Phylogenetic Analysis of <i>CG4715</i> Homologs

<div><p>(A) <i>CG4715</i> has been preserved in its syntenic location in <i>Drosophila</i> species. In species from the <i>takahashii/suzukii</i> species groups like <i>D. lutescens,</i> an additional paralog, <i>CG4715-B</i> (gray shading) is found in tandem orientation. <i>D. ananassae</i> has an additional transposon insertion in this syntenic location between <i>CG4715</i> and <i>CG4552,</i> while the genomes of <i>D. mojavensis</i> and <i>D. virilis</i> lack <i>CG4715</i> orthologs between <i>CG4577</i> and <i>CG4552</i>. For <i>D. ananassae</i> and <i>D. pseudoobscura,</i> sequence was obtained from genome sequencing data (indicated with an asterisk) and confirmed by sequencing.</p><p>(B) An “expected” phylogeny of <i>Drosophila</i> species is shown, summarizing results from many genes [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010044#pgen-0010044-b30" target="_blank">30</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010044#pgen-0010044-b31" target="_blank">31</a>].</p><p>(C) A neighbor-joining phylogeny of <i>CG4715</i> orthologs based on C-terminal amino acid sequence is presented. (For some species, only the C-terminal sequence was obtained (indicated by a “p” for partial)). This phylogeny is largely in agreement with the accepted species phylogeny in (B), indicating that the gene has been inherited by strict vertical inheritance. Although there is a slight discordance in phylogenetic placement of the <i>D. ananassae, D. eugracilis,</i> and <i>D. auraria,</i> these branches have only a low bootstrap support. A second lineage of <i>CG4715</i> paralogs, <i>CG4715-B</i> is evident (gray shading) in the <i>takahashii/suzukii</i> species groups.</p>