MBE Advance Access published online on May 30, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg136
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, UK
* To whom correspondence should be addressed. E-mail: s.creer{at}bangor.ac.uk.
A number of methods have been proposed addressing how to optimise the analysis of multiple datasets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous and conditional data combination methods to analyse 3135 b.p. of data from four mitochondrial partitions, and the 7th intron of the Key Words:
phylogeny, gene partitions, partitioned Bremer support, Trimeresurus
© 2003 Society for Molecular Biology and Evolution
Original Articles
Assessing the Phylogenetic Utility of Four Mitochondrial Genes and a Nuclear Intron in the Asian Pitviper Genus, Trimeresurus: Separate, Simultaneous, and Conditional Data Combination Analyses
Abstract 
fibrinogen gene in the Asian pitviper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron, resulted in much lower levels of homoplasy compared to the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa which were unresolved throughout all individual gene trees, and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b, and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships, than the 12S and 16S ribosomal RNA partitions, at the taxonomic levels under consideration.
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