Molecular evolution and codon bias of chloroplast DNA

Molecular evolutionary dynamics of chloroplast DNA are examined in two parts. The first in an investigation of the evolution of a noncoding segment in the grass family (Poaceae) regarding the mechanisms of change and the potential role of noncoding DNA in determining phylogenetic relationships. In addition, substitutional dynamics of noncoding sequence and four-fold degenerate sites of rbcL are determined in light of the phylogeny generated by analysis of rbcL. It is shown that in the absence of selection, substitutional dynamics are different in regions with different A+T content. The second part is an examination of the codon bias of chloroplast genes of plants and green algae. Two major patterns of codon use are shown to exist, one is proposed to be the result of selection for translation efficiency the second a result of a substitutional bias. All plant chloroplast genes follow the second pattern with the exception of psbA. The possible role of selection is examined in other chloroplast genes of Marchantia polymorpha and Nicotiana tabacum by estimating codon adaptation based on psbA codon use. Evidence is presented that selection may affect codon use in M. polymorpha. Selection on angiosperm psbA genes is then examined more closely by inferring the ancestral psbA gene and investigating the evolution of codon use. The data are consistent with the absence of selection indicating that the psbA codon use of angiosperms is an historical artifact.