The olfactory receptor gene repertoire in primates and mouse: evidence for reduction of the functional fraction in primates

Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex

Sexual reproduction is the dominant reproductive mode in eukaryotes but, in many taxa, it has never been observed. Molecular methods that detect evidence of sex are largely based on the genetic consequences of sexual reproduction. Here we describe a powerful new approach to directly search genomes for genes that function in meiosis. We describe a "meiosis detection toolkit", a set of meiotic genes that represent the best markers for the presence of meiosis. These genes are widely present in eukaryotes, function only in meiosis and can be isolated by degenerate PCR. The presence of most, or all, of these genes in a genome would suggest they have been maintained for meiosis and, implicitly, sexual reproduction. In contrast, their absence would be consistent with the loss of meiosis and asexuality. This approach will help to understand both meiotic gene evolution and the capacity for meiosis and sex in putative obligate asexuals.

Pattern of the divergence of olfactory receptor genes during tetrapod evolution

The olfactory receptor (OR) multigene family is responsible for the sense of smell in vertebrate species. OR genes are scattered widely in our chromosomes and constitute one of the largest gene families in eutherian genomes. Some previous studies revealed that eutherian OR genes diverged mainly during early mammalian evolution. However, the exact period when, and the ecological reason why eutherian ORs strongly diverged has remained unclear. In this study, I performed a strict data mining effort for marsupial opossum OR sequences and bootstrap analyses to estimate the periods of chromosomal migrations and gene duplications of OR genes during tetrapod evolution. The results indicate that chromosomal migrations occurred mainly during early vertebrate evolution before the monotreme-placental split, and that gene duplications occurred mainly during early mammalian evolution between the bird-mammal split and marsupial-placental split, coinciding with the reduction of opsin genes in primitive mammals. It could be thought that the previous chromosomal dispersal allowed the OR genes to subsequently expand easily, and the nocturnal adaptation of early mammals might have triggered the OR gene expansion.

Olfactory sensitivity for putrefaction-associated thiols and indols in three species of non-human primate

Using a conditioning paradigm, the olfactory sensitivity of four spider monkeys, three squirrel monkeys and three pigtail macaques to four thiols and two indols, substances characteristic of putrefaction processes and faecal odours, was assessed. With all odorants, the animals significantly discriminated concentrations below 1 p.p.m. (part per million) from the odourless solvent, and in several cases individual animals even demonstrated thresholds below 1 p.p.t. (part per trillion). The detection thresholds of 0.03 p.p.t. for indol in Saimiri sciureus and Macaca nemestrina and 0.96 p.p.t. for ethanethiol in Ateles geoffroyi represent the lowest values among the more than 50 odorants tested so far with these species and are in the same order of magnitude as the lowest detection thresholds reported so far in the rat and the mouse. The results showed (a) all three species of non-human primate to have a highly developed olfactory sensitivity for putrefaction-associated odorants, and (b) a significant correlation between perceptibility in terms of olfactory detection threshold and carbon chain length of the thiols, and a marked effect of the presence vs absence of a methyl group on perceptibility of the indols tested in two of the three species. The results support the hypotheses that (a) between-species differences in neuroanatomical or genetic features may not be indicative of olfactory sensitivity, and (b) within-species differences in olfactory sensitivity may reflect differences in the behavioural relevance of odorants.

The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans

An olfactory receptor (OR) multigene family is responsible for the well-developed sense of smell possessed by terrestrial tetrapods. Mammalian OR genes had diverged greatly in the terrestrial environment after the fish-tetrapod split, indicating their importance to land habitation. In this study, we analysed OR genes of marine tetrapods (minke whale Balaenoptera acutorostrata, dwarf sperm whale Kogia sima, Dall's porpoise Phocoenoides dalli, Steller's sea lion Eumetopias jubatus and loggerhead sea turtle Caretta caretta) and revealed that the pseudogene proportions of OR gene repertoires in whales were significantly higher than those in their terrestrial relative cattle and also in sea lion and sea turtle. On the other hand, the pseudogene proportion of OR sequences in sea lion was not significantly higher compared with that in their terrestrial relative (dog). It indicates that secondary perfectly adapted marine vertebrates (cetaceans) have lost large amount of their OR genes, whereas secondary-semi-adapted marine vertebrates (sea lions and sea turtles) still have maintained their OR genes, reflecting the importance of terrestrial environment for these animals.

Degeneration of the olfactory guanylyl cyclase D gene during primate evolution

BACKGROUND

The mammalian olfactory system consists of several subsystems that detect specific sets of chemical cues and underlie a variety of behavioral responses. Within the main olfactory epithelium at least three distinct types of chemosensory neurons can be defined by their expression of unique sets of signal transduction components. In rodents, one set of neurons expresses the olfactory-specific guanylyl cyclase (GC)-D gene (Gucy2d, guanylyl cyclase 2d) and other cell-type specific molecules. GC-D-positive neurons project their axons to a small group of atypical "necklace" glomeruli in the olfactory bulb, some of which are activated in response to suckling in neonatal rodents and to atmospheric CO2 in adult mice. Because GC-D is a pseudogene in humans, signaling through this system appears to have been lost at some point in primate evolution.

PRINCIPAL FINDINGS

Here we used a combination of bioinformatic analysis of trace-archive and genome-assembly data and sequencing of PCR-amplified genomic DNA to determine when during primate evolution the functional gene was lost. Our analysis reveals that GC-D is a pseudogene in a large number of primate species, including apes, Old World and New World monkeys and tarsier. In contrast, the gene appears intact and has evolved under purifying selection in mouse, rat, dog, lemur and bushbaby.

