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figure from manuscript showing island sampled

Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment".

Dataset type: Metabarcoding, Imaging
Data released on September 14, 2015

Drummond AJ; Newcomb RD; Buckley TR; Xie D; Dopheide A; Potter BCM; Heled J; Ross HA; Tooman L; Grosser S; Park D; Demetras NJ; Stevens MI; Russell JC; Anderson SH; Carter A; Nelson N (2015): Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment". GigaScience Database. https://doi.org/10.5524/100144

DOI10.5524/100144

There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20 × 20 metre plots, each comprising sixteen 5 × 5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem.
Across five molecular markers (16S, 18S, ITS, COI and trnL) we collected 3,537,908 sequence reads. From six eDNA data sets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 65 NCBI taxonomy-define phyla or equivalent high-level taxa, ranging from 12 (ITS) to 34 phyla (18S) for a given eDNA marker.

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Additional details

Read the peer-reviewed publication(s):

  • Drummond, A. J., Newcomb, R. D., Buckley, T. R., Xie, D., Dopheide, A., Potter, B. C., Heled, J., Ross, H. A., Tooman, L., Grosser, S., Park, D., Demetras, N. J., Stevens, M. I., Russell, J. C., Anderson, S. H., Carter, A., & Nelson, N. (2015). Evaluating a multigene environmental DNA approach for biodiversity assessment. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0086-1

Additional information:

https://github.com/walterxie/eDNA-pipeline

Accessions (data included in GigaDB):

BioProject: PRJNA267737

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Table Settings
Sample ID Common Name Scientific Name Sample Attributes Taxonomic ID Genbank Name
Plot 1-B Soil Metagenome soil metagenome PH method:http://trove.nla.gov.au/version/42620262
Nitrate:0.753777
Broad-scale environmental context:temperate broadl...
... 		410658
Plot 1-L Soil Metagenome soil metagenome Current vegetation:Kanuka scrub/forest - VS2
Phosphorus (Olsen.P):82.876913
Mean annual and seasonal temperature:15.28
... 		410658
Plot 2-C Soil Metagenome soil metagenome Sample storage duration:2
Carbon/nitrogen ratio:25.087251
Broad-scale environmental context:temperate broadl...
... 		410658
Plot 2-M Soil Metagenome soil metagenome pH:4.95
Electrical Conductivity(EC):0.103172
PH method:http://trove.nla.gov.au/version/42620265
... 		410658
Plot 3-H Soil Metagenome soil metagenome Phosphorus (Olsen.P):6.502267
Total nitrogen:0.223264
Broad-scale environmental context:temperate broadl...
... 		410658
Plot 3-N Soil Metagenome soil metagenome Geographic location (longitude):175.073758
Sample storage temperature:-80
Mean annual and seasonal temperature:14.48
... 		410658
Plot 4-A Soil Metagenome soil metagenome Organic carbon:32.085568
pH:6.24
Electrical Conductivity(EC):0.52014
... 		410658
Plot 4-N Soil Metagenome soil metagenome Nitrate:0.385856
Total nitrogen:1.875464
Slope aspect:260
... 		410658
Plot 5-I Soil Metagenome soil metagenome Nitrate:0.114747
Broad-scale environmental context:temperate broadl...
Elevation:240
... 		410658
Plot 5-N Soil Metagenome soil metagenome Collection date:2010-Dec-05
Slope gradient:23
Geographic location (latitude):-36.21535703
... 		410658
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Table Settings

File Name Description Sample ID Data Type File Format Size Release Date File Attributes Download
Community matrices at 97% clustering threshold of 16S Other CSV 861.80 kB 2015-06-02 MD5 checksum: 8c5d355079fcd6b0e259f1d3d0847382
Community matrices at 97% clustering threshold of 18S Other CSV 369.62 kB 2015-06-02 MD5 checksum: 690a9a8f72a28a44210a7c222f2d6a96
table of bird counts per plot Other CSV 972 B 2015-06-02 MD5 checksum: 6c8c77e57281ff95090484a4aeb8f22f
Invertebrate, pitfall trap survey data Other CSV 10.62 kB 2015-06-02 MD5 checksum: 96ffae8c397b3723efe6e1e614de8abe
Invertebrate, leaf litter survey data Other CSV 12.46 kB 2015-06-02 MD5 checksum: 51fe9f8add6ce29f05985bc9b7e9dbd1
Community matrices at 97% clustering threshold of COI Other CSV 797.45 kB 2015-06-02 MD5 checksum: eebce66a2588b375883fee7dab1c57fd
Community matrices at 97% clustering threshold of COI-spun Other CSV 156.34 kB 2015-06-02 MD5 checksum: 2663b01565e67537a818e3b751d69725
Vegetation (trees) survey data for Hauturu (Little Barrier island) in Jan 2011 (http://nvs.landcareresearch.co.nz). Other CSV 2.32 kB 2015-06-02 MD5 checksum: b43d38947fa58d17ba1c080b6a6e5255
compressed archive of drummond_images directory containing all exempler images of large invertebrates from sampling sites test Image zip 67.36 MB 2015-06-02 MD5 checksum: 0d4ba65d0e6f7f972c2cf4f62b4f18ee
Community matrices at 97% clustering threshold of ITS Other CSV 394.37 kB 2015-06-02 MD5 checksum: 74946dff0ef31e9464edd565b56edc3c
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Displaying 10 files of 44
Date Action
September 14, 2015 Dataset publish
September 14, 2015 Title updated from : Supporting data for "Evaluating a multigene environmental DNA approach for comprehensive biodiversity assessment".
June 13, 2016 Manuscript Link added : 10.1186/s13742-015-0086-1