Evolution of Higher-Plant Chloroplast DNA-Encoded Genes: Implications for Structure-Function and Phylogenetic Studies

INTRODUCTION 392 THE NATURE OF NUCLEOTIDE SUBSTITUTIONS IN CHLOROPLAST DNA EVOLUTION 393 Estimating the Number of Nucleotide Substitutions for rbeL, atpBE, and rp12...... 394 IDENTIFICATION OF FUNCTIONALLY IMPORT ANT SEQUENCES USING THE EVOLUTIONARY FILTERING PROCEDURE 399 Promoters 399 Leaders . ........ ... ....... ...... ....... . .. ..... 402 Ribosome-Binding Sites 402 Protein-Coding Regions 404 Intervening Sequences .... ......... 407 Transcription Terminators ...... 409 ESTIMATING PHYLOGENETIC TOPOLOGIES FROM CHLOROPLASTDNA SEQUENCE DATA 411 Protein-Coding Regions ....... ..... ' 412 Noncoding Regions .. . ...... ... 413 CONCLUSIONS 414