CONCLUSIONS

These data suggest that signaling through GC-D-expressing cells was probably compromised more than 40 million years ago, prior to the divergence of New World monkeys from Old World monkeys and apes, and thus cannot be involved in chemosensation in most primates.

A framework for exploring functional variability in olfactory receptor genes

Background

Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested.

Methodology

Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region.

Conclusions

Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability.

The how and why of adult neurogenesis

Brain plasticity refers to the brain's ability to change structure and/or function during maturation, learning, environmental challenges, or disease. Multiple and dissociable plastic changes in the adult brain involve many different levels of organization, ranging from molecules to systems, with changes in neural elements occurring hand-in-hand with changes in supportive tissue elements, such as glia cells and blood vessels. There is now substantial evidence indicating that new functional neurons are constitutively generated from endogenous pools of neural stem cells in restricted areas of the mammalian brain, throughout life. So, in addition to all the other known structural changes, entire new neurons can be added to the existing network circuitry. This addition of newborn neurons provides the brain with another tool for tinkering with the morphology of its own functional circuitry. Although the ongoing neurogenesis and migration have been extensively documented in non-mammalian species, its characteristics in mammals have just been revealed and thus several questions remain yet unanswered. "Is adult neurogenesis an atavism, an empty-running leftover from evolution? What is adult neurogenesis good for and how does the brain 'know' that more neurons are needed? How is this functional demand translated into signals a precursor cell can detect? "[corrected].Adult neurogenesis may represent an adaptive response to challenges imposed by an environment and/or internal state of the animal. To ensure this function, the production, migration, and survival of newborn neurons must be tightly controlled. We attempt to address some of these questions here, using the olfactory bulb as a model system.

Olfactory discrimination ability of CD-1 mice for aliphatic aldehydes as a function of stimulus concentration

Using an operant conditioning paradigm, we tested the ability of CD-1 mice to discriminate between members of a homologous series of aliphatic aldehydes presented at four different concentrations. We found that the mice were clearly capable of discriminating between all odorant pairs when stimuli were presented at concentrations of 1, 0.01, and 0.001 ppm (corresponding to four, two, and one log unit above the highest individual detection threshold) with no significant difference in performance between these concentrations. In contrast, the animals generally failed to discriminate above chance level when stimuli were presented at 0.0001 ppm (corresponding to the highest individual detection threshold) although stimuli were clearly detectable. Further, we found a significant negative correlation between discrimination performance and structural similarity of odorants in terms of differences in carbon chain length. These findings suggest that an increase in stimulus concentration of only one log unit above detection threshold appears to be sufficient for recruitment of additional subpopulations of odorant receptors to allow for qualitative recognition of aliphatic aldehydes.

The evolution of mammalian gene families

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

Olfactory receptor gene repertoires in mammals

In mammals, olfaction is mediated by two distinct organs that are located in the nasal cavity: the main olfactory epithelium (MOE) that binds volatile odorants is responsible for the conscious perception of odors, and the vomeronasal organ (VNO) that binds pheromones is responsible for various behavioral and neuroendocrine responses between individuals of a same species. Odorants and pheromones bind to seven transmembrane domain G-protein-coupled receptors that permit signal transduction. These receptors are encoded by large multigene families that evolved in mammal species in function of specific olfactory needs.

The relevance of genetically altered mouse models of human disease

The impetus to develop useful models of human disease and toxicity has resulted in a number of large-scale mouse mutagenesis programmes. This, in turn, has stimulated considerable concern regarding the scientific validity and welfare of genetically altered mice, and the large numbers of mice that are required by such programmes. In this paper, the scientific advantages and limitations of genetically altered mice as models of several human diseases are discussed. We conclude that, while the use of some such mouse models has contributed considerably to an understanding of human disease and toxicity, other genetically altered mouse models have limited scientific relevance, and fewer have positively contributed to the development of novel human medicines. Suggestions for improving this unsatisfactory situation are made.

Ancient genomic architecture for mammalian olfactory receptor clusters

A new tool for genome-wide definition of genomic gene clusters conserved in multiple species was applied to olfactory receptors in five mammals, demonstrating that most mammalian olfactory receptor clusters have a common ancestry.

Background

Mammalian olfactory receptor (OR) genes reside in numerous genomic clusters of up to several dozen genes. Whole-genome sequence alignment nets of five mammals allow their comprehensive comparison, aimed at reconstructing the ancestral olfactory subgenome.

Results

We developed a new and general tool for genome-wide definition of genomic gene clusters conserved in multiple species. Syntenic orthologs, defined as gene pairs showing conservation of both genomic location and coding sequence, were subjected to a graph theory algorithm for discovering CLICs (clusters in conservation). When applied to ORs in five mammals, including the marsupial opossum, more than 90% of the OR genes were found within a framework of 48 multi-species CLICs, invoking a general conservation of gene order and composition. A detailed analysis of individual CLICs revealed multiple differences among species, interpretable through species-specific genomic rearrangements and reflecting complex mammalian evolutionary dynamics. One significant instance involves CLIC #1, which lacks a human member, implying the human-specific deletion of an OR cluster, whose mouse counterpart has been tentatively associated with isovaleric acid odorant detection.

Conclusion

The identified multi-species CLICs demonstrate that most of the mammalian OR clusters have a common ancestry, preceding the split between marsupials and placental mammals. However, only two of these CLICs were capable of incorporating chicken OR genes, parsimoniously implying that all other CLICs emerged subsequent to the avian-mammalian divergence.

