Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics

Abstract

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20-600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor-joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.

Phylogenetic relationships of the Dactyloa clade of Anolis lizards based on nuclear and mitochondrial DNA sequence data

“…Genes coding for tRNAs were aligned manually to incorporate secondary structure information, following Kumazawa and Nishida's (1993) structural model for mitochondrial transfer RNAs. Sequences were strictly aligned following this model (i.e., no gaps were introduced in areas with conserved lengths: AA, AC, TWC and D-stems, junctions between AA-and D-stems, D-and AC-stems, and AC-and TWC-stems, and the anticodon loop).…”

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

“…DNA sequences were aligned in ClustalX 1.83 (Thompson et al, 1997) with default gap costs. Sequences encoding tRNAs were aligned by inferring secondary structures from primary structures of the corresponding tRNA genes based on standard tRNA models (Kumazawa and Nishida, 1993;Macey and Verma, 1997). Protein-coding sequences (i.e., ND1, ND2, COI, BDNF, RAG1) were translated into amino acids using MacClade 4.03 (Maddison and Maddison, 2001) for confirmation of alignment.…”

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

“…Alignment of the mtDNA sequences was performed manually using amino-acid sequence translations for protein-coding genes and secondary-structural models for tRNA genes (Kumazawa and Nishida, 1993). Length-variable regions whose alignment was ambiguous, including many loop regions of tRNAs and much of the origin for light-strand replication (O L ), were excluded from phylogenetic analyses.…”