Figure 1. Detection of ‘elusive’ genes.

(a) Pipeline of ortholog group clustering and gene loss detection. (b) Definition of an elusive gene schematized with ortholog presence/absence pattern referring to a taxonomic hierarchy. Red and orange crosses denote the gene loss in the common ancestor of a taxon and the loss specific to a single species, respectively. (c) A representative phylogeny of the elusive gene encoding Chitinase 3-like 2 (CHI3L2). Taxa shown in the tree were used to investigate the presence or absence of orthologs. The Sciuromorpha, Hystricognathi, Eulipotyphla, Carnivora, and Chiroptera are absent from the tree, indicating that the CHI3L2 orthologs were lost somewhere along the branches framed in gray in the tree. In addition, the orthologs of many members of the Myomorpha were not found, suggesting that gene loss occurred in this lineage.