General patterns of diversity in major marine microeukaryote lineages

PLoS One. 2013;8(2):e57170. doi: 10.1371/journal.pone.0057170. Epub 2013 Feb 21.

Abstract

Microeukaryotes have vital roles for the functioning of marine ecosystems, but still some general characteristics of their current diversity and phylogeny remain unclear. Here we investigated both aspects in major oceanic microeukaryote lineages using 18S rDNA (V4-V5 hypervariable regions) sequences from public databases that derive from various marine environmental surveys. A very carefully and manually curated dataset of 8291 Sanger sequences was generated and subsequently split into 65 taxonomic groups (roughly to Class level based on KeyDNATools) prior to downstream analyses. First, we calculated genetic distances and clustered sequences into Operational Taxonomic Units (OTUs) using different distance cut-off levels. We found that most taxonomic groups had a maximum pairwise genetic distance of 0.25. Second, we used phylogenetic trees to study general evolutionary patterns. These trees confirmed our taxonomic classification and served to run Lineage Through Time (LTT) plots. LTT results indicated different cladogenesis dynamics across groups, with some displaying an early diversification and others a more recent one. Overall, our study provides an improved description of the microeukaryote diversity in the oceans in terms of genetic differentiation within groups as well as in the general phylogenetic structure. These results will be important to interpret the large amount of sequence data that is currently generated by High Throughput Sequencing technologies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alveolata / classification
  • Alveolata / genetics
  • Aquatic Organisms*
  • Eukaryota / classification*
  • Eukaryota / genetics*
  • Genetic Speciation
  • Genetic Variation*
  • High-Throughput Nucleotide Sequencing
  • Phylogeny
  • RNA, Ribosomal, 18S / classification*
  • RNA, Ribosomal, 18S / genetics*
  • Rhizaria / classification
  • Rhizaria / genetics
  • Sequence Analysis, DNA
  • Stramenopiles / classification
  • Stramenopiles / genetics

Substances

  • RNA, Ribosomal, 18S

Grants and funding

Funding has been provided by projects FLAME (CGL2010-16304, MICINN, Spain) and BioMarKs (2008-6530, ERA-net Biodiversa, EU) to RM, by project GEMMA (CTM2007-63753-C02-01/MAR, MEC, Spain) to Carlos Pedrós-375 Alió, by a FPI fellowship from the Spanish Ministry of Education and Science to MCP, and by a Marie Curie Intra-European Fellowship grant PIEF-GA-2009-235365 to RL. Original sequence database was built under the frame of the French ANR-Biodiversité project AQUAPARADOX. High-performance computing resources were provided by the Barcelona Supercomputing Center at the MareNostrum (grants BCV-2011-2-0003 & BCV-2011-3-0005) to RM and RL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.