EVOLUTION STUDIED USING PROTEIN STRUCTURE

One of the principle goals of evolutionary biology is to generate phylogeny that best represents the evolutionary histories of all organisms on earth. Aside from directly investigating the fossil records of ancestor species, all phylogenetic methods depend on the comparison of specific features (homologous characteristics) of contemporary organisms to determine the evolutionary relationships between different organisms. Among the features are morphological, physiological, genetic, and genomic which changed as the organisms evolved. The study of evolution changed dramaticallywith the discovery ofDNA and the evolutionaryfingerprint it represents. Evolutionary relationships betweenorganisms can be studied by comparing their DNA sequences (Zuckerkandl and Pauling, 1965). Gene mutation is the primary cause of evolution, so utilizing the universal carrier of genetic information as the characteristic by which phylogenetic comparison is made makes sense. This approach has significant advantages over the classical approach in which morphological and physiological characteristics are used. This is exemplified by the discovery of a third branch of life, the archaea, which have no substantial morphological or physiological differences to other prokaryotes. Archaeawere discovered to be a separate domain of life by analyzing small subunit ribosomal RNAs (SSU rRNA) (Woese and Fox, 1977). While studyingphylogenyusingDNAsequencedatahasprovenvery successful, it has its limitations. Since individual genes have different evolutionary rates in different lineages, phylogenies built from individual genes do not always agree (Doolittle, 1995a; Doolittle, 1995b).As a consequence, although efforts have beenmade to generate a universal tree of life (Woese,1998a;Woese,1998b;ForterreandPhilippe,1999),manypartsofthetreearestillunresolved and highly debated, especially at the root of the treewhere the three superkingdoms— archaea, bacteria, and eukaryotes—diverged (Mayr, 1998; Woese, 1998a; Woese, 1998b). Advances in large-scale sequencing technology enable the acquisition of the complete genome of an organism. There are currently hundreds of complete genomes available from