Table Of Content

Contents of Volume 42 (1996) No. 1, January 1996 R.R. Wagner, M.A. Riley Low Synonymous Site Variation at the JacY Locus in Escherichia coli Suggests the Action of Special Issue: SINEs, LINEs, and Retrotransposable Positive Selection 79 Elements A. Del Campillo Campbell, A. Campbell Introduction 1 Alternative Gene for Biotin Sulfoxide Reduction in Escherichia coliK-12 85 M.A. Batzer, P.L. Deininger, U. Hellmann-Blumberg, J. Jurka, D. Labuda, A. Jeltsch, A. Pingoud C.M. Rubin, C.W. Rubin, C.W. Schmid, Horizontal Gene Transfer Contributes to the Wide E. Zietkiewicz, E. Zuckerkandl Distribution and Evolution of Type II Restriction- Standardized Nomenclature for Alu Repeats 3 Modification Systems 91 D.H. Kass, J. Kim, P.L. Deininger P.L. Bollyky, A. Rambaut, P.H. Harvey, Sporadic Amplification of ID Elements in Rodents 7 E.C. Holmes Recombination Between Sequences of Hepatitis B T.H. Shaikh, P.L. Deininger Virus from Different Genotypes 97 The Role and Amplification of the HS Alu Subfamily Founder Gene 15 N. Takasaki, L. Park, M. Kaeriyama, A.J. Gharrett, N. Okada M.A. Batzer, S.S. Arcot, J.W. Phinney, Characterization of Species-Specifically Amplified M. Alegria-Hartman, D.H. Kass, S.M. Milligan, SINEs in Three Salmonid Species—Chum Salmon, C. Kimpton, P. Gill, M. Hochmeister, P.A. loannou, Pink Salmon, and Kokanee: The Local Environment R.J. Herrera, D.A. Boudreau, W.D. Scheer, of the Genome May Be Important for the Generation B.J.B. Keats, P.L. Deininger, M. Stoneking of a Dominant Source Gene at a Newly Genetic Variation of Recent Alu Insertions in Retroposed Locus 103 Human Populations 22 D.M. Milewicz, P.H. Byers, J. Reveille, I. Chesnokov, C.W. Schmid A.L. Hughes, M. Duvic Flanking Sequences of an Alu Source Stimulate A Dimorphic Alu Sb-Like Insertion in COL3A1 Is Transcription In Vitro by Interacting with Ethnic-Specific 117 Sequence-Specific Transcription Factors 30 Z.-H. Su, T. Ohama, T.S. Okada, K. Nakamura, C. Prades, A.-M. Laurent, J. Puechberty, Y. Yurov, R. Ishikawa, S. Osawa G. Roizes Phylogenetic Relationships and Evolution of the SINE and LINE Within Human Centromeres 37 Japanese Carabinae Ground Beetles Based on Mitochondrial ND5 Gene Sequences 124 R.N. Lee, J.C. Jaskula, R.A. Van Den Bussche, R.J. Baker, H.A. Wichman Z.-H. Su, T. Ohama, T.S. Okada, K. Nakamura, Retrotransposon Mys Was Active During Evolution of R. Ishikawa, S. Osawa the Peromyscus leucopus-maniculatus Complex 44 Geography-Linked Phylogeny of the Damaster Ground Beetles Inferred from Mitochondrial ND5 J.E. Clough, J.A. Foster, M. Barnett, Gene Sequences 130 H.A. Wichman Computer Simulation of Transposable Element C. Ledje, U. Arnason Evolution: Random Template and Strict Phylogenetic Analyses of Complete Cytochrome b Master Models 52 Genes of the Order Carnivora with Particular Emphasis on the Caniformia 135 V. Kapitonov, J. Jurka The Age of Alu Subfamilies 59 U. Arnason, X. Xu, A. Gullberg Comparison Between the Complete E. Zietkiewicz, D. Labuda Mitochondrial DNA Sequences of Homo and the Mosaic Evolution of Rodent B1 Elements 66 Common Chimpanzee Based on Nonchimeric Sequences 145 A. Janke, N.J. Gemmell, G. Feldmaier-Fuchs, A. Von Haeseler, S. Paabo The Mitochondrial Genome of a Monotreme—The No. 2, February 1996 Platypus (Ornithorhynchus anatinus) 153 A. Eyre-Walker J.A. Terrett, S. Miles, R.H. Thomas The Close Proximity of Escherichia coli Genes: Complete DNA Sequence of the Mitochondrial Consequences for Stop Codon and Synonymous Genome of Cepaea nemoralis (Gastropoda: Codon Use 73 Pulmonata) 160 G. Orti, P. Petry, J.I.R. Porto, M. Jégu, A. Meyer J. Sullivan, K.E. Holsinger, C. Simon Patterns of Nucleotide Change in Mitochondrial The Effect of Topology on Estimates of Among-Site Ribosomal RNA Genes and the Phylogeny Rate Variation 308 of Piranhas 169 J.M. Koshi, R.A. Goldstein S. Kumar, A. Rzhetsky Probabilistic Reconstruction of Ancestral Evolutionary Relationships of Eukaryotic Protein Sequences 313 Kingdoms 183 Letter to the Editor B. Nelissen, R. De Baere, A. Wilmotte, T.H. Jukes, S. Osawa R. De Wachter CUG Codons in Candidaspp. 