Phylogenetic relationships and unusual diversity in histone H4 proteins within the Tetrahymena pyriformis complex

The 29 species of the Tetrahymena pyriformis complex are morphologically identical while being quite diverse at the molecular level. These species are also diverse relative to other eukaryotes. Phylogenetic relationships within the complex have been difficult to determine, because there are groups of closely related species, as well as individual species, that are highly divergent. We have sequenced portions of two highly conserved histone genes and the more rapidly evolving intergenic region between them. These sequences have been used to construct a phylogeny for the complex. A comparison of the amino-terminal portion of the histone H4 proteins from the species of the complex reveals a high degree of sequence diversity relative to that of other organisms. In contrast, the amino-terminal portions of the histone H3 proteins of the species in the complex are identical to each other. We also find that the pattern of nucleotide substitution in the intergenic region differs from that described for higher eukaryotes.