Improved Inference of Taxonomic Richness from Environmental DNA

Matthew J. Morgan, Anthony A. Chariton, Diana M. Hartley, Leon N. Court, Christopher M. Hardy

Research output: Contribution to journalArticle

29 Citations (Scopus)
10 Downloads (Pure)


Accurate estimation of biological diversity in environmental DNA samples using high-throughput amplicon pyrosequencing must account for errors generated by PCR and sequencing. We describe a novel approach to distinguish the underlying sequence diversity in environmental DNA samples from errors that uses information on the abundance distribution of similar sequences across independent samples, as well as the frequency and diversity of sequences within individual samples. We have further refined this approach into a bioinformatics pipeline, Amplicon Pyrosequence Denoising Program (APDP) that is able to process raw sequence datasets into a set of validated sequences in formats compatible with commonly used downstream analyses packages. We demonstrate, by sequencing complex environmental samples and mock communities, that APDP is effective for removing errors from deeply sequenced datasets comprising biological and technical replicates, and can efficiently denoise single-sample datasets. APDP provides more conservative diversity estimates for complex datasets than other approaches; however, for some applications this may provide a more accurate and appropriate level of resolution, and result in greater confidence that returned sequences reflect the diversity of the underlying sample.

Original languageEnglish
Article numbere71974
Pages (from-to)1-13
Number of pages13
JournalPLoS ONE
Issue number8
Publication statusPublished - 26 Aug 2013
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2013. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Fingerprint Dive into the research topics of 'Improved Inference of Taxonomic Richness from Environmental DNA'. Together they form a unique fingerprint.

Cite this