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. 2007 Dec 18;104(51):20421-6.
doi: 10.1073/pnas.0709956104. Epub 2007 Dec 5.

Genomic drift and copy number variation of sensory receptor genes in humans

Masafumi Nozawa  1 , Yoshihiro Kawahara, Masatoshi Nei
Affiliations

Genomic drift and copy number variation of sensory receptor genes in humans

Masafumi Nozawa et al. Proc Natl Acad Sci U S A. .

Abstract

The number of sensory receptor genes varies extensively among different mammalian species. This variation is believed to be caused partly by physiological requirements of animals and partly by genomic drift due to random duplication and deletion of genes. If the contribution of genomic drift is substantial, each species should contain a significant amount of copy number variation (CNV). We therefore investigated CNVs in sensory receptor genes among 270 healthy humans by using published CNV data. The results indicated that olfactory receptor (OR), taste receptor type 2, and vomeronasal receptor type 1 genes show a high level of intraspecific CNVs. In particular, >30% of the approximately 800 OR gene loci in humans were polymorphic with respect to copy number, and two randomly chosen individuals showed a copy number difference of approximately 11 in functional OR genes on average. There was no significant difference in the amount of CNVs between functional and nonfunctional OR genes. Because pseudogenes are expected to evolve in a neutral fashion, this observation suggests that functional OR genes also have evolved in a similar manner with respect to copy number change. In addition, we found that the evolutionary change of copy number of OR genes approximately follows the Gaussian process in probability theory, and the copy number divergence between populations has increased with evolutionary time. We therefore conclude that genomic drift plays an important role for generating intra- and interspecific CNVs of sensory receptor genes. Similar results were obtained when all annotated genes were analyzed.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Distribution of the number of polymorphic loci in which a sampled individual shows a copy number different from that of the reference individual. All annotated loci were used. Mean and SD represent the mean and the standard deviation of the number of polymorphic loci, respectively.
Fig. 2.
Fig. 2.
Distribution of relative copy number for all annotated genes. A curve represents the normal distribution fitted to the data. Mean and SD represent the mean and the standard deviation of gene copy number, respectively.
Fig. 3.
Fig. 3.
Distributions of relative copy number for all annotated genes in three human populations. N, sample size.
Fig. 4.
Fig. 4.
Distributions of relative copy number of sensory receptor genes.
Fig. 5.
Fig. 5.
Distributions of relative copy number of OR genes in three human populations.
Fig. 6.
Fig. 6.
Schematic diagram of copy number evolution in sensory receptor genes. (A) CNV within a population. (B) CNVs in two geographical populations. (C) CNVs in two species. Each color line represents the distributions of gene copy number for each species or population, whereas different color shades show different environmental conditions. A solid arrow indicates that a group of individuals with a larger number of genes than the average (B) moves to a new niche and establishes a new species (C).
See this image and copyright information in PMC

Comment in

  • The drifting human genome.
    Zhang J. Zhang J. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20147-8. doi: 10.1073/pnas.0710524104. Proc Natl Acad Sci U S A. 2007. PMID: 18093959 Free PMC article. No abstract available.

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