Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Foraminifera have one of the best known fossil records among theunicellular eukaryotes. However, the origin and phylogenetic relationshipsof the extant foraminiferal lineages are poorly understood. To test thecurrent paleontological hypotheses on evolution of foraminifera, wesequenced about 1,000 base pairs from the 3' end of the small subunit rRNAgene (SSU rDNA) in 22 species representing all major taxonomic groups.Phylogenies were derived using neighbor- joining, maximum-parsimony, andmaximum-likelihood methods. All analyses confirm the monophyletic origin offoraminifera. Evolutionary relationships within foraminifera inferred fromrDNA sequences, however, depend on the method of tree building and on thechoice of analyzed sites. In particular, the position of planktonicforaminifera shows important variations. We have shown that these changesresult from the extremely high rate of rDNA evolution in this group. Bycomparing the number of substitutions with the divergence times inferredfrom the fossil record, we have estimated that the rate of rDNA evolutionin planktonic foraminifera is 50 to 100 times faster than in some benthicforaminifera. The use of the maximum-likelihood method and limitation ofanalyzed sites to the most conserved parts of the SSU rRNA molecule rendermolecular and paleontological data generally congruent.