Open Access Highly Accessed Research article

A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits

Karin C Kiontke1*, Marie-Anne Félix2, Michael Ailion36, Matthew V Rockman14, Christian Braendle5, Jean-Baptiste Pénigault2 and David HA Fitch1

  • * Corresponding author: Karin C Kiontke kk52@nyu.edu

  • † Equal contributors

Author Affiliations

1 Department of Biology, New York University, 100 Washington Square East New York, New York 10003, USA

2 CNRS-Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France

3 Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA

4 Center for Genomics and Systems Biology, New York University, New York, USA

5 Institute of Developmental Biology and Cancer, CNRS-University of Nice, Sophia-Antipolis, Parc Valrose, 06108 NICE cedex 2, France

6 Department of Biochemistry, University of Washington, Seattle, WA, USA

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BMC Evolutionary Biology 2011, 11:339  doi:10.1186/1471-2148-11-339

Published: 21 November 2011

Additional files

Additional file 1:

Crosses between strains and species. A table showing the results of crosses between strains of the same species and of different species.

Format: XLS Size: 41KB Download file

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Additional file 2:

Primer sequences. Primer sequences for amplification and sequencing of 9 genes.

Format: XLS Size: 28KB Download file

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Additional file 3:

Accession numbers. GenBank Accession numbers of the sequences used in this study.

Format: XLS Size: 46KB Download file

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Additional file 4:

Matrix of molecular sequence data. Data matrix with concatenated sequences of 11 genes with additional information for maximum parsimony analysis.

Format: NXS Size: 332KB Download file

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Additional file 5:

Drosophila RNAP2 sequences. Alignment of RNA polymerase II sequences for 12 Drosophila species.

Format: NXS Size: 79KB Download file

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Additional file 6:

Aligned ITS2 sequences. Alignment of the region between the genes for 5.8S and LSU rRNA (ITS2) for 50 Caenorhabditis strains.

Format: NXS Size: 34KB Download file

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Additional file 7:

New isolates of described Caenorhabditis species. A table which lists strains of described Caenorhabditis species that were sampled from rotting plant material.

Format: DOC Size: 218KB Download file

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Additional file 8:

Isolates of new Caenorhabditis species. A table which lists strains of the new Caenorhabditis species with location and habitat.

Format: DOC Size: 149KB Download file

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Additional file 9:

Drosophila RNAP2 phylogram. Likelihood phylogram for Drosophila species calculated for RNA polymerase II (215 kD subunit) genes.

Format: PDF Size: 116KB Download file

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Additional file 10:

Distribution of phenotypic characters. Matrix for phenotypic characters and phylogeny. In MacClade or Mesquite, this file will provide a visualization of the distribution of the characters on the trees and the evolutionary changes.

Format: NEX Size: 6KB Download file

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Additional file 11:

Differences in the ITS2 region. Number and kind of differences in the ITS2 region between Caenorhabditis strains.

Format: DOC Size: 49KB Download file

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Additional file 12:

Geographic distribution of previously known Caenorhabditis species used in this study. Map showing the geographic distribution of C. elegans and C. briggsae and second map showing the distribution of previously known gonochoristic Caenorhabditis species.

Format: PPT Size: 1.4MB Download file

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Additional file 13:

Large sperm in C. sp. 18. Micrographs showing the large sperm size in C. sp. 18 compared to typical sperm size in C. sp. 17.

Format: PPT Size: 772KB Download file

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