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Ane Kirstine Brunbjerg

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

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DOI

  • Tobias Guldberg Froslev, Univ Copenhagen, University of Copenhagen, Ctr Star & Planet Format, Nat Hist Museum Denmark
  • ,
  • Rasmus Kjoller, Univ Copenhagen, University of Copenhagen, Dept Biol
  • ,
  • Hans Henrik Bruun, Univ Copenhagen, University of Copenhagen, Dept Biol
  • ,
  • Rasmus Ejrnaes
  • Ane Kirstine Brunbjerg
  • Carlotta Pietroni, Univ Copenhagen, University of Copenhagen, Ctr Star & Planet Format, Nat Hist Museum Denmark
  • ,
  • Anders Johannes Hansen, Univ Copenhagen, University of Copenhagen, Ctr Star & Planet Format, Nat Hist Museum Denmark

DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves alpha-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.

OriginalsprogEngelsk
Artikelnummer1188
TidsskriftNature Communications
Vol/bind8
Antal sider11
ISSN2041-1723
DOI
StatusUdgivet - 30 okt. 2017

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