| Announcements | | iii |
| Letter from the editor | BG Hall | 1 |
| The Cairo spiny mouse Acomys cahirinus shows a strong affinity to the Mongolian gerbil Meriones unguiculatus | SI Agulnik, LM Silver | 3 |
| Conflicting character distribution within different data sets on cardueline finches: artifact or history? | J Fehrer | 7 |
| Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes | C Krajewski, DG King | 21 |
| Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews | L Fumagalli, P Taberlet, L Favre, J Hausser | 31 |
| Gene transfer is a major factor in bacterial evolution | R Lan, PR Reeves | 47 |
| The divergence of major histocompatibility complex class I genes in Sciurus aberti | PJ Wettstein, M Strausbauch, SL Johnston, J States | 56 |
| Evolution of the diatoms (Bacillariophyta). II. Nuclear-encoded small- subunit rRNA sequence comparisons confirm a paraphyletic origin for the centric diatoms | LK Medlin, WH Kooistra, R Gersonde, U Wellbrock | 67 |
| First molecular evidence for the existence of a Tardigrada + Arthropoda clade | G Giribet, S Carranza, J Baguna, M Riutort, C Ribera | 76 |
| Variations in ribosomal DNA and mitochondrial DNA among chromosomal species of subterranean mole rats | H Suzuki, S Wakana, H Yonekawa, K Moriwaki, S Sakurai | 85 |
| A Hidden Markov Model approach to variation among sites in rate of evolution | J Felsenstein, GA Churchill | 93 |
| Estimating synonymous and nonsynonymous substitution rates | SV Muse | 105 |
| Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences | KA Crandall | 115 |
| Molecular phylogeny and genome evolution in the Drosophila virilis species group: duplications of the alcohol dehydrogenase gene | DI Nurminsky, EN Moriyama, ER Lozovskaya, DL Hartl | 132 |
| Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA | RE Hickson, C Simon, A Cooper, GS Spicer, J Sullivan | 150 |
| The root of the phylogenetic tree of human populations | M Nei, N Takezaki | 170 |
| Mitochondrial DNA phylogeny and the reconstruction of the population history of a species: the case of the European anchovy (Engraulis encrasicolus) | A Magoulas, N Tsimenides, E Zouros | 178 |
| Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila | ML Wayne, D Contamine, M Kreitman | 191 |
| Tempo and mode of synonymous substitutions in mitochondrial DNA of primates | J Adachi, M Hasegawa | 200 |
| Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes | M Lynch | 209 |
| Similar evolutionary patterning among repeated and single copy nematode mitochondrial genes | BC Hyman, JL Azevedo | 221 |
| Extensive gene rearrangements in the chloroplast DNAs of Chlamydomonas species featuring multiple dispersed repeats | E Boudreau, M Turmel | 233 |
| Intra-specific heterogeneity of the rDNA internal transcribed spacer in the Simulium damnosum (Diptera: Simuliidae) complex | J Tang, L Toe, C Back, TR Unnasch | 244 |
| Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence | JH McDonald | 253 |
| Intraspecific nuclear DNA variation in Drosophila | EN Moriyama, JR Powell | 261 |
| Codon usage and the origin of P elements | JR Powell, JM Gleason | 278 |
| Interspecific RNA in situ hybridization reveals perinuclear mastermind transcripts in drosophila virilis | AT Schmid, SJ Newfeld, B Yedvobnick | 280 |
| Reproducibility of ancient DNA sequences from extinct Pleistocene fauna | PG Taylor | 283 |
| Society for Molecular Biology and Evolution council meeting minutes | | 286 |
| Instructions to authors | | 289 |
