eDNA Data Pipeline

Multigene environmental DNA approach for biodiversity assessment

Project on GitHub

Analysis of DNA extraction and PCR methods:

DNA extraction and PCR replication comparison from one site (i.e. the second Waitakere samples experiment).

Andrew Dopheide, Dong Xie, Thomas R. Buckley, Alexei J. Drummond, and Richard D. Newcomb, 2018. Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity, Methods in Ecology and Evolution, doi: 10.1111/2041-210X.13086.

The pipeline: andrewdopheide/DNA_extr_PCR_impacts

Multigene metabarcoding analysis of Hauturu biodiversity:

Andrew Dopheide, Dong Xie, Laura Ward, Nicola Nelson, Thomas R Buckley, Alexei J Drummond, and Richard D Newcomb, (submitted in 2017). Simultaneous DNA meta-barcoding analysis of soil prokaryotes and eukaryotes in a forested island ecosystem reveals contrasting patterns of biodiversity, .

The pipeline: walterxie/eDNA-pipeline/tree/hauturu

Invertebrate biodiversity analysis:

Andrew Dopheide, Leah K. Tooman, Stefanie Grosser, Barbara Agabiti, Birgit Rhode, Dong Xie, Mark I. Stevens, Nicola Nelson, Alexei J. Drummond, Thomas R. Buckley, and Richard D. Newcomb, Ecological Applications (accepted in 2019). Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data.

The pipeline: andrewdopheide/Barcoding_invertebrate_biodiversity

Hauturu eDNA pilot study:

Alexei J Drummond, Richard D Newcomb, Thomas R Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A Ross, Leah Tooman, Stefanie Grosser, Duckchul Park, Nicholas J Demetras, Mark I Stevens, James C Russell, Sandra H Anderson, Anna Carter and Nicola Nelson, 2015. Evaluating a multigene environmental DNA approach for biodiversity assessment, GigaScience.

The online version of this article (doi: 10.1186/s13742-015-0086-1) or http://link.springer.com/article/10.1186/s13742-015-0086-1

Supporting data in GigaScience Database: http://dx.doi.org/10.5524/100144

The pipeline: walterxie/eDNA-pipeline/tree/pilot