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Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1 (2009)
| Venue: | Systematic Biology |
| Citations: | 8 - 3 self |
BibTeX
@ARTICLE{Mauro09experimentaldesign,
author = {Diego San Mauro and David J. Gower and Tim Massingham and Mark Wilkinson and Rafael Zardoya and James A. Cotton},
title = {Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1},
journal = {Systematic Biology},
year = {2009},
pages = {425--438}
}
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Abstract
Abstract.—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 com-bined (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 tere-
Keyphrases
experimental design nuclear rag1 phylogenetic information caecilian systematics mitochondrial genome caecilian tree mt transfer caecilian amphibian controversial relationship different gene major aspect context specific previous study ribosomal rna gene overall phylogenetic information estimate molecular phylogenetic study phylogenetic utility mt genome different part taxon addition phylogenetic performance hypothetical new taxon specific estimate controversial branch data set taxon sampling informative data set
