The Eukaryotic Taxonomy Working Group (ETWG) has been founded in October 2011 to create a unified taxonomy for Eukaryotes based on 18S/28S ribosomal RNA gene sequences.

The goals of ETWG are:

1. Identify reliable resources for eukaryotic taxonomic classification
2. Create a consensus taxonomic hierarchy for eukaryotic organisms
3. Implement this consensus hierarchy onto 18S and 28S sequences
4. Promote dissemination and access to the classification and sequences

• Pelin Yilmaz, MPI-Bremen (Chair)
• Frank Oliver Glöckner, MPI-Bremen
• Laura Wegener Parfrey, Department of Chemistry and Biochemistry University of Colorado
• Rob Knight, Department of Chemistry and Biochemistry University of Colorado
• James R. Cole, Center for Microbial Ecology, Michigan State University
• Linda Amaral Zettler, Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole
• Susan M. Huse, Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole
• Alastair Simpson, Department of Biology Dalhousie University
• Colomban de Vargas, Station biologique de Roscoff, CNRS, France
• Alexandra Z. Worden, Monterey Bay Aquarium Research Institute
• Brian Leander, Departments of Zoology and Botany The University of British Columbia
  
• Chris Lane, Department of Biological Sciences, University of Rhode Island
  
• Daniel McDonald, Department of Chemistry and Biochemistry University of Colorado
• George M. Garrity, Department of Microbiology and Molecular Genetics Michigan State University
  
• Holly Bik, UC Davis Genome Center University of California, Davis
  
• Jason Stajich, Dept of Plant Pathology & Microbiology University of California
• Naiara Rodríguez-Ezpeleta, AZTI Tecnalia
• Noah Fierer, Department of Ecology & Evolutionary Biology University of Colorado
  
• Philip Hugenholtz, Australian Centre for Ecogenomics
  
• Scott Bates, Department of Ecology & Evolutionary Biology University of Colorado
• Sina Adl, College of Agriculture and Bioresources University of Saskatchewan
  
• Virginia Edgcomb, Woods Hole Oceanographic Institution

The first version of the new  Eukaryotic Taxonomy with SILVA is now available with the SILVA release 111. In this first version, the taxonomy of Protist lineages (Alveolata, Stramenopiles, Excavata, etc...) have been reconciled with the Adl et al. 2005 publication (http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2005.00053.x/full). An early draft from the ISOP committee (Adl et al. 2012 (in prep)) was also used to further improve the Protist classification, where possible.
Moreover, higher level ranks have been also revised for higher plants, fungi and animals. However, these groups are still "work in progress", and the classification should be used with caution.
This new classification introduced the concept of "rankless" taxa, i.e. the position of the taxon in the taxonomic hierarchy does not imply rank as is the case with Bacteria and Archaea. Although this concept is biologically sound, we recognize the difficulties that this may bring in computational analyses. Therefore, a separate ranks mapping file will also be provided with the new Eukaroyotic Taxonomy, which assigns reasonable ranks to taxa to make different levels comparable.

Classification ranks for eukaryotes are provided to help users address the practical challenges of using bioinformatic tools that are designed for or require explicit rank information. These classification ranks are based on a combination of ranks assigned by NCBI/EMBL with additional information coming from current views on the deep relationships among eukaryotic groups. Rank designations were made according to the overall goal of assigning the same rank to roughly equivalent levels across the tree. Only taxonomic levels that are distinguishable in the Silva guide tree are included (so many levels of animal, plant and fungal taxonomy are not in the table). The meaning of classification ranks is variable across the major clades of eukaryotes in terms of the timing of clade divergence, overall diversity, and genetic distance. As such, ranks are not used in overall eukaryotic classification schema (see Adl et al. 2005). Thus, we ask that you use the ranks as a guideline. Users are welcome to change the ranks to reflect the desired taxonomic depth for individual studies.

The spreadsheet file is available for download under Release 111 Exports Archive.