Color vision is the ability to distinguish light of different wavelengths. This property has arisen independently in vertebrates and invertebrates through duplications of the genes encoding ciliary opsins and rhabdomeric opsins, respectively . In the vertebrates, three types of cones displaying distinct wavelength properties were initially described by Ragnar Granit who received the Nobel Prize for these achievements in 1967. Later studies, including molecular cloning of the visual opsins in various vertebrates, have shown that four major color opsin subtypes existed in early vertebrates [2–4]. Thus, together with the dim-light (scotopic) receptor rhodopsin expressed in rods, the family of visual opsins encompassed five members in early vertebrates: RH1 (rhodopsin), RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin).
Subsequently, the gene repertoire has changed by gains and losses of opsin genes in the different vertebrate lineages. For instance, the ancestor of placental mammals lost RH2 and SWS2 and extant mammals use SWS1 for vision in the blue part of the spectrum. Primates have a duplicate of LWS that has mutated to have its absorption maximum in green, namely OPN1MW. The platypus has retained SWS2 but lost SWS1. Other losses have occurred in frogs (RH2), in the coelacanth Latimeria chalumnae, and in cartilaginous fishes. In teleost fishes, on the other hand, many additional duplicates have arisen .
Phylogenetic analyses of the five visual opsin sequences in chicken showed that the rhodopsin sequence RH1 was most closely related to the green opsin RH2, suggesting that this gene duplication was the most recent and that the four color opsins existed before rhodopsin . Thus, it appeared that color vision was ancestral to the dim-light vision and the appearance of rhodopsin and rod photoreceptors facilitated the adaptation to nocturnal environments. As a rhodopsin sequence had already been described in a lamprey, this implied that all five opsins existed before the divergence of lampreys and gnathostomes, i.e., jawed vertebrates. Subsequently, also the four color opsins have been described in pouched lamprey (Geotria australis) .
Although the visual opsin gene duplications must have taken place before the lamprey-gnathostome divergence, it has remained unclear how they happened. We and others have previously reported that numerous gene families expanded in the two genome doublings, i.e. tetraploidizations, that took place before the radiation of gnathostomes [8–11] usually called 2R for two rounds of genome doubling. The two tetraploidizations resulted in a large number of quartets of related chromosome regions, and each such quartet is called a paralogon. Subsequently, a third tetraploidization, 3R, took place in the lineage leading to teleost fishes . By investigating gene families sharing chromosome regions, we have been able to deduce the evolution of multiple neuronal and endocrine gene families as well as their neighbors, namely the opioid peptides  and receptors , neuropeptide Y-family peptides  and receptors [16, 17], voltage-gated sodium channels and their neighboring TGF-β receptors , the IGFBP family , the paralemmin family  and, more recently, the three transducin subunit gene families activated by visual opsins . All of these families received additional members in 2R and all but one expanded further in 3R. Chromosomal positions thereby constitute a useful additional type of information for analyses of gene families, especially families that display different evolutionary rates among members or over time, both of which seem to afflict the visual opsins.
We have previously performed sequence-based phylogenetic analyses of several gene families in the phototransduction cascade, and also investigated their chromosomal positions in the human genome [21–23]. These analyses suggested that most of the phototransduction gene families expanded in the basal vertebrate tetraploidizations, including the visual opsin family. In our first study, we proposed that RH1, SWS1 and LWS arose as a result of duplications of a large chromosome block . Because teleost fishes and birds have the LWS and SWS2 genes in close proximity on the same chromosome [24–26], we suggested a scenario where two adjacent visual opsin genes were quadrupled by chromosome duplications . However, the paralogon harboring the opsin genes seemed to have undergone major rearrangements and only a few adjacent gene families were identified, thereby making our conclusions uncertain. Interestingly, one of the neighboring gene families was the transducin alpha subunit family (GNAT), involved in the phototransduction cascade, as well as its adjacent relative G protein alpha inhibiting subunit (GNAI) gene [21–23]. The GNAT family includes three genes located on three of the visual opsin chromosomes in several vertebrates, each flanked by a more distantly related GNAI gene [21, 27, 28].
In parallel, independent analyses in our laboratory of the oxytocin/vasopressin receptor (OT/VP-R) genes and the L-type voltage-gated calcium channel alpha subunit (CACNA1-L) genes converged to reveal large chromosomal regions that share evolutionary history with the visual opsin, GNAT and GNAI genes. The pituitary peptide hormones oxytocin and vasopressin have previously been reported to have five to six ancestral vertebrate receptors (OT/VP-R) based on phylogenetic analyses [29, 30]: one oxytocin receptor, OTR, encoded by OXTR genes, and four to five vasopressin receptors, including V1A (AVPR1A), V1B (AVPR1B) as well as several types of V2 receptors. We report here that the OT/VP-R family genes are located in the proposed visual opsin paralogon, thus resolving the issue of the evolutionary relationships between the ancestral members. Finally, the L-type voltage-gated calcium channel alpha subunits (CACNA1-L) form a family with four members whose genes are located on the visual opsin chromosomes.
We have used these gene families as starting points for extensive analyses of conserved synteny in species representing several vertebrate classes. We report here that these five main gene families and 34 neighboring gene families comprise large paralogous chromosomal regions with extensive similarities to one another that can most parsimoniously be explained by quadruplication of a large ancestral chromosome region. These results define the time points for expansion of the visual opsin family as well as the transducin alpha family, the oxytocin/vasopressin receptors, and the L-type voltage-gated calcium channels. Furthermore, our results have implications for the divergence time point of lampreys and jawed vertebrates relative to the two basal vertebrate tetraploidizations.