. Darling, M. Molina, B. Johnson, and L. Yuan. Characterizing temporal variability in streams supports nutrient indicator development using diatom and bacterial DNA metabarcoding. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 831: 154960, (2022).