Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences

Using two sets of nucleotide sequences of the human and simian T-cellleukemia/lymphoma virus type I (HTLV-I/STLV-I), one consisting of 522 bp ofthe env gene from 70 viral strains and the other a 140-bp segment from thepol gene of 52 viral strains, I estimated cladograms based on a statisticalparsimony procedure that was developed specifically to estimatewithin-species gene trees. An extension of a nesting procedure is offeredfor sequence data that forms nested clades used in hypothesis testing. Thenested clades were used to test three hypotheses relating to transmissionof HTLV/STLV sequences: (1) Have cross-species transmissions occurred and,if so, how many? (2) In what direction have they occurred? (3) What are thegeographic relationships of these transmission events? The analyses supporta range of 11-16 cross-species transmissions throughout the history ofthese sequences. Additionally, outgroup weights were assigned to haplotypesusing arguments from coalescence theory to infer directionality oftransmission events. Conclusions on geographic origins of transmissionevents and particular viral strains are inconclusive due to small samplesand inadequate sampling design. Finally, this approach is compared directlyto results obtained from a traditional maximum parsimony approach and foundto be superior at establishing relationships and identifying instances oftransmission.