Data from: Estimating species richness using environmental DNA

Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA

Date Published: May 31, 2016

DOI: http://dx.doi.org/10.5061/dryad.d63sc

 

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Title Actino12s OTU Centroid Sequences
Downloaded 4 times
Description List of centroid sequences generated in OTU formation after HMMER filtering
Download Actino12s.OTU.ID.hmm.fasta (15.92 Kb)
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Title Actino16s OTU Centroid Sequences
Downloaded 5 times
Description List of centroid sequences generated in OTU formation after HMMER filtering
Download Actino16s.OTU.ID.hmm.fasta (8.385 Kb)
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Title Amphibia12s OTU Centroid Sequences
Downloaded 3 times
Description List of centroid sequences generated in OTU formation after HMMER filtering
Download Amphibia12s.OTU.ID.hmm.fasta (11.25 Kb)
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Title Cytb OTU Centroid Sequences
Downloaded 4 times
Description List of centroid sequences generated in OTU formation after HMMER filtering
Download Cytb.OTU.ID.hmm.fasta (7.681 Kb)
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Title Supplement Table 1
Downloaded 7 times
Description Electrofishing derived species counts in Juday Creek for each reach from September 2013. Samples are ordered from the most downstream reach (R1) to the most upstream reach (R4).
Download Supplement Table 1.xlsx (13.01 Kb)
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Title Supplement Table 2
Downloaded 7 times
Description Number of reads from each sample (i.e. library) run on the Illumina MiSeq platform for each step of the bioinformatic pipeline.
Download Supplement Table 2.xlsx (13.83 Kb)
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Title Supplement Table 3
Downloaded 3 times
Description Results for all species identified with OTU species assignment. Values of P1 – P7 represent the pathway taken to arrive at species assignment using SAP and USearch (Fig. S1).
Download Supplement Table 3.xlsx (9.777 Kb)
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Title Supplement Table 4
Downloaded 6 times
Description Raw read counts of each species identified, for each sample and all four markers.
Download Supplement Table 4.xlsx (14.21 Kb)
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Title Supplement Table 5
Downloaded 6 times
Description Putative false positive OTUs and the corresponding read number of each marker in each sample.
Download Supplement Table 5.xlsx (10.21 Kb)
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Title Supplement Table 6
Downloaded 6 times
Description List of species for which we had a reference sequence for each of the four markers used.
Download Supplement Table 6.xlsx (14.67 Kb)
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Title Supplement Table 7
Downloaded 5 times
Description This table shows read counts after filtering. The eDNA column shows the species detected in the actual Juday Creek samples with some reads counts in any of these control samples. The P/A columns shows Presence (1) or Absence (0) given our criteria of >1 read and reads in multiple markers or samples.
Download Supplement Table 7.xlsx (13.99 Kb)
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When using this data, please cite the original publication:

Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA (2016) Estimating species richness using environmental DNA. Ecology and Evolution 6(12): 4214-4226. http://dx.doi.org/10.1002/ece3.2186

Additionally, please cite the Dryad data package:

Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA (2016) Data from: Estimating species richness using environmental DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.d63sc
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