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rithms for phylogenetic inference when based on molecular data. In the interim, one must view molecular phylogenetic reconstructions as approximate, especially at very deep levels of evolution.
Comparative sequence analyses have utility beyond the study of phylogeny. The pattern of amino acid replacements observed over evolutionary time reflects the pattern of functional constraints that are evolutionary time reflects the pattern of functional constraints that are imposed by natural selection on the protein molecule. Natural selection is a sensitive filter because it is capable of detecting subtle changes associated with small fitness effects. Regions that do not accept change are clearly strongly constrained by functional requirements, but those regions that do accept change may be simply unconstrained, or in a few cases they may reflect responses to adaptive change. It is difficult to distinguish these latter two possibilities, but unusual patterns, such as the repeated replacement of Ala-103 by Cys, may be suggestive of adaptive change.
Comparative molecular sequence analyses also reveal aspects of the evolutionary process that would otherwise be opaque. For example, the recombinational processes that acted to convert Ψrpl23 to the functional gene are only resolvable at the sequence level. Similarly, the identification of labile sites for indel mutation, and more importantly, the identification of local sequence features that may promote indel mutation, depend on a substantial comparative sequence base. When viewed broadly, comparative sequence analyses reveal the rich variety of mutational mechanisms that subsume the processes of molecular evolution.
The chloroplast genome (cpDNA) of plants has been a focus of research in plant molecular evolution and systematics. Several features of this genome have facilitated molecular evolutionary analyses. First, the genome is small and constitutes an abundant component of cellular DNA. Second, the chloroplast genome has been extensively characterized at the molecular level providing the basic information to support comparative evolutionary research. And third, rates of nucleotide substitution are relatively slow and therefore provide the appropriate window of resolution to study plant phylogeny at deep levels of evolution. Despite a conservative rate of evolution and a relatively stable gene content, comparative molecular analyses reveal complex patterns of mutational change. Noncoding regions of cpDNA diverge through insertion/deletion changes that are sometimes site dependent. Coding genes exhibit different patterns of codon bias that appear to violate the equilibrium assumptions of some evolutionary models. Rates of molec-