| Summary: | <p>Abstract</p> <p>Background</p> <p>During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements <it>Bari</it> and <it>412</it> in the sequenced genomes of the <it>Drosophila melanogaster</it> group and in the sibling species <it>D. melanogaster</it> and <it>D. simulans</it> using traditional phylogenetic and network approaches.</p> <p>Results</p> <p>Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the <it>Bari</it> and <it>412</it> elements. The DNA transposon <it>Bari</it> within the <it>D. ananassae</it> genome is more closely related to the element of the <it>melanogaster</it> complex than to the sequence in <it>D. erecta</it>, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the <it>Bari</it> and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving <it>D. melanogaster</it>, <it>D. simulans</it> and <it>D. sechellia</it>. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between <it>D. melanogaster</it> and <it>D. simulans</it>. The divergence values of the elements between these species support this conclusion.</p> <p>Conclusions</p> <p>We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the <it>Bari</it> and <it>412</it> elements in the <it>melanogaster</it> group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of <it>D. melanogaster</it> and <it>D. simulans</it>.</p>
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