Approaches for detecting orthology and loss events: example of gene trees.

<p>Gene appearance detected by the phylogeny is depicted by the yellow star and the red circle represents gene duplication event. In bold is the gene used as input to build the tree. Based on the orthologous group from the Eth ancestor (blue frame) no lineage-specific loss is evidenced because each species has an ortholog to Mus. Based on the Ctr ancestor orthologous group, there are two orthologous groups, but only one group has an lineage-specific loss (red frame). Note that all abbreviations concerning species name and their ancestors are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038792#pone-0038792-g006" target="_blank">Figure 6</a>.