Journal Article

Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear <i>rag1</i>

Diego San Mauro, David J. Gower, Tim Massingham, Mark Wilkinson, Rafael Zardoya and James A. Cotton

in Systematic Biology

Published on behalf of Society of Systematic Biologists

Volume 58, issue 4, pages 425-438
Published in print August 2009 | ISSN: 1063-5157
Published online August 2009 | e-ISSN: 1076-836X | DOI: https://dx.doi.org/10.1093/sysbio/syp043
Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1

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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

Journal Article.  8023 words.  Illustrated.

Subjects: Biological Sciences

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