Phylogeny of HML endogenous elements. A Bayesian inference tree of the pol gene from prototypical members of HML 1-10 families (indicated by "REF") along with exogenous betaretroviruses MMTV, MPMV, and JSRV was generated to characterize proviruses identified through our BLAT search (black). Sequences were colored according to LTR5 subgroup and annotated with filled diamonds for type 1 proviruses and open diamonds for proviruses of undetermined type. Colored sequences without diamonds represent type 2 proviruses. Posterior probability values > 70 are shown for the tree rooted on the exogenous betaretrovirus sequences.