@ARTICLE{TreeBASE2Ref15104, author = {Simon Creer and Catharine Emma Pook and Anita Malhotra and Roger S Thorpe}, title = {Optimal Intron Analyses in the Trimeresurus Radiation of Asian Pitvipers.}, year = {2006}, keywords = {}, doi = {10.1080/10635150500431213}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {55}, number = {1}, pages = {57--72}, abstract = {Nuclear introns are commonly used as phylogenetic markers, but a number of issues related to alignment strategies, indel treatments and the incorporation of length variant heterozygotes (LVHs) are not routinely addressed when generating phylogenetic hypotheses. Topological congruence in relation to an extensive mitochondrial DNA multigene phylogeny (derived from 2423 b.p. of 12S, 16S, ND4 and CYTB genes) of the Asian pitviper Trimeresurus radiation was used to compare combinations of ?by eye? and ClustalX 1.8 assisted alignments of two nuclear introns. Indels were treated as missing data, fifth character states and assigned simple and multistate codes. Upon recovery of the optimal alignment and indel treatment strategy, a total evidence approach was used to investigate the phylogenetic utility of the indels and test new generic arrangements within Trimeresurus. Approximately one third of the intron data partitions exhibited LVHs suggesting that they are common in introns. Furthermore, a simple concatenation approach can facilitate the incorporation of LVHs into phylogenetic analyses to make use of all available data and investigate mechanisms of molecular evolution. Analyses of ClustalX 1.8 assisted alignments were generally more congruent than the ?by eye? alignment and the analysis of a simple coded, ClustalX 1.8 (gap opening cost 5, gap extension cost 1) alignment revealed the most congruent tree. The total evidence approach supported the new arrangements within Trimeresurus suggesting that the phylogeny should be considered as a working benchmark in Asian pitviper systematics. Finally, a critical appraisal of the diverse array of indels (56--57 per intron, ranging from 1--151 b.p. in length) suggested that they are a combination of homologous and homoplasious events unrelated to indel size or location within the intron.} }

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