Les récepteurs des molécules odorantes et le codage olfactif

The first step of olfactory detection involves interactions between odorant molecules and neuronal protein receptors. Odour coding results from the combinatory activation of a set of receptors and rests on their clonal expression and olfactory neurone connexion, which lead to formation of a specific sensory map in the cortex. This system, sufficient to discriminate myriads of odorants with a mere 350 different receptors, allows humans to smell molecules that are not natural (new cooking flavours, synthetic chemicals...). The extreme olfactory genome diversity explains the absence of odour semantics. Olfactory receptors are also involved in cellular chemotaxis.

Genetic basis of olfactory communication in primates

The genes involved in olfactory communication in mammals via the vomeronasal system are summarized, and studies investigating these genes in primates are reviewed. Only five potentially functional vomeronasal receptor genes (V1RL s) have been found in humans, and only one of these (V1RL1) has been studied in other primates. V1RL1 has become a pseudogene repeatedly during primate evolution, but patterns of natural selection on primate V1RL genes demonstrate that this gene family diverged under natural selection throughout at least part of primate evolution. Evolution of the TRP2 gene, which encodes for an ion channel that is important in vomeronasal organ (VNO) signalling, strongly suggests that this signalling function was lost in ancestral Catarrhines. Overall, much work remains to be done to elucidate the repertoire of genes that are involved in pheromonal communication, particularly in Strepsirhines. Such studies promise unique insights into the evolution of this modality.

The frequency of occurrence of acyclic monoterpene alcohols in the chemical environment does not determine olfactory sensitivity in nonhuman primates

Using a conditioning paradigm, the olfactory sensitivity of five spider monkeys, three squirrel monkeys, and three pigtail macaques for six acyclic monoterpene alcohols that differ markedly in their frequency of occurrence in plant odors was assessed. The results showed that: (1) all three primate species have a well-developed olfactory sensitivity for acyclic monoterpene alcohols; (2) squirrel monkeys are significantly more sensitive for members of this class of odorants than the other two species and are able to detect all six odorants at concentrations below 0.1 ppm; and (3) there is a lack of positive correlations between olfactory sensitivity and the abundance of the acyclic monoterpene alcohols in flower odors and etheric oils. The results lend support to the growing body of evidence that suggests between-species comparisons of the number of functional olfactory receptor genes or of neuroanatomical features are poor predictors of olfactory performance. The findings do not support the hypothesis that olfactory sensitivity for members of a chemical class may be related to the frequency of occurrence of such odorants in a species' chemical environment.

Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup

We examine the pattern of molecular evolution of the beta-esterase gene cluster, including the Est-6 and psiEst-6 genes, in eight species of the Drosophila melanogaster subgroup. Using maximum likelihood estimates of nonsynonymous/synonymous rate ratios, we show that the majority of Est-6 sites evolves under strong (48% of sites) or moderate (50% of sites) negative selection and a minority of sites (1.5%) is under significant positive selection. Est-6 sites likely to be under positive selection are associated with increased intraspecific variability. One positively selected site is responsible for the EST-6 F/S allozyme polymorphism; the same site is responsible for the EST-6 functional divergence between species of the melanogaster subgroup. For psiEst-6 83.7% sites evolve under negative selection, 16% sites evolve neutrally, and 0.3% sites are under positive selection. The positively selected sites of psiEst-6 are located at the beginning and at the end of the gene, where there is reduced divergence between D. melanogaster and D. simulans; these regions of psiEst-6 could be involved in regulation or some other function. Branch-site-specific analysis shows that the evolution of the melanogaster subgroup underwent episodic positive selection. Collating the present data with previous results for the beta-esterase genes, we propose that positive and negative selection are involved in a complex relationship that may be typical of the divergence of duplicate genes as one or both duplicates evolve a new function.

Plant Volatile Compounds: Sensory Cues for Health and Nutritional Value?

Plants produce many volatile metabolites. A small subset of these compounds is sensed by animals and humans, and the volatile profiles are defining elements of the distinct flavors of individual foods. Flavor volatiles are derived from an array of nutrients, including amino acids, fatty acids, and carotenoids. In tomato, almost all of the important flavor-related volatiles are derived from essential nutrients. The predominance of volatiles derived from essential nutrients and health-promoting compounds suggests that these volatiles provide important information about the nutritional makeup of foods. Evidence supporting a relation between volatile perception and nutrient or health value will be reviewed.

Subarachnoid injection of Microfil reveals connections between cerebrospinal fluid and nasal lymphatics in the non-human primate

Based on quantitative and qualitative studies in a variety of mammalian species, it would appear that a significant portion of cerebrospinal fluid (CSF) drainage is associated with transport along cranial and spinal nerves with absorption taking place into lymphatic vessels external to the central nervous system. CSF appears to convect primarily through the cribriform plate into lymphatics associated with the submucosa of the olfactory and respiratory epithelium. However, the significance of this pathway for CSF absorption in primates has never been established unequivocally. In past studies, we infused Microfil into the subarachnoid compartment of numerous species to visualize CSF transport pathways. The success of this method encouraged us to use a similar approach in the non-human primate. Yellow Microfil was injected post mortem into the cisterna magna of 6 years old Barbados green monkeys (Cercopithecus aethiops sabeus, n = 6). Macroscopic and microscopic examination revealed that Microfil was (1) distributed throughout the subarachnoid compartment, (2) located in the perineurial spaces associated with the fila olfactoria, (3) present within the olfactory submucosa, and (4) situated within an extensive network of lymphatic vessels in the nasal submucosa, nasal septum and turbinate tissues. We conclude that the Microfil distribution patterns in the monkey were very similar to those observed in many other species suggesting that significant nasal lymphatic uptake of CSF occurs in the non-human primate.

