Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Author:

Ewers Isabelle1ORCID,Rajter Lubomír12ORCID,Czech Lucas3ORCID,Mahé Frédéric45ORCID,Stamatakis Alexandros67ORCID,Dunthorn Micah8ORCID

Affiliation:

1. Eukaryotic Microbiology, Faculty of Biology University of Duisburg‐Essen Essen Germany

2. Phycology, Faculty of Biology University of Duisburg‐Essen Essen Germany

3. Department of Plant Biology Carnegie Institution for Science Stanford California USA

4. CIRAD, UMR PHIM Montpellier France

5. PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD University of Montpellier Montpellier France

6. Computational Molecular Evolution Group Heidelberg Institute for Theoretical Studies Heidelberg Germany

7. Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe Germany

8. Natural History Museum University of Oslo Oslo Norway

Abstract

AbstractTaxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic‐placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA‐ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA‐ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA‐ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

Publisher

Wiley

Subject

Microbiology

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