Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia)

Abstract

The complete 12S rRNA gene has been sequenced in 4 Ungulata (hoofed eutherians) and 1 marsupial and compared to 38 available mammalian sequences in order to investigate the molecular evolution of the mitochondrial small-subunit ribosomal RNA molecule. Ungulata were represented by one artiodactyl (the collared peccary, Tayassu tajacu, suborder Suiformes), two perissodactyls (the Grevy's zebra, Equus grevyi, suborder Hippomorpha; the white rhinoceros, Ceratotherium simum, suborder Ceratomorpha), and one hyracoid (the tree hyrax, Dendrohyrax dorsalis). The fifth species was a marsupial, the eastern gray kangaroo (Macropus giganteus). Several transition/transversion biases characterized the pattern of changes between mammalian 12S rRNA molecules. A bias toward transitions was found among 12S rRNA sequences of Ungulata, illustrating the general bias exhibited by ribosomal and protein-encoding genes of the mitochondrial genome. The derivation of a mammalian 12S rRNA secondary structure model from the comparison of 43 eutherian and marsupial sequences evidenced a pronounced bias against transversions in stems. Moreover, transversional compensatory changes were rare events within double-stranded regions of the ribosomal RNA. Evolutionary characteristics of the 12S rRNA were compared with those of the nuclear 18S and 28S rRNAs. From a phylogenetic point of view, transitions, transversions and indels in stems as well as transversional and indels events in loops gave congruent results for comparisons within orders. Some compensatory changes in double-stranded regions and some indels in single-stranded regions also constituted diagnostic events. The 12S rRNA molecule confirmed the monophyly of infraorder Pecora and order Cetacea and demonstrated the monophyly of the suborder Ruminantia was not supported and the branching pattern between Cetacea and the artiodacytyl suborders Ruminantia and Suiformes was not established. The monophyly of the order Perissodactyla was evidenced, but the relationships between Artiodactyla, Cetacea, and Perissodactyla remained unresolved. Nevertheless, we found no support for a Perissodactyla + Hyracoidea clade, neither with distance approach, nor with parsimony reconstruction. The 12S rRNA was useful to solve intraordinal relationships among Ungulata, but it seemed to harbor too few informative positions to decipher the bushlike radiation of some Ungulata orders, an event which has most probably occurred in a short span of time between 55 and 70 MYA.

Lineage-Specific Evolutionary Rate in Mammalian mtDNA

“…This could be explained with the peculiar substitution pattern in rRNA genes, where compensatory changes occur in the stem regions and insertion/deletions are common in the loop regions. Particularly in the 12S rRNA molecule, the heterogeneity of the transition/transversion bias between stems and loops and the rapid saturation of transitions reduce the resolution of this gene for interordinal relationships among Eutheria, particularly when only stem regions are considered (Douzery and Catzeflis 1995;Springer and Douzery 1996). The same pattern should hold for the 16S rRNA; thus, some interordinal distances calculated on a ribosomal supergene might be underestimated.…”

Multiple molecular evidences for a living mammalian fossil

“…We excluded the third codon position of this gene because preliminary analysis has shown that this position was saturated. The alignment of 12S rRNA was performed with ClustalX (20) with default parameter settings and refined by hand to minimize the number of indels (insertions-deletions) in stems (21,22). Finally, gaps present in Ͼ25% of the taxa were removed from the analyses for each data set.…”

Evolutionary Spread and Recombination of Porcine Endogenous Retroviruses in the Suiformes

“…They are listed below in decreasing order of relationship to Sus scrofa. The epoch when the phylogenetic split occurred, as determined by archaeological evidence (43,44) and genetic reconstruction (8,11,15,24), is given in parentheses: Sus barbatus, Sus celebensis (Holocene), Potamochorus porcus, Potamochorus larvatus (Pleistocene), Phacochorus africanus, Babyrousa babyrussa (Pliocene), and Tayassuidae pecari (Eocene). A detailed classification of the families of Suidae and Tayassuidae, including subfamilies and genera, is given in Fig.…”