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

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

(1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,715

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,647

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778

Sequence and organization of the human mitochondrial genome

Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H. L., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., et al. (1981) · Nature · doi:10.1038/290457a0 · Cited by 9,636

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

Kocher, T. D., Thomas, W. K., Meyer, A., Edwards, S. V., Pääbo, S., Villablanca, F. X., & Wilson, A. C. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.16.6196 · Cited by 4,969

Comparison of phylogenetic trees

Robinson, D. F., & Foulds, L. R. (1981) · Mathematical Biosciences · doi:10.1016/0025-5564(81)90043-2 · Cited by 2,701

Evolution of the cytochromeb gene of mammals

Irwin, D. M., Kocher, T. D., & Wilson, A. C. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02515385 · Cited by 2,315

PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY

Felsenstein, J. (1988) · Annual Review of Genetics · doi:10.1146/annurev.ge.22.120188.002513 · Cited by 2,128

Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki012 · Cited by 1,914

Sequence and gene organization of mouse mitochondrial DNA

Bibb, M. J., Van Etten, R. A., Wright, C. T., Walberg, M. W., & Clayton, D. A. (1981) · Cell · doi:10.1016/0092-8674(81)90300-7 · Cited by 1,710

Evolution Of Animal Mitochondrial Dna: Relevance For Population Biology And Systematics

Moritz, C. (1987) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.18.1.269 · Cited by 1,566

Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus.

Gyllensten, U. B., & Erlich, H. A. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.20.7652 · Cited by 1,560

Mitochondrial DNA sequences of primates: tempo and mode of evolution

Brown, W. M., Prager, E. M., Wang, A., & Wilson, A. C. (1982) · Journal of Molecular Evolution · doi:10.1007/bf01734101 · Cited by 1,554

Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome

Anderson, S., de Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., & Young, I. G. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90137-1 · Cited by 1,472

Mitochondrial DNA and two perspectives on evolutionary genetics

WILSON, A. C., CANN, R. L., CARR, S. M., GEORGE, M., GYLLENSTEN, U. B., HELM-BYCHOWSKI, K. M., HIGUCHI, R. G., PALUMBI, S. R., PRAGER, E. M., SAGE, R. D., et al. (1985) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.1985.tb02048.x · Cited by 1,222

Sequence and gene organization of the chicken mitochondrial genome

Desjardins, P., & Morais, R. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90225-b · Cited by 1,048

Compilation of small ribosomal subunit RNA sequences

De Rijk, P., Neefs, J.-M., Van de Peer, Y., & De Wachter, R. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.suppl.2075 · Cited by 967

The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.

Roe, B. A., Ma, D. P., Wilson, R. K., & Wong, J. F. (1985) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)39303-1 · Cited by 733

Comparative Anatomy of 16-S-like Ribosomal RNA

Gutell, R. R., Weiser, B., Woese, C. R., & Noller, H. F. (1985) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(08)60348-7 · Cited by 668

Transfer RNA: Molecular Structure, Sequence, and Properties

Rich, A., & RajBhandary, U. L. (1976) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.45.070176.004105 · Cited by 650

The Absence of a Pyrimidine Dimer Repair Mechanism in Mammalian Mitochondria

Clayton, D. A., Doda, J. N., & Friedberg, E. C. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.7.2777 · Cited by 530

The complete nucleotide sequence of theRattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates

Gadaleta, G., Pepe, G., De Candia, G., Quagliariello, C., Sbisa, E., & Saccone, C. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02602930 · Cited by 518

Rates of mitochondrial DNA evolution in sharks are slow compared with mammals

Martin, A. P., Naylor, G. J. P., & Palumbi, S. R. (1992) · Nature · doi:10.1038/357153a0 · Cited by 513

GENE TREES AND ORGANISMAL HISTORIES: A PHYLOGENETIC APPROACH TO POPULATION BIOLOGY

Avise, J. C. (1989) · Evolution · doi:10.1111/j.1558-5646.1989.tb02568.x · Cited by 481

HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS

Aquadro, C. F., & Greenberg, B. D. (1983) · Genetics · doi:10.1093/genetics/103.2.287 · Cited by 442

Nucleotide sequence and gene organization of sea urchin mitochondrial DNA

Jacobs, H. T., Elliott, D. J., Math, V. B., & Farquharson, A. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90452-4 · Cited by 326

Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms.

Wolstenholme, D. R., Macfarlane, J. L., Okimoto, R., Clary, D. O., & Wahleithner, J. A. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.5.1324 · Cited by 269

Ribosomal RNA In Vertebrates: Evolution And Phylogenetic Applications

Mindell, D. (1990) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.21.1.541 · Cited by 234

Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish

Meyer, A., & Wilson, A. C. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02106050 · Cited by 211

The Complete Nucleotide Sequence, Gene Organization, and Genetic Code of the Mitochondrial Genome of Paracentrotus lividus

Cantatore, P., Roberti, M., Rainaldi, G., Gadaleta, M. N., & Saccone, C. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)60413-2 · Cited by 208

Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes

Cantatore, P., Gadaleta, M. N., Roberti, M., Saccone, C., & Wilson, A. C. (1987) · Nature · doi:10.1038/329853a0 · Cited by 198

The evolutionary relationships among known life forms

Cedergren, R., Gray, M. W., Abel, Y., & Sankoff, D. (1988) · Journal of Molecular Evolution · doi:10.1007/bf02143501 · Cited by 177

A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given.

