RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences

Abstract

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes.3

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

“…Compared with the basic assumptions of parsimony analysis, the model-based Bayesian analyses generally should be preferred, in that it can accommodate better estimates of appropriate models to deal with the functional constraints of maintaining base pairing on stem regions (Hudelot et al, 2003;Kjer, 2004;Brown, 2005). Likelihood-based phylogenetic analyses can be demonstrated to be more effective in improving the phylogenetic performance than weighted parsimony analysis (Table 5).…”

“…The Bayesian framework employed in PHASE used random starting trees and the parameters of the substitution models were estimated during the analysis. Following Hudelot et al (2003), we adopted a conservative burn-in period and used 2,000,000 initial generations. Later, another 1,000,000 generations were run with sampling every 500 generations.…”

Evolutionary patterns of non-coding RNAs

“…in [362,205,358,311]. The phase package [190,173] implements such a model and is specifically designed to infer phylogenies from RNAs that have a conserved secondary structure.…”

“…The evolution of mitochondrial tRNA was studied in detail by Paul Higgs and collaborators [173,154,183]. In particular, they present evidence that the two animal tRNA-Leu variants (one with anticodon UAG, the other with anticodon UAA) evolve by a peculiar mechanism of gene duplication, followed by mutation of the anticodon and subsequent gene loss.…”

“…In fact, much of our knowledge about the deepest branches of the tree of life has been inferred from 16S/18S sequence data [85,308,415,327,51]. Besides the 16S/18S and the 28S/23S large subunit rRNA, other classes of RNAs, however, have been used only sporadically for these purposes, although it has been shown that they are phylogenetically informative [42,66,173]. Telomerase RNA structures were used to elucidate the phylogeny of tetrahymenine ciliates [445].…”