Sex-Specific Differences in Olfactory Sensitivity for Putative Human Pheromones in Nonhuman Primates

In humans, the volatile C19-steroids androsta-4,16-dien-3-one (AND) and estra-1,3,5(10),16-tetraen-3-ol (EST) have been shown to modulate autonomic nervous system responses, and to cause hypothalamic activation in a gender-specific manner. Using two conditioning paradigms, the authors here show that pigtail macaques and squirrel monkeys of both sexes were able to detect AND and EST at concentrations in the micromolar and mM range, respectively. Male and female spider monkeys, in contrast, differed markedly in their sensitivity to these two odorous steroids, with males not showing any behavioral responses to the highest concentrations of AND tested and females not responding to the highest concentrations of EST. These data provide the first examples of sex-specific bimodal distributions of olfactory sensitivity in a nonhuman primate species.

Scaling of mammalian ethmoid bones can predict olfactory organ size and performance

The relation between size and performance is central for understanding the evolution of sensory systems, and much interest has been focused on mammalian eyes and ears. However, we know very little about olfactory organ size (OOS), as data for a representative set of mammals are lacking. Here, we present a cranial endocast method for estimating OOS by measuring an easily accessible part of the system, the perforated part of the ethmoid bone, through which the primary olfactory axons reach the olfactory bulb. In 16 species, for which relevant data are available, the area of the perforated ethmoid bone is directly proportional to the area of the olfactory epithelium. Thus, the ethmoid bone is a useful indicator enabling us to analyse 150 species, and describe the distribution of OOS within the class Mammalia. In the future, a method using skull material may be applied to fossil skulls. In relation to skull size, humans, apes and monkeys have small olfactory organs, while prosimians have OOSs typical for mammals of their size. Large ungulates have impressive olfactory organs. Relating anatomy to published thresholds, we find that sensitivity increases with increasing absolute organ size.

Olfactory responsiveness to two odorous steroids in three species of nonhuman primates

Social communication by means of odor signals is widespread among mammals. In pigs, for example, the C19-steroids 5-alpha-androst-16-en-3-one and 5-alpha-androst-16-en-3-ol are secreted by the boar and induce the mating stance in the sow. In humans, the same substances have been shown to be compounds of body odor and are presumed to affect human behavior. Using an instrumental conditioning paradigm, we here show that squirrel monkeys, spider monkeys and pigtail macaques are able to detect androstenone at concentrations in the micromolar range and thus at concentrations at least as low as those reported in pigs and humans. All three species of nonhuman primates were considerably less sensitive to androstenol, which was detected at concentrations in the millimolar range. Additional tests, using a habituation-dishabituation paradigm, showed that none of the 10 animals tested per species was anosmic to the two odorous steroids. These results suggest that androstenone and androstenol may be involved in olfactory communication in the primate species tested and that the specific anosmia to these odorants found in approximately 30% of human subjects may be due to their reduced number of functional olfactory receptor genes compared with nonhuman primates.

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Olfactory receptor (OR) genes constitute the basis of the sense of smell and are encoded by the largest mammalian gene superfamily, with >1000 members. In humans, but not in mice or dogs, the majority of OR genes have become pseudogenes, suggesting that OR genes in humans evolve under different selection pressures than in other mammals. To explore this further, we compare the OR gene repertoire of human with its closest living evolutionary relative, by taking advantage of the recently sequenced genome of the chimpanzee. In agreement with previous reports based on a small number of ORs, we find that humans have a significantly higher proportion of OR pseudogenes than chimpanzees. Moreover, we can reject the possibility that humans have been accumulating OR pseudogenes at a constant neutral rate since the divergence of human and chimpanzee. The comparison of the two repertoires reveals two chimpanzee-specific OR subfamily expansions and three expansions specific to humans. It also suggests that a subset of OR genes are under positive selection in either the human or the chimpanzee lineage. Thus, although overall there is relaxed constraint on human olfaction relative to chimpanzee, species-specific sensory requirements appear to have shaped the evolution of the functional OR gene repertoires in both species.

Evolution of the special senses in primates: past, present, and future

The present special issue of The Anatomical Record is the result of a symposium entitled Evolution of the Special Senses in Primates. Considered together, the special senses of primates are remarkable because they constitute a singular and definitive suite of mammalian characteristics. Examining their evolution is pivotal for understanding the origin and present-day variation of primate behavior and ecology. Accordingly, the 14 articles assembled here consider the different constraints and opportunities associated with the uptake and use of physical and chemical stimuli. The present issue brings together experts on different primate sensory modalities and stresses events at the sensory periphery, where the organism is exposed to and comes into contact with its environment. Key topics include color vision, the genetics of olfaction, the morphological basis and significance of chemical communication, and the neural organization and scaling of primate sensory systems. The result is a special issue that both reflects our current understanding of primate sensory modalities and challenges certain fundamental assumptions concerning their evolution.

Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages

The numbers of functional olfactory receptor (OR) genes are quite variable among mammalian species. Previously we have reported that humans have 388 functional OR genes and 414 pseudogenes, while mice have 1037 functional genes and 354 pseudogenes. These observations suggest either that humans lost many functional OR genes after the human-mouse divergence (HMD) or that mice gained many functional genes. To distinguish between these two hypotheses, we devised a new method of inferring the number of functional OR genes in the most recent common ancestor (MRCA) of humans and mice. An application of this method suggested that the MRCA had approximately 750 functional OR genes and that mice acquired approximately 350 new OR genes after the HMD whereas approximately 430 OR genes in the MRCA have become pseudogenes or eliminated in the human lineage. Therefore, the two evolutionary hypotheses mentioned above are not mutually exclusive and both are nearly equally responsible for the difference in the number of OR genes between humans and mice.

Microsmatic primates: reconsidering how and when size matters

The terms "microsmatic" and "macrosmatic" refer to species with lesser or greater levels, respectively, of olfactory function. Historically, primates are considered microsmats (olfactory sense reduced) with a concomitant increased emphasis on vision. The olfactory bulbs (forebrain centers that receive peripheral olfactory input) are proportionately smaller in primates compared to most other mammals. Similarly, the regions of the nasal cavity that are covered with olfactory epithelium (containing receptor cells) have proportionately less surface area in primates than other mammals. Thus, the generalization that primates are microsmatic is most frequently stated in terms of the proportional rather than absolute size of olfactory structures. Yet the importance of scaling to body size is unclear in regard to the chemical senses such as the olfactory or vomeronasal systems-do chemosensory structures such as olfactory bulbs and olfactory epithelium exhibit the same neural relationship to body mass that is seen for neural tissues that supply innervation to musculature or the skin? Previous studies examining neuronal density, volume, and/or surface area of the olfactory epithelium illustrate that different conclusions may be supported based on the parameter used. Plots of olfactory bulb volume versus body mass that generated for large-scale taxonomic studies or growth studies benefit from body mass (or total brain volume) with a comparative perspective. However, our examination of proportional versus absolute measurements implies that in comparisons within taxa, body size adjustments needlessly distort the data. As a final consideration, another embryonic derivative of the nasal placode, the vomeronasal organ, may warrant consideration regarding a definition of microsomia versus macrosomia.

Information processing in the mammalian olfactory system

Recently, modern neuroscience has made considerable progress in understanding how the brain perceives, discriminates, and recognizes odorant molecules. This growing knowledge took over when the sense of smell was no longer considered only as a matter for poetry or the perfume industry. Over the last decades, chemical senses captured the attention of scientists who started to investigate the different stages of olfactory pathways. Distinct fields such as genetic, biochemistry, cellular biology, neurophysiology, and behavior have contributed to provide a picture of how odor information is processed in the olfactory system as it moves from the periphery to higher areas of the brain. So far, the combination of these approaches has been most effective at the cellular level, but there are already signs, and even greater hope, that the same is gradually happening at the systems level. This review summarizes the current ideas concerning the cellular mechanisms and organizational strategies used by the olfactory system to process olfactory information. We present findings that exemplified the high degree of olfactory plasticity, with special emphasis on the first central relay of the olfactory system. Recent observations supporting the necessity of such plasticity for adult brain functions are also discussed. Due to space constraints, this review focuses mainly on the olfactory systems of vertebrates, and primarily those of mammals.

Olfactory sensitivity for aliphatic alcohols and aldehydes in spider monkeys (Ateles geoffroyi)

Using a conditioning paradigm, the olfactory sensitivity of five spider monkeys for homologous series of aliphatic 1-alcohols (1-propanol to 1-octanol) and n-aldehydes (n-butanal to n-nonanal) was investigated. With the exception of 1-propanol, the animals significantly discriminated concentrations below 1 ppm from the odorless solvent, and in several cases, individual monkeys even demonstrated detection thresholds below 10 ppb. The results showed 1) spider monkeys to have a well-developed olfactory sensitivity for both substance classes, which for the majority of alcohols tested matches or even is better than that of the rat, and 2) a significant negative correlation between perceptibility in terms of olfactory detection thresholds and carbon chain length of the alcohols, but not of the aldehydes tested. These findings lend further support to the growing body of evidence suggesting that between-species comparisons of the number of functional olfactory receptor genes or of neuroanatomical features are poor predictors of olfactory performance, and that general labels such as "microsmat" or "macrosmat" (which are usually based on allometric comparisons of olfactory brain structures) are inadequate to describe a species' olfactory capabilities.

Olfactory sensitivity for aliphatic ketones in squirrel monkeys and pigtail macaques

Using a conditioning paradigm, the olfactory sensitivity of three squirrel monkeys and three pigtail macaques for homologous series of aliphatic 2-ketones (2-butanone to 2-nonanone), symmetrical ketones (3-pentanone to 6-undecanone), and C7-ketones (2-heptanone to 4-heptanone) was assessed. In the majority of cases, the animals of both species significantly discriminated concentrations below 1 ppm from the odorless solvent, and with 2-nonanone and 5-nonanone the monkeys even demonstrated thresholds below 1 ppb. The results showed both primate species have a well-developed olfactory sensitivity for aliphatic ketones, and pigtail macaques generally perform better than squirrel monkeys in detecting members of this class of odorants. Further, in both species tested, we found a significant negative correlation between perceptibility in terms of olfactory detection thresholds and carbon-chain length of both the 2-ketones and the symmetrical ketones, but not between detection thresholds and position of the functional group with the C7-ketones. These findings lend further support to the growing body of evidence suggesting that between-species comparisons of the number of functional olfactory receptor genes or of neuroanatomical features are poor predictors of olfactory performance.

The human sense of smell: are we better than we think?

