@ARTICLE{TreeBASE2Ref18639, author = {Dawn M Simon and Scot A. Kelchner and Steven Zimmerly}, title = {A broad-scale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases}, year = {2009}, keywords = {}, doi = {10.1093/molbev/msp193}, url = {}, pmid = {}, journal = {Molecular Biology and Evolution}, volume = {26}, number = {12}, pages = {2795--2808}, abstract = {Group II introns are self-splicing RNAs that are frequently assumed to be the ancestors of spliceosomal introns. They are widely distributed in bacteria and are also found in organelles of plants, fungi, and protists. In this study, we present a broad-scale phylogenetic analysis of group II introns using sequence data from both the conserved RNA structure and the intron-encoded reverse transcriptase (RT). Two similar phylogenies are estimated for the RT ORF, based on either amino acid or nucleotide sequence, while one phylogeny is produced for the RNA. In making these estimates, we confronted nearly all of the classic challenges to phylogenetic inference including positional saturation, base composition heterogeneity, short internodes with low support, and sensitivity to taxon sampling. While the major lineages are well-defined, robust resolution of topology is not possible between these lineages. The approximately unbiased (AU) and Shimodaira-Hasegawa (SH) topology tests indicated that the RT ORF and RNA ribozyme data sets are in significant conflict under a variety of models, revealing the possibility of imperfect coevolution between group II introns and their intron-encoded ORFs. The high level of sequence divergence, large time scale, and limited number of alignable characters in our study are representative of many reverse transcriptases and group I introns, and our results suggest that phylogenetic analyses of any of these sequences could suffer from the same sources of error and instability identified in this study.} }

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