321 Phylogenetic Relationships of Nonaxenic Filamentous Cyanobacterial Strains Based on 16S rRNA Sequence Analysis 194 Y. Van De Peer, G. Van Der Auwera, R. De Wachter No. 3, March 1996 The Evolution of Stramenopiles and Alveolates as Derived by “Substitution Rate Calibration” of Small Ribosomal Subunit RNA 201 D. Proudhon, J. Wei, J.-F. Briat, E.C. Theil Ferritin Gene Organization: Differences Between G.B. Nunn, B.F. Theisen, B. Christensen, Plants and Animals Suggest Possible P. Arctander Kingdom-Specific Selective Constraints 325 Simplicity-Correlated Size Growth of the Nuclear 28S Ribosomal RNA D3 Expansion Segment in the W.S. Modi, D.S. Gallagher, J.E. Womack Crustacean Order lsopoda 211 Evolutionary Histories of Highly Repeated DNA Families Among the Artiodactyla (Mammalia) 337 G. Thode, J.A. Garcia-Ranea, J. Jimenez Search for Ancient Patterns in Protein Sequences 224 . Ugarkovic, S. Durajlija, M. Plohl Evolution of Tribolium madens (Insecta, Coleoptera) Satellite DNA Through DNA Inversion and C.A. Ouzounis, N.C. Kyrpides Insertion 350 Parallel Origins of the Nucleosome Core and Eukaryotic Transcription from Archaea 234 P. Capy, R. Vitalis, T. Langin, D. Higuet, C. Bazin Relationships Between Transposable Elements C. Rocchini, R.M. Marx, J. Schnorr Von Carosfeld, Based Upon the Integrase-Transposase Domains: Is H.E. Kasinsky, E. Rosenberg, F. Sommer, J. Ausio There a Common Ancestor? 359 Replacement of Nucleosomal Histones by Histone H1-Like Proteins During Spermiogenesis in Cnidaria: Evolutionary Implications 240 M.D. Moltd, N. Paricio, M.A. Lépez-Preciado, V.F. Semeshin, M.J. Martinez-Sebastian A.L. Hughes Tirant: A New Retrotransposon-Like Element in Evolution of the src-Related Protein Tyrosine Drosophila melanogaster 369 Kinases 247 T. Kamaishi, T. Hashimoto, Y. Nakamura, F. Nakamura, S. Murata, N. Okada, K.-I. Okamoto, M. Shimizu, M. Hasegawa Protein Phylogeny of Translation Elongation Factor No. 4, April 1996 EF-1a Suggests Microsporidians Are Extremely Ancient Eukaryotes 257 T.H. Jukes On the Prevalence of Certain Codons (“RNY”) in K.D. Mehta, R. Chang, J. Norman Genes for Proicins 377 Chiloscyllium plagiosum Low-Density Lipoprotein Receptor: Evolutionary Conservation of Five Different Functional Domains 264 E.M. Denovan-Wright, D. Sankoff, D.F. Spencer, R.W. Lee Evolution of Fragmented Mitochondrial Ribosomal P.A. McLenachan, P.J. Lockhart, H.R. Faber, RNA Genes in Chlamydomonas 382 B.C. Mansfield Evolutionary Analysis of the Multigene Pregnancy-Specific 8,-Glycoprotein Family: E. Rosato, A.A. Peixoto, A. Gallippi, Separation of Historical and Nonhistorical C.P. Kyriacou, R. Costa Signals 273 Mutational Mechanisms, Phylogeny, and Evolution of a Repetitive Region Within a Clock Gene of J.H. Parish, J. Bentley Drosophila melanogaster 392 Relationships Between Bacterial Drug Resistance Pumps and Other Transport Proteins 281 H. Hachler, S.P. Cohen, S.B. Levy Untranslated Sequence Upstream of MarA in the Z. Yang Multiple Antibiotic Resistance Locus of Escherichia Phylogenetic Analysis Using Parsimony and coli |s Related to the Effector-Binding Domain of the Likelihood Methods 294 XylS Transcriptional Activator 409 D. Rouhbakhsh, C.