Multiple alignment of <i>DINE-1</i>copies in syntenic regions of <i>D. melanogaster</i> and <i>D. simulans/D. sechellia</i>.

<p>(<b>A</b>) Alignment of known and novel <i>DINE-1</i> copies with <i>D. melanogaster DINE-1</i> consensus sequence (DINEYang) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; consensus regions are designated according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; (<b>B</b>) Alignment of the <i>simINE_ben</i> and <i>DNAREP1_DM</i> consensus sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Kapitonov3" target="_blank">[36]</a>.</p

Recombination between the ancestor <i>CK2βtes</i>-<i>like</i> gene (GD15860 or GM17570) and <i>NACβtes</i> promoter region.

<p>Signature sequence of putative <i>CK2βtes</i>-like partner is designated in bold italics. The distances in nucleotides from the start of signature sequence and ORF start are indicated in brackets. Broken line shows the site of fusion of the <i>CK2βtes</i>-like and <i>NACβtes</i> sequences as a result of recombination. The tree represents the similarity of the nucleotide sequences in the selected box measured as the number of base differences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-S1" target="_blank">[42]</a> and was constructed using the UPGMA method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Sneath1" target="_blank">[43]</a>. The percentage of replicate trees in which the associated sequence clustered together in the bootstrap test (500 iterations) are shown next to the branches. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed.</p

Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.

<p>Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.</p