Evolutionary Analysis of Plant DNA Sequences

The comparative analysis of DNA sequence data reveals much about plant evolution. We have used maximum-likelihood algorithms, based on sequence comparisons for homologous chloroplast-encoded genes, to investigate plant phylogeny. These analyses show that the origin of three subclasses of dicots (represented by pea, spinach, and tobacco) occurred during approximately the same epoch in evolution. It is also possible to extend the phylogenetic analyses to green algae and cyanobacteria, such that virtually the entire spectrum of evolution in the plant kingdom is included. The analyses of chloroplast DNA sequences among higher plants are remarkably consistent, in that different coding and noncoding sequences yield the same phylogenies. This overall consistency is apparent despite different rates of evolution by codon position, differential rates of evolution for some branches of the phylogenetic topologies, and differences in model constraints. We conclude from these analyses that DNA sequence comparisons of chloroplast-encoded genes will be particularly useful in phylogenetic analyses of higher taxonomic categories. DNA sequence comparisons for two families of nuclear genes are also presented. The analysis of a family of transposable elements of maize (Ds1 family) yielded a star phylogeny for seven of the eight elements for which sequence data are available, and equal branch lengths were found among seven of the eight maize Ds1 sequences. The eighth element (Wₓ) diverged about twice as fast and was placed on the branch leading to two Tripsacum elements. These Tripsacum elements originated during a radiation of the Ds1 family, probably in the progenitor of maize and Tripsacum. Most of the maize elements appear to have evolved independently since the period of radiation, and the two Tripsacum elements have diverged much more recently. The pattern of sequence evolution exhibited by a multigene family with tandem repeats associated with knob heterochromatin is quite different from that of the Ds1 family. The repeating units of this multigene family evolve in a highly correlated fashion on account of concerted evolution. Comparisons among maize, teosinte, and Tripsacum suggest that the rate of gene exchange associated with concerted evolution is not rapid.