Origins and antiquity of X-linked triallelic color vision systems in New World monkeys

Abstract

It is known that the squirrel monkey, marmoset, and other related New World (NW) monkeys possess three high-frequency alleles at the single X-linked photopigment locus, and that the spectral sensitivity peaks of these alleles are within those delimited by the human red and green pigment genes. The three alleles in the squirrel monkey and marmoset have been sequenced previously. In this study, the three alleles were found and sequenced in the saki monkey, capuchin, and tamarin. Although the capuchin and tamarin belong to the same family as the squirrel monkey and marmoset, the saki monkey belongs to a different family and is one of the species that is most divergent from the squirrel monkey and marmoset, suggesting the presence of the triallelic system in many NW monkeys. The nucleotide sequences of these alleles from the five species studied indicate that gene conversion occurs frequently and has partially or completely homogenized intronic and exonic regions of the alleles in each species, making it appear that a triallelic system arose independently in each of the five species studied. Nevertheless, a detailed analysis suggests that the triallelic system arose only once in the NW monkey lineage, from a middle wavelength (green) opsin gene, and that the amino acid differences at functionally critical sites among alleles have been maintained by natural selection in NW monkeys for >20 million years. Moreover, the two X-linked opsin genes of howler monkeys (a NW monkey genus) were evidently derived from the incorporation of a middle (green) and a long wavelength (red) allele into one chromosome; these two genes together with the (autosomal) blue opsin gene would immediately enable even a male monkey to have trichromatic vision.

Figure 1

Neighbor-joining tree derived from an analysis of intron 4 sequences. The distances were computed by using Kimura’s (26) two-parameter method. The number at each node denotes the proportion of 500 bootstrap replicates that supported the subset of sequences. The number in brackets below each branch denotes the number of indels supporting the monophyly of the three alleles in each species. A dashed arrow with a number in brackets denotes the number of indels shared by two alleles. The seven numbers listed vertically at the upper right of the tree refer to the positions of the seven critical amino acid sites. The sequence alignment and the positions and sizes of indels are available on request from W.-H.L.

Figure 2

Variable sites in exons 3, 4, and 5 and intron 4 of the P562 allele and the two P535 alleles (P535 and P535c) of the capuchin. The numbers at the top refer to the positions of the sites on the complete coding sequence (for exons 3, 4, and 5) and to the positions on an alignment of intron 4 sequences (available on request). The five positions in boldface are the five critical amino acid residues, respectively, at positions 180, 229, 233, 277, and 285.

Figure 3

Histograms showing pairwise variation in divergence as a function of position in intron 4. Horizontally, each bar represents a 100-bp segment. Vertically, each bar shows the number of nucleotide differences per segment. Three within-species and two between-species comparisons are shown (Mar, marmoset; Tam, tamarin; Sqm, squirrel monkey).

Figure 4

Neighbor-joining tree derived from an analysis of exon 3, 4, and 5 sequences. The distances were computed by using the method of W.-H.L. (27), with weights of 80% and 20% for nonsynonymous and synonymous substitutions, respectively. The number at each node denotes the percent of 500 bootstrap replicates that supported the subset of sequences. The galago sequences of Zhou et al. (30) were used to root the tree (CAP, capuchin; HUM, human; HOW, howler monkey; MAR, marmoset; SAK, saki monkey; SQM, squirrel monkey; TAM, tamarin).

Figure 5

Tree that requires the minimal number of amino acid changes at the five critical sites under the constraint of the species phylogeny in Fig. 1. Substitutions along branches are indicated as the ancestral amino acid followed by its position on the complete coding sequence and then followed by the new amino acid. Two equally parsimonious pathways are shown; one pathway is above branches (italics) and one is below branches. A shorter tree (11 steps instead of 12 steps) is obtained if the marmoset and tamarin P556 alleles have a recent origin and was derived from the P562 allele, as indicated by the arrow. However, this alternative tree is less likely (see Results).