Final answer:
LTR-retrotransposons share common features with retroviruses, such as flanking long terminal repeats and similar gene products necessary for reverse transcription and integration, supporting their common ancestry and suggesting that retroviruses evolved from retrotransposon lineages.
Step-by-step explanation:
The gene homologies found in LTR-retrotransposons that are shared with retroviruses include the presence of flanking long terminal repeats, an integration domain, and enzymes such as reverse transcriptase, integrase, protease, and structural proteins like Gag. These common features support the hypothesis that retroviruses and LTR-retrotransposons share a common ancestry. By comparing DNA sequences, scientists can reconstruct phylogenetic trees that show how closely related certain retrotransposons are to retroviruses, suggesting that LTR-retrotransposons such as TY3 and the Gypsy ERVs evolved from a common ancestor with certain retroviruses like MMTV and HTLV. The evolutionary path suggests that retroviruses likely evolved from a retrotransposon lineage, as opposed to originating independently.