-Y. Lai, C.D. von Dohlen, S.G.E. Andersson, P.M. Sharp M.A. Clark, L. Baumann, P. Baumann, N.A. Moran, Codon Usage and Base Composition in D.J. Voegtlin Rickettsia prowazekii 525 The Tryptophan Biosynthetic Pathway of Aphid Endosymbionts (Buchnera): Genetics and Evolution C. Buades, A. Moya of Plasmid-Associated Anthranilate Synthase (trpEG) Phylogenetic Analysis of the Isopenicillin-N- Within the Aphididae 414 Synthetase Horizontal Gene Transfer 537 M. Sahrawy, V. Hecht, J. Lopez-Jaramillo, A. Chueca, Y. Chartier, Y. Meyer A. Van Wormhoudt, D. Sellos Intron Position as an Evolutionary Marker of Cloning and Sequencing Analysis of Three Amyase Thioredoxins and Thioredoxin Domains 422 cDNAs in the Shrimp Penaeus vannamei (Crustaceia decapoda): Evolutionary Aspects 543 J. Zhou, A. Kleinhofs Molecular Evolution of Nitrate Reductase L.Y. Mackey, B. Winnepenninckx, R. De Wachter, Genes 432 T. Bakeljau, P. Emcshermann, J.R. Garey 18S rRNA Suggests That Entoprocta Are C. Vieira, C. Biémont Protosomes, Unrelated to Ectoprocta 552 Geographical Variation in Insertion Site Number of Retrotransposon 412 in Drosophila simulans 443 B. Prakash, S. Selvaraj, M.R.N. Murthy, Y.N. Sreerama, D.R. Rao, L.R. Gowda Analysis of the Amino Acid Sequences of Plan S. Niewiesk, C.R.M. Bangham Evolution in a Chronic RNA Virus Infection: Selection Bowman-Birk Inhibitors 560 on HTLV-I Tax Protein Differs Between Healthy Carriers and Patients with Tropical Spastic L. Guan, J.G. Scandalios Paraparesis 452 Molecular Evolution of Maize Catalases and Their Relationship to Other Eukaryotic and Prokaryotic Catalases 570 J. Adachi, M. Hasegawa Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA 459 G.-J. Caspers, G.-J. Reinders, J.A.M. Leunissen, J. Wattel, W.W. De Jong Protein Sequences Indicate That Turtles Branched Letters to the Editor Off from the Amniote Tree After Mammals 580 J.E. Mayfield, M.R. Duvall Anomalous Phylogenies Based on Bacterial Catalase Gene Sequences 469 Z. Yang Maximum-Likelihood Models for Combined Analysis of Multiple Sequence Data 587 G. Lucotte, S. Hazout Y-Chromosome DNA Haplotypes in Basques 472 Letter to the Editor D.W. Schultz, M. Yarus L.S. Jermiin, P.G. Foster, D. Graur, R.M. Lowe, On Malleability in the Genetic Code 597 R.H. Crozier Unbiased Estimation of Symmetrical Directional ISME Membership Listing 603 Mutation Pressure from Protein-Coding DNA 476 No. 6, June 1996 No. 5, May 1996 R.P. Ambler Random Walking 481 The Distance Between Bacterial Species in Sequence Space 617 J.F. Allen, J.A. Raven Free-Radical-Induced Mutation vs Redox Regulation: K.E.M. Hastings Costs and Benefits of Genes in Organelles 482 Strong Evolutionary Conservation of Broadly Expressed Protein Isoforms in the Troponin | Gene M. Beljanski Family and Other Vertebrate Gene Families 631 De Novo Synthesis of DNA-Like Molecules by Polynucleotide Phosphorylase In Vitro 493 A.M. Jellie, W.P. Tate, C.N.A. Trotman Evolutionary History of Introns in a Multidomain Globin Gene 641 M.C. Field, J.C. Boothroyd Sequence Divergence in a Family of Variant Surface Glycoprotein Genes from Trypanosomes: Coding Y. Satta, W.E. Mayer, J. Klein Region Hypervariability and Downstream Evolutionary Relationship of HLA-DRB Genes Recombinogenic Repeats 500 Inferred from Intron Sequences 648 J. DoskoGil C.M. Westhoff, D.E. Wylie The Amplification of Oligonucleotide Themes in the Investigation of the RH Locus in Gorillas Evolution of the myc Protooncogene Family 512 and Chimpanzees 658 F. Brunet, F. Godin, C. Bazin, J.R. David, P. Capy S. Evers, B. Casadewall, M. Charles, The mariner Transposable Element in Natural S. Dutka-Malen, M. Galimand, P. Courvalin Populations of Drosophila teissieri 669 Evolution of Structure and Substrate Specificity in b-Alanine:p-Alanine Ligases and Related J.R. Kornegay Enzymes 706 Molecular Genetics and Evolution of Stomach and Nonstomach Lysozymes in the Hoatzin 676 T. Burmester, K. Scheller Common Origin of Arthropod Tyrosinase, Arthropod R.C. Cronn, X. Zhao, A.H. Paterson, J.F. Wendel Hemocyanin, Insect Hexamerin, and Dipteran Polymorphism and Concerted Evolution in a Arylphorin Receptor 713 Tandemly Repeated Gene Family: 5S Ribosomal DNA in Diploid and Allopolyploid Cottons 685 Index to Volume 42 729