Systematic Biology Advance Access originally published online on August 18, 2009
Systematic Biology 2009 58(4):425-438; doi:10.1093/sysbio/syp043
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© Society of Systematic Biologists
Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1
1 Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
2 The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
3 Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales - CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
4 School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
* Correspondence to be sent to: Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; E-mail: d.san-mauro{at}nhm.ac.uk.
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Abstract |
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In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. Although previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.
Keywords: Experimental design; Gymnophiona; mitochondrial genes; mitochondrial genome; phylogenetic information; rate of evolution; rag1; taxon sampling
Received May 12, 2008; Revised July 17, 2008; Accepted June 29, 2009