Figure 1. Distribution of OR genes on human chromosomes. (a) Vertical bars above and below the chromosomes represent locations of functional OR genes and OR pseudogenes, respectively. The height of each bar indicates the number of OR genes present in a nonoverlapping 500-kb window. (b) Distribution of OR genes in a 0.6-Mb region indicated by an arrow in (a) on chromosome 3. ‘’ represents a pseudogene. (c) Neighbour-joining phylogenetic tree for the genes contained in a genomic cluster shown in (b). Each gene is indicated by a number in (b). A scale bar shows the number of amino acid substitutions per site. Modified from Niimura and Nei (2003). Copyright (2003) National Academy of Sciences, U.S.A.

Figure 2. Relationships between genomic clusters and phylogenetic clades. (a) Neighbour-joining phylogenetic tree for all functional OR genes in humans. These genes are classified into Class I and Class II genes, and Class II genes are further classified into clades A–S. Several genes remain unclassified. (b) Arrangement of OR genes in three genomic clusters, which are located on chromosomes 1, 11 and 14. Vertical bars above and below the horizontal line indicate OR genes in opposite transcriptional orientations. Alphabets indicate the phylogenetic clades defined in (a). ‘X’ represents an unclassified gene. A pseudogene is shown by a shorter bar. Modified from Niimura and Nei (2003). Copyright (2003) National Academy of Sciences, U.S.A.

Figure 3. Phylogenetic tree of primates. Catarrhines and the howler monkey (shown in blue) have full trichromatic vision and show high fractions of OR pseudogenes. A triangle indicates a branch in which the duplication of red/green opsin genes and deterioration of OR genes occurred. A blue opsin gene is not shown.

Figure 4. Evolutionary dynamics of OR genes in mammals (a) and in vertebrates (b). (a) The numbers in rectangles are those of functional OR genes in the extant species or in the ancestral species. The numbers with plus and minus signs indicate those of gene gains and losses, respectively, along each branch. Modified from Niimura and Nei (2007). (b) The MRCA between jawed and jawless vertebrates and that between fishes and tetrapods were estimated to have had at least two and nine functional OR genes. The size of a coloured circle or triangle at the bottom represents the number of genes originated from each ancestral gene in the MRCA between fishes and tetrapods. MYA, million years ago. Modified from Niimura and Nei (2005). Copyright (2005) National Academy of Sciences, U.S.A.