Domain insertions in the presence of gene loss. (a)Embedded trees showing the co-evolution of domains, genes, and species in the hypothetical family in Fig. 3. (b)An extended reconciled gene tree for the gene family. Inferred gene losses (ℓ
) and pseudonodes (open circles, ϕ
) representing the location of the missing taxa in the gene tree are shown in grey. The pseudonodes are used to distinguish between gene losses and domain losses in the reconciled domain tree. Gene duplication is represented as a black square; filled circles represent co-divergences. (c)A reconciled tree for the domain family, showing a domain insertion (arrow, edge (u, v)) and a domain loss (d2 g2 B). Domains that are missing due to gene loss (ℓ
) are shown in grey. Co-divergence due to gene duplication is represented by an open square.