Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

摘要: The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within diverse and economically important subfamily Cyprininae. Within a biased nucleotide composition (A > T, C G) was observed in loop regions of gene, stem apparent selective pressures base pairing showed bias favor G over T A. may be associated with transition-transversion bias. Rates substitution lower stems than loops. Analysis compensatory substitutions across these taxa demonstrates 68% covariation logical weighting factor account for dependence mutations inference should 0.66. Comparisons varied stem-loop schemes indicate that down-weightings could improve analysis degree non-independence not as expected. Bayesian under four models indicated likelihood-based analyses more effective improving performance weighted parsimony analysis. In analyses, resolution phylogenies 16-state paired regions, incorporating GTR + I unpaired better those other models. Cyprininae resolved monophyletic group, well tribe Labein several genera. However, monophyly currently recognized tribes, such Schizothoracin, Barbin, Cyprinion Onychostoma lineages, some genera rejected. Furthermore, comparisons results variable length bootstrap indicates rRNA contain character variation recover well-supported phylogeny whose divergences occurred recent 8 MY, but provide power deep spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.