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References from Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities. Local targets link to admitted publications; unresolved targets remain external evidence.
Scrutinizing key steps for reliable metabarcoding of environmental samples
10.1111/2041-210x.12849 · 2018 · External reference
An economic valuation of southern California coastal wetlands.
2018 · External reference
Marine bacteriophages
10.1016/b978-0-12-809633-8.20988-6 · 2021 · External reference
DNAqua‐Net conference unites participants from around the world with the quest to standardize and implement DNA‐based aquatic biomonitoring
10.1002/edn3.207 · 2021 · External reference
The family Cryomorphaceae
10.1007/978-3-642-38954-2_135 · 2014 · External reference
Is the detection of aquatic environmental DNA influenced by substrate type?
10.1371/journal.pone.0183371 · 2017 · External reference
DADA2: High-resolution sample inference from Illumina amplicon data
10.1038/nmeth.3869 · 2016 · External reference
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
10.1038/ismej.2012.8 · 2012 · External reference
Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples
10.1101/2020.01.22.915009 · 2020 · External reference
VennDiagram: Generate high-resolution Venn and Euler plots (R Package)
2018 · External reference
The Anacapa Toolkit
2018 · External reference
CRUX: Creating reference libraries using eXisting tools
2018 · External reference
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
10.1111/mec.14350 · 2017 · External reference
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
10.1016/j.biocon.2014.11.018 · 2015 · External reference
Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus
10.1111/j.1365-2664.2012.02171.x · 2012 · External reference
Degradation and turnover of extracellular DNA in marine sediments: ecological and methodological considerations
10.1128/aem.70.7.4384-4386.2004 · 2004 · External reference
Isopropanol precipitation method for collecting fish environmental DNA
10.1002/lom3.10161 · 2017 · External reference
Rangewide microsatellite phylogeography of the endangered tidewater goby, Eucyclogobius newberryi (Teleostei: Gobiidae), a genetically subdivided coastal fish with limited marine dispersal
10.1007/s10592-009-0008-9 · 2010 · External reference
Accurate multiplexing and filtering for high-throughput amplicon-sequencing
10.1093/nar/gkv107 · 2015 · External reference
FASTX-Toolkit
2010 · External reference
ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq
10.1371/journal.pone.0067019 · 2013 · External reference
Species detection using environmental DNA from water samples
10.1098/rsbl.2008.0118 · 2008 · External reference
A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy
10.1186/s12859-017-1670-4 · 2017 · External reference
Occurrence Download
10.15468/dl.htj3ht · 2022 · External reference
Critical considerations for the application of environmental DNA methods to detect aquatic species
10.1111/2041-210x.12595 · 2016 · External reference
Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds
10.1007/s10750-018-3750-5 · 2019 · External reference
Methods to maximise recovery of environmental DNA from water samples
10.1371/journal.pone.0179251 · 2017 · External reference
Historical Weather Summer 2018 at Point Mugu Naval Air Warfare Center
External reference
Classification of California estuaries based on natural closure patterns: Templates for restoration and management (Technical Report)
2011 · External reference
ranacapa: Utility functions and “shiny” app for simple environmental DNA visualizations and analyses (0.1.0)
2020 · External reference
Understanding PCR processes to draw meaningful conclusions from environmental DNA studies
10.1038/s41598-019-48546-x · 2019 · External reference
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
10.1093/nar/gkr771 · 2012 · External reference
One size does not fit all: Tuning eDNA protocols for high‐ and low‐turbidity water sampling
10.1002/edn3.235 · 2022 · External reference
Differential effects of frozen storage on the molecular detection of bacterial taxa that inhabit the nasopharynx
10.1186/1472-6890-11-2 · 2011 · External reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms
10.3133/tm2a13 · 2015 · External reference
Computational correction of index switching in multiplexed sequencing libraries
10.1038/nmeth.4666 · 2018 · External reference
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
10.1186/1742-9994-10-34 · 2013 · External reference
Cycling of extracellular DNA in the soil environment
10.1016/j.soilbio.2007.06.020 · 2007 · External reference
The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding
10.1111/1755-0998.12899 · 2018 · External reference
Filtration recovery of extracellular DNA from environmental water samples
10.1021/es401342b · 2013 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Environmental DNA filtration techniques affect recovered biodiversity
10.1038/s41598-018-23052-8 · 2018 · External reference
Cutadapt removes adapter sequences from high-throughput sequencing reads
10.14806/ej.17.1.200 · 2011 · External reference
phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