Gordon Shepherd challenges the notion - based on genetic evidence - that olfaction is less well developed in humans as compared to other mammals

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Neuropoietin, a new IL-6-related cytokine signaling through the ciliary neurotrophic factor receptor

A structural profile-based computational screen was used to identify neuropoietin (NP), a new cytokine. The np gene is localized in tandem with the cardiotrophin-1 gene on mouse chromosome 7. NP shares structural and functional features with ciliary neurotrophic factor (CNTF), cardiotrophin-1, and cardiotrophin-like cytokine. It acts through a membrane receptor complex comprising CNTF receptor-alpha component (CNTFRalpha), gp130, and leukemia inhibitory factor receptor to activate signal transducer and activator of transcription 3 signaling pathway. NP is highly expressed in embryonic neuroepithelia. Strikingly, CNTFRalpha, but not its alternate ligands, CNTF and cardiotrophin-like cytokine, is expressed at the same developmental stages. NP is also observed in retina and to a lesser extent in skeletal muscle. Moreover, NP could sustain the in vitro survival of embryonic motor neurons and could increase the proliferation of neural precursors when associated to epidermal growth factor and fibroblast growth factor 2. Thus, NP is a new ligand for CNTFRalpha, with important implications for murine nervous system development.

The canine olfactory subgenome

We identified 971 olfactory receptor (OR) genes in the dog genome, estimated to constitute approximately 80% of the canine OR repertoire. This was achieved by directed genomic DNA cloning of olfactory sequence tags as well as by mining the Celera canine genome sequences. The dog OR subgenome is estimated to have 12% pseudogenes, suggesting a functional repertoire similar to that of mouse and considerably larger than for humans. No novel OR families were discovered, but as many as 34 gene subfamilies were unique to the dog. "Fish-like" Class I ancient ORs constituted 18% of the repertoire, significantly more than in human and mouse. A set of 122 dog-human-mouse ortholog triplets was identified, with a relatively high fraction of Class I ORs. The elucidation of a large portion of the canine olfactory receptor gene superfamily, with some dog-specific attributes, may help us understand the unique chemosensory capacities of this species.

Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates

Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of pseudogenes in the OR gene family is significantly larger in humans than in other apes and significantly larger in apes than in the mouse. To investigate the process of degeneration of the olfactory repertoire in primates, we estimated the proportion of OR pseudogenes in 19 primate species by surveying randomly chosen subsets of 100 OR genes from each species. We find that apes, Old World monkeys and one New World monkey, the howler monkey, have a significantly higher proportion of OR pseudogenes than do other New World monkeys or the lemur (a prosimian). Strikingly, the howler monkey is also the only New World monkey to possess full trichromatic vision, along with Old World monkeys and apes. Our findings suggest that the deterioration of the olfactory repertoire occurred concomitant with the acquisition of full trichromatic color vision in primates.

Examination of olfactory receptor genes in 19 primate species suggests that the olfactory repertoire lost complexity as our ancestors acquired full-color vision

Olfactory fossa ofTremacebus harringtoni (platyrrhini, early Miocene, Sacanana, Argentina): Implications for activity pattern

CT imaging was undertaken on the skull of approximately 20-Myr-old Miocene Tremacebus harringtoni. Here we report our observations on the relative size of the olfactory fossa and its implications for the behavior of Tremacebus. The endocranial surface of Tremacebus is incomplete, making precise estimate of brain size and olfactory fossa size imprecise. However, olfactory fossa breadth and maximum endocranial breadth measured from CT images of one catarrhine species and eight platyrrhine species for which volumes of the olfactory bulb and brain are known show that the osteological proxies give a reasonably accurate indication of relative olfactory bulb size. Nocturnal Aotus has the largest relative olfactory fossa breadth and the largest olfactory bulb volume compared to brain volume among extant anthropoids. Tremacebus had a much smaller olfactory fossa breadth and, by inference, bulb volume--within the range of our sample of diurnal anthropoids. Variations in the relative size of the olfactory bulbs in platyrrhines appear to relate to the importance of olfaction in daily behaviors. Aotus has the largest olfactory bulbs among platyrrhines and relies more on olfactory cues when foraging than Cebus, Callicebus, or Saguinus. As in other examples of nocturnal versus diurnal primates, nocturnality may have been the environmental factor that selected for this difference in Aotus, although communication and other behaviors are also likely to select for olfactory variation in diurnal anthropoids. Considering the olfactory fossa size of Tremacebus, olfactory ability of this Miocene monkey was probably not as sensitive as in Aotus and counts against the hypothesis that Tremacebus was nocturnal. This finding accords well with previous observations that the orbits of Tremacebus are not as large as nocturnal Aotus.

Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse

In the mouse olfactory system, each olfactory sensory neuron (OSN) expresses only one odorant receptor (OR) gene in a monoallelic and mutually exclusive manner. Such expression forms the genetic basis for OR-instructed axonal projection of OSNs to the olfactory bulb of the brain during development. Here, we identify an upstream cis-acting DNA region that activates the OR gene cluster in mouse and allows the expression of only one OR gene within the cluster. Deletion of the coding region of the expressed OR gene or a naturally occurring frame-shift mutation allows a second OR gene to be expressed. We propose that stochastic activation of only one OR gene within the cluster and negative feedback regulation by that OR gene product are necessary to ensure the one receptor-one neuron rule.

Comparison of the canine and human olfactory receptor gene repertoires

In this study, 817 novel canine olfactory receptor (OR) sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse.

