Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer...

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Bibliographic Details
Published in:Molecular biology and evolution 2014-04, Vol.31 (4), p.993-1009
Main Authors: Dunthorn, Micah, Otto, Johannes, Berger, Simon A, Stamatakis, Alexandros, Mahé, Frédéric, Romac, Sarah, de Vargas, Colomban, Audic, Stéphane, Stock, Alexandra, Kauff, Frank, Stoeck, Thorsten
Format: Article
Language:English
Subjects:
Bayes Theorem
Ciliophora - genetics
Deoxyribonucleic acid
DNA
DNA, Ribosomal Spacer - genetics
Environmental Sciences
Eukaryotes
Evolution, Molecular
Fresh Water - microbiology
Freshwater organisms
Genes, Protozoan
Genetic Speciation
Genetic Variation
High-Throughput Nucleotide Sequencing
Life Sciences
Marine environment
Models, Genetic
Molecular biology
Phylogenetics
Phylogeny
Ribosome Subunits, Small - genetics
Seawater - microbiology
Sequence Analysis, DNA
Water Microbiology
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Summary:Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msu055