10.1371/journal.pone.0061217 · 2013 · External reference
Waste not, want not: Why rarefying microbiome data is inadmissible
10.1371/journal.pcbi.1003531 · 2014 · External reference
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
10.1098/rsos.150088 · 2015 · External reference
Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries
10.1007/s12237-022-01080-y · 2022 · External reference
vegan: Community Ecology Package (2.5-6)
2019 · External reference
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods
10.1016/j.scitotenv.2021.151783 · 2022 · External reference
Sediment composition influences spatial variation in the abundance of human pathogen indicator bacteria within an estuarine environment
10.1371/journal.pone.0112951 · 2014 · External reference
Extracellular DNA in soil and sediment: Fate and ecological relevance
10.1007/s00374-008-0345-8 · 2009 · External reference
Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples
10.1139/cjfas-2013-0047 · 2013 · External reference
Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA
10.1111/mec.13481 · 2016 · External reference
R: A language and environment for statistical computing. R Foundation for Statistical Computing
2018 · External reference
REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology
10.1111/1365-2664.12306 · 2014 · External reference
Fine-tuning for the tropics: Application of eDNA technology for invasive fish detection in tropical freshwater ecosystems
10.1111/1755-0998.12505 · 2016 · External reference
RStudio: Integrated development for R. RStudio, PBC
2020 · External reference
Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river
10.1002/edn3.14 · 2019 · External reference
Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean
10.1073/pnas.1416223112 · 2015 · External reference
Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
10.1002/edn3.38 · 2019 · External reference
PairwiseCI: Confidence Intervals for Two Sample Comparisons (0.1-27).
2019 · External reference
Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies
10.1111/1755-0998.12402 · 2015 · External reference
Wetlands on the edge: The future of southern California’s wetlands: Regional strategy 2018 (p. 142). California State Coastal Conservancy.
2018 · External reference
Effect of freezing on PCR amplification of 16S rRNA genes from microbes associated with black band disease of corals
10.1128/aem.01500-08 · 2009 · External reference
Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex
10.1111/j.1365-294x.2004.02285.x · 2004 · External reference
Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding
10.1002/ece3.8239 · 2021 · External reference
Assessing the cost‐efficiency of environmental DNA sampling
10.1111/2041-210x.12598 · 2016 · External reference
Wetlands of the southern California coast: Historical extent and change over time (SFEI Report 720; SCCWRP Technical Report 826; p. 58). Southern California Coastal Water Research Project and San Francisco Estuary Institute
2014 · External reference
Freezing induces biased results in the molecular detection of Flavobacterium columnare
10.1128/aem.72.2.1702-1704.2006 · 2006 · External reference
The status and distribution of the freshwater fishes of southern California
10.3160/0038-3872-92.3.101 · 1993 · External reference
A new species of the bay goby genus Eucyclogobius, endemic to southern California: Evolution, conservation, and decline
10.1371/journal.pone.0158543 · 2016 · External reference
Towards next-generation biodiversity assessment using DNA metabarcoding: Next-generation DNA metabarcoding
10.1111/j.1365-294x.2012.05470.x · 2012 · External reference
Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies: Extraction of extracellular DNA from soil
10.1111/j.1365-294x.2011.05317.x · 2012 · External reference
Effects of sample processing on the detection rate of environmental DNA from the Common Carp (Cyprinus carpio)
10.1016/j.biocon.2014.11.014 · 2015 · External reference
Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
10.1016/j.biocon.2014.11.019 · 2015 · External reference
Origin, dynamics, and implications of extracellular DNA pools in marine sediments
10.1016/j.margen.2015.08.007 · 2015 · External reference
The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection
10.1002/edn3.21 · 2019 · External reference
Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities (Scripts, Code and Dataset)
10.5068/d1bq25 · 2023 · External reference
Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities (Supplementary material)
10.5281/zenodo.7762005 · 2023 · External reference
Particle size distribution and optimal capture of aqueous macrobial eDNA
10.1111/2041-210x.12206 · 2014 · External reference
Fish environmental DNA is more concentrated in aquatic sediments than surface water
10.1016/j.biocon.2014.11.017 · 2015 · External reference
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
10.1111/mec.15592 · 2021 · External reference
Clearing muddied waters: Capture of environmental DNA from turbid waters
10.1371/journal.pone.0179282 · 2017 · External reference
metabaR: an R package for the evaluation and improvement of DNA metabarcoding data quality
10.1101/2020.08.28.271817 · 2020 · External reference