Background

Olfactory receptors (ORs), the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation, constitute the largest gene family in vertebrates, including around 900 genes in human and 1,500 in the mouse. Whereas dogs, like many other mammals, have a much keener olfactory potential than humans, only 21 canine OR genes have been described to date.

Results

In this study, 817 novel canine OR sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse. Phylogenetic analysis of 403 canine OR sequences identified 51 families, and radiation-hybrid mapping of 562 showed that they are distributed on 24 dog chromosomes, in 37 distinct regions. Most of these regions constitute clusters of 2 to 124 closely linked genes. The two largest clusters (124 and 109 OR genes) are located on canine chromosomes 18 and 21. They are orthologous to human clusters located on human chromosomes 11q11-q13 and HSA11p15, containing 174 and 115 ORs respectively.

Conclusions

This study shows a strongly conserved genomic distribution of OR genes between dog and human, suggesting that OR genes evolved from a common mammalian ancestral repertoire by successive duplications. In addition, the dog repertoire appears to have expanded relative to that of humans, leading to the emergence of specific canine OR genes.

Evolution of olfactory receptor genes in the human genome

Olfactory receptor (OR) genes form the largest known multigene family in the human genome. To obtain some insight into their evolutionary history, we have identified the complete set of OR genes and their chromosomal locations from the latest human genome sequences. We detected 388 potentially functional genes that have intact ORFs and 414 apparent pseudogenes. The number and the fraction (48%) of functional genes are considerably larger than the ones previously reported. The human OR genes can clearly be divided into class I and class II genes, as was previously noted. Our phylogenetic analysis has shown that the class II OR genes can further be classified into 19 phylogenetic clades supported by high bootstrap values. We have also found that there are many tandem arrays of OR genes that are phylogenetically closely related. These genes appear to have been generated by tandem gene duplication. However, the relationships between genomic clusters and phylogenetic clades are very complicated. There are a substantial number of cases in which the genes in the same phylogenetic clade are located on different chromosomal regions. In addition, OR genes belonging to distantly related phylogenetic clades are sometimes located very closely in a chromosomal region and form a tight genomic cluster. These observations can be explained by the assumption that several chromosomal rearrangements have occurred at the regions of OR gene clusters and the OR genes contained in different genomic clusters are shuffled.

Natural selection on the olfactory receptor gene family in humans and chimpanzees

The olfactory receptor (OR) genes constitute the largest gene family in mammalian genomes. Humans have >1,000 OR genes, of which only approximately 40% have an intact coding region and are therefore putatively functional. In contrast, the fraction of intact OR genes in the genomes of the great apes is significantly greater (68%-72%), suggesting that selective pressures on the OR repertoire vary among these species. We have examined the evolutionary forces that shaped the OR gene family in humans and chimpanzees by resequencing 20 OR genes in 16 humans, 16 chimpanzees, and one orangutan. We compared the variation at the OR genes with that at intergenic regions. In both humans and chimpanzees, OR pseudogenes seem to evolve neutrally. In chimpanzees, patterns of variability are consistent with purifying selection acting on intact OR genes, whereas, in humans, there is suggestive evidence for positive selection acting on intact OR genes. These observations are likely due to differences in lifestyle, between humans and great apes, that have led to distinct sensory needs.

Evolutionary relationships of the Tas2r receptor gene families in mouse and human

The early molecular events in the perception of bitter taste start with the binding of specific water-soluble molecules to G protein-coupled receptors (GPCRs) encoded by the Tas2r family of taste receptor genes. The identification of the complete TAS2R receptor family repertoire in mouse and a comparative study of the Tas2r gene families in mouse and human might help to better understand bitter taste perception. We have identified, cloned, and characterized 13 new mouse Tas2r sequences, 9 of which encode putative functional bitter taste receptors. The encoded proteins are between 293 and 333 amino acids long and share between 18% and 54% sequence identity with other mouse TAS2R proteins. Including the 13 sequences identified, the mouse Tas2r family contains approximately 30% more genes and 60% fewer pseudogenes than the human TAS2R family. Sequence and phylogenetic analyses of the proteins encoded by all mouse and human Tas2r genes indicate that TAS2R proteins present a lower degree of sequence conservation in mouse than in human and suggest a classification in five groups that may reflect a specialization in their functional activity to detect bitter compounds. Tas2r genes are organized in clusters in both mouse and human genomes, and an analysis of these clusters and phylogenetic analyses indicates that the five TAS2R protein groups were present prior to the divergence of the primate and rodent lineages. However, differences in subsequent evolutionary processes, including local duplications, interchromosomal duplications, divergence, and deletions, gave rise to species-specific sequences and shaped the diversity of the current TAS2R receptor families during mouse and human evolution.

Complex evolution of 7E olfactory receptor genes in segmental duplications

Large segmental duplications (SDs) constitute at least 3.6% of the human genome and have increased its size, complexity, and diversity. SDs can mediate ectopic sequence exchange resulting in gross chromosomal rearrangements that could contribute to speciation and disease. We have identified and evaluated a subset of human SDs that harbor an 88-member subfamily of olfactory receptor (OR)-like genes called the 7Es. At least 92% of these genes appear to be pseudogenes when compared to other OR genes. The 7E-containing SDs (7E SDs) have duplicated to at least 35 regions of the genome via intra- and interchromosomal duplication events. In contrast to many human SDs, the 7E SDs are not biased towards pericentromeric or subtelomeric regions. We find evidence for gene conversion among 7E genes and larger sequence exchange between 7E SDs, supporting the hypothesis that long, highly similar stretches of DNA facilitate ectopic interactions. The complex structure and history of the 7E SDs necessitates extension of the current model of large-scale DNA duplication. Despite their appearance as pseudogenes, some 7E genes exhibit a signature of purifying selection, and at least one 7E gene is expressed.

