Extreme variability among mammalian V1R gene families

Pheromones are chemical signals used for intraspecies communication that affect many important mammalian behaviors, including aggression, maternal behavior, courtship, and mating (Wyatt 2003). In rodents, pheromone detection was previously thought to be accomplished solely through the vomeronasal organ (VNO), but it is now recognized that the main olfactory epithelium is also involved in pheromone sensing (Brennan and Zufall 2006). Neurons of the vomeronasal epithelium project to the accessory olfactory bulb (AOB), from which signals are passed on to various other areas of the brain, including some areas that seem to control innate and stereotyped behavioral and endocrine responses (Dulac and Axel 1995). Several large families of 7-transmembrane G-protein–coupled receptors (GPCRs) are expressed in neurons of the vomeronasal and main olfactory epithelia and recognize odorant and pheromone ligands directly. These GPCR families include olfactory receptors (ORs) and trace-amine associated receptors (TAARs) in the main olfactory epithelium and three families expressed in the vomeronasal organ (V1Rs, V2Rs, and formyl peptide receptor-like proteins [FPRs]) (Dulac and Axel 1995; Mombaerts 2004; Liberles and Buck 2006; Riviere et al. 2009). Based on analysis of a limited number of genome assemblies, the size and composition of these gene families are known to differ between mammalian species (Ache and Young 2005; Grus et al. 2005; Young et al. 2005; Liberles and Buck 2006; Shi and Zhang 2007; Young and Trask 2007; Riviere et al. 2009), with the V1R and V2R families appearing especially variable. There are over 100 functional V1Rs in the rat and mouse genomes, but only five (or fewer) intact V1Rs in the human and chimpanzee genomes along with a large number of pseudogenes (Liman 2006). The platypus possesses the largest V1R repertoire of any mammal studied to date, with more than 270 intact V1Rs (Grus et al. 2007). Here, we examine V1Rs in a much larger and more diverse set of 37 mammalian genomes to address several questions that were difficult to examine with smaller data sets. Is the variation in V1R family size seen in the eight previously analyzed species a prevalent feature across the mammalian tree? Are the large V1R repertoires seen in platypus, rat, and mouse exceptional among mammals, with most mammalian genomes encoding small functional V1R repertoires like primates and dog? Or do most mammals, like rodents, have large V1R repertoires? Can any correlations between V1R family size and ecological or behavioral observations be seen by studying a much larger range of mammalian species? And, with data from many more primate genomes, we could examine a previous hypothesis that functional decline of the V1R family in humans and other apes and Old World monkeys might reflect a decreased reliance on chemical sensing due to the acquisition of trichromatic visual abilities (Liman and Innan 2003; Zhang and Webb 2003). In order to address these questions, we took advantage of ongoing efforts to generate low-redundancy comparative sequence data on numerous mammalian genomes (Margulies et al. 2005). Such data, although not providing full coverage of the genomes being sequenced, allow both the estimation of the number of V1Rs possessed by various mammals and the generation of partial phylogenies of mammalian V1Rs. We show that the size of the V1R repertoire varies widely among mammals and that most mammals examined appear to have experienced species-specific duplications resulting in “semi-private” functional V1R repertoires. We also generated additional sequence from V1R family members in wolves to examine the evolutionary timing of the decline of the dog V1R repertoire to only approximately nine apparently intact V1R genes and ∼60 pseudogenes (Grus et al. 2005; Young et al. 2005). Dog also has only pseudogenes in the V2R family (Shi and Zhang 2007; Young and Trask 2007) and possesses a relatively thin vomeronasal epithelium and relatively small AOB (Dennis et al. 2003). Vomeronasal decline is surprising given that dogs and wolves appear to exhibit pheromone-based behaviors (Anisko 1976; Goodwin et al. 1979), such as the well-known effect of a female in heat on males, and urine-marking and examination of urine marks. We and others considered the idea that selective pressures imposed by humans during dog domestication favoring more docile, human-centric animals might have led to a rapid, recent degeneration of the dog V1R repertoire to pseudogenes (Grus et al. 2005; Young et al. 2005). Here, we disprove that hypothesis by sequencing the least degenerated dog V1R pseudogenes (i.e., those most likely to be recently inactivated) from wolf DNA, finding that they are also pseudogenes in wolf. Our result implies that loss of functional V1R genes occurred before dogs were domesticated.