18S Ribosomal RNA and Tetrapod Phylogeny

Abstract

Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms" (p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11:152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by (1) the misalignment of the sequences, (2) the inappropriate use of the frequency parameters, and (3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species.

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

“…However, these weighting schemes have provide nearly equivalent resolu-tions of relationships relative to equal weighting, largely due to the previous studies not accounting for different selective pressures on stem positions (Wang and Lee, 2002). Recently, simulation studies (Savill et al, 2001) and studies of experimental phylogenies (Higgs, 1998(Higgs, , 2000Xia et al, 2003;Kjer, 2004;Brown, 2005) had developed likelihood-based methods to evaluate phylogeny and these have resulted in improved phylogenetic resolution. However, these previous studies have mostly focused on lineages diverging across expansive time scales and not on relatively closely related taxa.…”

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

“…Considering these secondary structural features, rRNA can be divided into paired (stem) and unpaired (loop) regions, and compensatory substitutions occur frequently in the paired regions, a property that contradicts the assumption of independent mutations. Recently, likelihood-based methods have been successfully developed to account for compensatory substitutions in the rRNA genes (e.g., Savill et al, 2001;Xia et al, 2003a;Brown, 2005). Moreover, the use of partitioned Bayesian analyses has facilitated the exploration of partition-specific evolutionary models and should reduce systematic error, thus providing more precise posterior probability estimates (e.g., Nylander et al, 2004;Brandley et al, 2005;Guo and Wang, 2007).…”

Compositional properties and thermal adaptation of 18S rRNA in vertebrates

“…Although a phylogenetic tree was presented (van Tuinen et al 2002) that indicated a certain distance among species, if we consider a potential GC tree made with CA, all the avian species are clustered together as if we were looking at only one species. Along the same line, Xia et al (2003) already reported the case of a phylogenetic tree in which birds appeared closer to mammals than to reptiles, contrary to other molecular and morphological results, and to their tree in which the rRNAs were aligned with the aide of the secondary structure. From these results and by referring to literature (Bernardi 1993), they suggested that such discrepancy could have been due to the common high body temperature and GC level in birds and mammals.…”

“…In fact, we observed a trend of increasing GC with increasing temperature already from the rough data of the global sequences, warm-blooded vertebrates having the highest GC level and Antarctic fishes the lowest one (together with Chondrichthyes, which, however, have more GC-rich stems compared with the rayfinned fishes). A comparison between the GC levels of global rRNA sequences of cold-blooded and warm-blooded vertebrates was already done with a similar result (Xia et al 2003), but at that time, the available sequences were few, and differences between fishes living in cold or hot environments were not taken into consideration.…”