(1989) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040577 · Cited by 174

Recognition of †RNAs by Aminoacyl-†RNA Synthetases

Schulman, L. H. (1991) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(08)60006-9 · Cited by 172

Variation in salmonid mitochondrial DNA: Evolutioinary constraints and mechanisms of substitution

Thomas, W. K., & Beckenbach, A. T. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100207 · Cited by 160

Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes

Miyata, T., Hayashida, H., Kikuno, R. F., Hasegawa, M., Kobayashi, M., & Koike, K. (1982) · Journal of Molecular Evolution · doi:10.1007/bf02100221 · Cited by 155

Rearrangements of mitochondrial transfer RNA genes in marsupials

Pääbo, S., Thomas, W. K., Whitfield, K., Kumazawa, Y., & Wilson, A. C. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02103134 · Cited by 149

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

Reeves, J. H. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00160257 · Cited by 147

Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes

Asakawa, S., Kumazawa, Y., Araki, T., Himeno, H., Miura, K., & Watanabe, K. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02102653 · Cited by 142

A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire ‘dihydrouridine’ loop and stem.

de Bruijn, M. H. L., & Klug, A. (1983) · The EMBO Journal · doi:10.1002/j.1460-2075.1983.tb01586.x · Cited by 139

Unusual genetic codes and a novel gene structure for tRNASer in starfish mitochondria! DNA

Hyouta, H., Masaki, H., Tatsushi, K., Ohta, T., Kumagai, I., Miura, K., & Watanabe, K. (1987) · Gene · doi:10.1016/0378-1119(87)90139-9 · Cited by 92

Role of the tertiary nucleotides in the interaction of yeast phenylalanine tRNA with its cognate synthetase

Sampson, J. R., DiRenzo, A. B., Behlen, L. S., & Uhlenbeck, O. C. (1990) · Biochemistry · doi:10.1021/bi00462a014 · Cited by 87

The Evolving Trna Molecul

Cedergren, R., Sankoff, D., Larue, B., Grosjean, H., & Söil, D. (1981) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238109108699 · Cited by 83

A novel cloverleaf structure found in mammalian mitochondrial tRNASer(UCN)

Yokogawa, T., Watanabe, Y., Kumazawa, Y., Ueda, T., Hirao, I., Miura, K., & Watanabe, K. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.22.6101 · Cited by 75

Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins

de Peer, Y. V., Neefs, J., & Wächter, R. D. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02101118 · Cited by 66

Conserved tRNA gene cluster in starfish mitochondrial DNA

Jacobs, H. T., Asakawa, S., Araki, T., Miura, K., Smith, M. J., & Watanabe, K. (1989) · Current Genetics · doi:10.1007/bf00435506 · Cited by 57

Purification and characterization of two serine isoacceptor tRNAs from bovine mitochondria by using a hybridization assay method

Yokogawa, T., Kumazawa, Y., Miura, K.-C., & Watanabe, K. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.7.2623 · Cited by 50

The aminoacylation of Structurally Variant Phenylalanine tRNAs from Mitochondria and Various Nonmitochondrial Sources by Bovine Mitochondrial Phenylalanyl-tRNA Synthetase

Kumazawa, Y., Yokogawa, T., Hasegawa, E., Miura, K., & Watanabe, K. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)51587-8 · Cited by 45

Interactions of bovine mitochondrial phenylalanyl-tRNA with ribosomes and elongation factors from mitochondria and bacteria

Kumazawa, Y., Schwartzbach, C. J., Liao, H., Mizumoto, K., Kaziro, Y., Miura, K., Watanabe, K., & Spremulli, L. L. (1991) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/0167-4781(91)90097-6 · Cited by 41

Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals.

Thomas, W. K., Maa, J.-S., & Wilson, A. C. C. (1989) · PubMed · Cited by 25

Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery

Hasegawa, M., Yano, T.-A., & Miyata, T. (1984) · Journal of Molecular Evolution · doi:10.1007/bf02101989 · Cited by 16

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences

Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J. G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., et al. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00332-9 · Cited by 758

Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome

Macey, J. R., Larson, A., Ananjeva, N. B., Fang, Z., & Papenfuss, T. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025706 · Cited by 656

Molecular Phylogenetics of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root of the Squamate Tree

Townsend, T. M., Larson, A., Louis, E., & Macey, J. R. (2004) · Systematic Biology · doi:10.1080/10635150490522340 · Cited by 458

Mitogenomic Exploration of Higher Teleostean Phylogenies: A Case Study for Moderate-Scale Evolutionary Genomics with 38 Newly Determined Complete Mitochondrial DNA Sequences

Miya, M., Kawaguchi, A., & Nishida, M. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003741 · Cited by 419

Organization of the Mitochondrial Genome of a Deep-Sea Fish, Gonostoma gracile (Teleostei: Stomiiformes): First Example of Transfer RNA Gene Rearrangements in Bony Fishes

Miya, M., & Nishida, M. (1999) · Marine Biotechnology · doi:10.1007/pl00011798 · Cited by 320