Identification and characterization of human taste receptor genes belonging to the TAS2R family

The sense of taste is a chemosensory system responsible for basic food appraisal. Humans distinguish between five primary tastes: bitter, sweet, sour, salty and umami. The molecular events in the perception of bitter taste are believed to start with the binding of specific water-soluble molecules to G-protein-coupled receptors encoded by the TAS2R/T2R family of taste receptor genes. TAS2R receptors are expressed at the surface of taste receptor cells and are coupled to G proteins and second messenger pathways. We have identified, cloned and characterized 11 new bitter taste receptor genes and four new pseudogenes that belong to the human TAS2R family. Their encoded proteins have between 298 and 333 amino acids and share between 23 and 86% identity with other human TAS2R proteins. Screening of a mono-chromosomal somatic cell hybrid panel to assign the identified bitter taste receptor genes to human chromosomes demonstrated that they are located in chromosomes 7 and 12. Including the 15 sequences identified, the human TAS2R family is composed of 28 full-length genes and 16 pseudogenes. Phylogenetic analyses suggest a classification of the TAS2R genes in five groups that may reflect a specialization in the detection of specific types of bitter chemicals.

Olfactory sensitivity for aliphatic aldehydes in squirrel monkeys and pigtail macaques

Using a conditioning paradigm, the olfactory sensitivity of three squirrel monkeys and three pigtail macaques for a homologous series of aliphatic aldehydes ( n-butanal to n-nonanal) was assessed. With only few exceptions, the animals of both species significantly discriminated concentrations below 1 ppm from the odorless solvent, and with n-butanal and n-hexanal individual pigtail macaques even demonstrated thresholds below 1 ppb. The results showed (1). both primate species to have a well-developed olfactory sensitivity for aliphatic aldehydes, (2). pigtail macaques to generally perform better than squirrel monkeys in detecting members of this class of odorants, and (3). no significant correlation between perceptibility in terms of olfactory detection thresholds and carbon chain length of the aliphatic aldehydes in both species tested. These findings lend further support to the growing body of evidence suggesting that between-species comparisons of the number of functional olfactory receptor genes or of neuroanatomical features are poor predictors of olfactory performance. Further, our findings suggest that olfaction may play an important and hitherto underestimated role in the regulation of behavior in the species tested.

Human specific loss of olfactory receptor genes

Olfactory receptor (OR) genes constitute the basis for the sense of smell and are encoded by the largest mammalian gene superfamily of >1,000 genes. In humans, >60% of these are pseudogenes. In contrast, the mouse OR repertoire, although of roughly equal size, contains only approximately 20% pseudogenes. We asked whether the high fraction of nonfunctional OR genes is specific to humans or is a common feature of all primates. To this end, we have compared the sequences of 50 human OR coding regions, regardless of their functional annotations, to those of their putative orthologs in chimpanzees, gorillas, orangutans, and rhesus macaques. We found that humans have accumulated mutations that disrupt OR coding regions roughly 4-fold faster than any other species sampled. As a consequence, the fraction of OR pseudogenes in humans is almost twice as high as in the non-human primates, suggesting a human-specific process of OR gene disruption, likely due to a reduced chemosensory dependence relative to apes.

Successful acquisition of an olfactory discrimination paradigm by spider monkeys, Ateles geoffroyi

The present study demonstrates that an operant conditioning paradigm-originally designed for assessing olfactory performance in an Old World primate, the pigtail macaque-can successfully be adapted for use with a New World primate, the spider monkey. Using a task based on a food-rewarded, two-choice discrimination of simultaneously presented odor stimuli, Ateles geoffroyi is capable of learning to discriminate between objects on the basis of odor cues. Moreover, animals could readily transfer to new S+ and S- stimuli, and could remember the significance of previously learned odor stimuli even after a 4-week break. We could also show that this method is suitable for obtaining reliable measures of olfactory sensitivity. Our results indicate that A. geoffroyi clearly outperforms Macaca nemestrina with regard to the speed of initial task acquisition and the ability to master transfer tasks, and shows a sensitivity to a food-related odorant which matches that of other primate species.

Isolation of novel olfactory receptor genes in marmosets (Callithrix): insights into pseudogene formation and evidence for functional degeneracy in non-human primates

Nineteen olfactory receptor (OR) genes were isolated from three OR subfamilies in two species of marmoset (Callithrix). Olfactory receptor 912-93 has high sequence similarity among marmosets and between marmosets and humans, suggesting strong conservation of function. All of the remaining seventeen OR genes identified from subfamilies 3A and 1E were pseudogenes. Following pseudogene formation, marmoset OR genes in both 1E and 3A subfamilies underwent duplications, indel events and a high rate of nucleotide substitution. These results provide a contrast to previous studies, and show that in spite of the keen olfactory sense of marmosets, they harbour many OR pseudogenes. A high rate of in vitro recombination using Pfu polymerase but not Taq polymerase was confirmed. The rapid molecular evolution of OR pseudogenes suggests that they do not provide a useful source of sequence variation for conversion to intact OR genes over evolutionary timescales. The overall pattern of OR evolution in marmosets is comparable to the 'birth-and-death' model of gene family evolution. An unbiased view on the evolutionary timing of the reduction of the functional olfactory repertoire in humans must await more data.