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

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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.

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Abbreviations

AA stem:

amino acid-acceptor stem

AC stem:

anticodon stem

COI:

cytochrome oxidase subunit I

cytb:

cytochrome b

D stem:

dihydrouridine stem

MP:

maximum parsimony

mtDNA:

mitochondrial DNA

Myr:

million years

NJ:

neighbor joining

PCR:

polymerase chain reaction

Ti:

transition

T stem:

tψC stem

Tv:

transversion

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Author notes

  1. Mutsumi Nishida

    Present address: Department of Marine Bioscience, Fukui Prefectural University, 917, Obama, Fukui, Japan

Authors and Affiliations

  1. Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, 414 Barker Hall, 94720, Berkeley, CA, USA

    Yoshinori Kumazawa & Mutsumi Nishida

  2. Department of Marine Sciences, University of the Ryukyus, 903-01, Okinawa, Japan

    Mutsumi Nishida

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  1. Yoshinori Kumazawa
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  2. Mutsumi Nishida
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Correspondence to: Y. Kumazawa

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Kumazawa, Y., Nishida, M. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 37, 380–398 (1993). https://doi.org/10.1007/BF00178868

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