PHYLOGENETIC ANALYSES OF 55 RETROELEMENTS ON THE BASIS OF THE NUCLEOTIDE AND PRODUCT AMINO-ACID-SEQUENCES OF THE POL GENE

Comparisons of pol gene nucleotide and reverse transcriptase (RT) amin o acid sequences of 47 retroviruses, 3 caulimoviruses, and 5 hepadnavi ruses showed that approximately one-third of the gene at the 5' end is much more conserved than other pol regions. The most conserved region s on both the nucleotide and amino acid sequences were chosen for cons truction of phylogenetic trees. The maximum-parsimony and distance-mat rix methods were used for analyses of aligned amino acid sequences; th ese two methods, and the compatibility method, were used to analyze th e aligned nucleotide sequences. Essentially identical majority-rule co nsensus trees were produced by these different methods from both the p ol gene nucleotide and RT amino acid sequences, which divided the 55 r etroelements into six major groups. The reliability of the phylogeneti c trees was probed with the bootstrapping of 100 replicates of the ori ginal sequence alignments. The grouping results were shown to be stati stically significant by multiple comparisons with the least-significan t-difference procedure.