Phylogenetic (neighbor-joining trees) relationship among pairs of genes of A. aegypti (gene ID begins with AAEL; gene structural pattern shown as light color bars next to branches) and A. gambiae (gene ID begins with AGAP; gene structural pattern shown as dark color bars next to branches). The gene pairs in each case are paralogous to each other within species and at the same time they are orthologous to each other between the two species. They either retain positional overlapping structure in both the genomes (A) or show overlapping in one but non-overlapping in the other (B). The tree shown in (C) represents phylogenetic relationship of the host gene (AAEL014407) with paralogous copies in the A. aegypti genome which are either embedded (within AAEL014407) or non-embedded (located outside AAEL014407). The genes that are embedded are marked so within brackets. The scale for branch length is shown below each tree.