Evolution of the cytochromeb gene of mammals

Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457–465

Anderson S, de Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol 156: 683–717

Aquadro CF, Greenberg BD (1983) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103: 287–312

Beintema JJ, Schüller C, Irie M, Carsana A (1988) Molecular evolution of the ribonuclease superfamily. Prog Biophys Mol Biol 51: 165–192

Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26: 167–180

Brown WM (1985) The mitochondrial genome of animals. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum, New York, pp 95–130

Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18: 225–239

Carroll RL (1988) Vertebrate paleontology and evolution. WH Freeman, New York

Carlson SS, Wilson AC, Maxson RD (1978) Do albumin clocks run on time? Science 200: 1183–1185

Czelusniak J, Goodman M, Moncrief ND, Kehoe SM (1990) Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences. Methods Enzymol 183: 601–615

de Jong WW (1985) Superordinal affinities of rodentia studied by sequence analysis of eye lens proteins. In: Luckett WP, Hartenberger J-L (eds) Evolutionary relationships among rodents. A multidisciplinary analysis. Plenum, New York, pp 211–226

di Rago J-P, Netter P, Slonimski PP (1990) Pseudo-wild type revertants from inactive apocytochromeb mutants as a tool for the analysis of the structure/function relationships of the mitochondrial ubiquinol-cytochromec reductase ofSaccharomyces cerevisiae. J Biol Chem 265: 3332–3339

Easteal S (1990) The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics 124: 165–173

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791

Fukuda M, Wakasugi S, Tsuzuki T, Nomiyama H, Shimada K, Miyata T (1985) Mitochondrial DNA-like sequences in the human nuclear genome. Characterization and implications in the evolution of mitochondrial DNA. J Mol Biol 186: 257–266

Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisà E, Saccone C (1989) The complete nucleotide sequence of theRattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol 28: 497–516

Gyllensten UB, Erlich HA (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of theHLA-DQA locus. Proc Natl Acad Sci USA 85: 7652–7656

Harrison RG (1989) Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol & Evol 4: 6–11

Hatefi Y (1985) The mitochondrial electron transport and oxidative phosphorylation system. Annu Rev Biochem 54: 1015–1069

Hayasaka K, Gojobori T, Horai S (1988) Molecular phylogeny and evolution of primate mitochondrial DNA. Mol Biol Evol 5: 626–644

Holmquist R, Goodman M, Conroy T, Czelusniak J (1983) The spatial distribution of fixed mutations within genes coding for proteins. J Mol Evol 19: 437–448

Howell N (1989) Evolutionary conservation of protein regions in the proton-motive cytochromeb and their possible roles in redox catalysis. J Mol Evol 29: 157–169

Howell N, Gilbert K (1988) Mutational analysis of the mouse mitochondrial cytochromeb gene. J Mol Biol 203: 607–618

Irwin DM, Wilson AC (1989) Multiple cDNA sequences and the evolution of bovine stomach lysozyme. J Biol Chem 264: 11387–11393

Irwin DM, Wilson AC (1990) Concerted evolution of ruminant stomach lysozymes. Characterization of lysozyme cDNA clones from sheep and deer. J Biol Chem 265: 4944–4952

Irwin DM, Wilson AC (1991) Limitations of molecular methods for establishing the phylogeny of mammals, with special reference to the position of elephants. In: Szalay FS, Novacek MJ, McKenna MC (eds) American Museum of Natural History symposium on mammalian phylogeny. Princeton University Press, Princeton NJ (in press)

Irwin DM, Sidow A, White RT, Wilson AC (1989) Multiple genes for ruminant lysozymes. In: Smith-Gill SJ, Sercarz EE (eds) The immune response to structurally defined proteins: the lysozyme model. Adenine Press, Schenectady NY, pp 73–85

Janis CM (1988) New ideas in ungulate phylogeny and evolution. Trends Ecol & Evol 3: 291–297

Jollès J, Jollès P, Bowman BH, Prager EM, Stewart C-B, Wilson AC (1989) Episodic evolution in the stomach lysozymes of ruminants. J Mol Evol 28: 528–535

Jollès J, Prager EM, Alnemri ES, Jollès P, Ibrahimi IM, Wilson AC (1990) Amino acid sequences of stomach and nonstomach lysozymes of ruminants. J Mol Evol 30: 370–382

Kamimura N, Ishii S, Liandong M, Shay JW (1989) Three separate mitochondrial DNA sequences are contiguous in human genomic DNA. J Mol Biol 210: 703–707

Keohavong P, Thilly WG (1989) Fidelity of DNA polymerases in DNA amplification. Proc Natl Acad Sci USA 86: 9253–9257

Kocher TD, White TJ (1989) Evolutionary analysis via PCR. In: Erlich HA (ed) PCR technology. Principles and applications for DNA amplification. Stockton Press, New York, pp 137–147

Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in mammals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86: 6196–6200

Koop BF, Goodman M (1988) Evolutionary and developmental aspects of two hemoglobin β-chain genes (∈M and βM) of opossum. Proc Natl Acad Sci USA 85: 3893–3897

Larson A, Wilson AC (1989) Patterns of ribosomal RNA evolution in salamanders. Mol Biol Evol 6: 131–154

Li W-H, Luo C-C, Wu C-I (1985) Evolution of DNA sequences. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum, New York, pp 1–94

Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor NY

Messing J (1983) New M13 vectors for cloning. Methods Enzymol 101: 20–78

Meyer A, Wilson AC (1990) Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J Mol Evol 31: 359–364

Miyamoto MM, Boyle SM (1989) The potential importance of mitochondrial DNA sequence data to eutherian mammal phylogeny. In: Fernholm B, Bremer K, Jörnvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 437–450

Mross GA, Doolittle RF (1967) Amino acid sequence studies on artiodactyl fibrinopeptides. II. Vicuna, elk, muntjak, pronghorn antelope, and water buffalo. Arch Biochem Biophys 122: 674–684

Nomiyama H, Fukuda M, Wakasugi S, Tsuzuki T, Shimada K (1985) Molecular structures of mitochondrial-DNA-like sequences in human nuclear DNA. Nucleic Acids Res 13: 1649–1658

Novacek MJ (1989) Higher mammal phylogeny: the morphological-molecular synthesis. In: Fernholm B, Bremer K, Jörnvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 421–435

Pääbo S, Wilson AC (1988) Polymerase chain reaction reveals cloning artefacts. Nature 334: 387–388

Prager EM, Wilson AC (1988) Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J Mol Evol 27: 326–335

Saccone C, Attimonelli M, Lanave C, Gallerani R, Pesole G (1987) The evolution of mitochondrially coded cytochrome genes: a quantitative estimate. In: Papa S, Chance B, Ernster L (eds) Cytochrome systems. Plenum, New York, pp 103–109

Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425

Sarich VM (1985) Rodent macromolecular systematics. In: Luckett WP, Hartenberger J-L (eds) Evolutionary relationships among rodents. A multidisciplinary analysis. Plenum, New York, pp 423–452

Savage DE, Russell DE (1983) Mammalian paleofaunas of the world. Addison-Wesley, Reading MA

Shoshani J (1986) Mammalian phylogeny: comparison of morphological and molecular results. Mol Biol Evol 3: 222–242

Sidow A, Wilson AC (1990) Compositional statistics: an improvement of evolutionary parsimony and its application to deep branches in the tree of life. J Mol Evol 31: 51–68

Simon C, Pääbo S, Kocher TD, Wilson AC (1990) Evolution of mitochondrial ribosomal RNA in insects as shown by the polymerase chain reaction. In: Clegg M, Clark S (eds) Molecular evolution. UCLA symposia on molecular and cellular biology, new series, vol 122. Alan R Liss, New York, pp 235–244

Simpson GG (1945) The principles of classification and a classification of mammals. Bull Am Mus Nat Hist 85: 1–350

Southern SO, Southern PJ, Dizon AE (1988) Molecular characterization of a cloned dolphin mitochondrial genome. J Mol Evol 28: 32–42

Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85: 2653–2657

Swofford DL (1989) PAUP: phylogenetic analysis using parsimony, version 3.0b. Illinois Natural History Survey, Champaign IL

Thomas WK, Beckenbach AT (1989) Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution. J Mol Evol 29: 233–245

Thomas WK, Maa J, Wilson AC (1989) Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals. New Biologist 1: 93–100

Tindall KR, Kunkel TA (1988) Fidelity of DNA synthesis by theThermus aquaticus DNA polymerase. Biochemistry 27: 6008–6013

Uzzell T, Corbin KW (1971) Fitting discrete probability distributions to evolutionary events. Science 172: 1089–1096

Watanabe T, Hayashi Y, Semba R, Ogasawara N (1985) Bovine mitochondrial DNA polymorphism in restriction endonuclease cleavage patterns and the location of the polymorphic sites. Biochem Genet 23: 947–957

Watanabe T, Masangkay JS, Wakana S, Saitou N, Tomita T (1989) Mitochondrial DNA polymorphism in native Philippine cattle based on restriction endonuclease cleavage patterns. Biochem Genet 27: 431–438

White TJ, Arnheim N, Erlich HA (1989) The polymerase chain reaction. Trends Genet 5: 185–189

Wilson AC, Cann RL, Carr SM, George M, Gyllensten UB, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26: 375–400

Wilson AC, Zimmer EA, Prager EM, Kocher TD (1989) Restriction mapping in the molecular systematics of mammals: a retrospective salute. In: Fernholm B, Bremer K, Jörnvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 407–419