Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

Abstract

Chemosensation is the most ubiquitous sense in animals, enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues. While there is a general conception that olfactory receptor (OR) genes evolve rapidly, the universality of this phenomenon across vertebrates, and its magnitude, are unclear. The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested. We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits. Using published genomes, we identified ORs in 21 tetrapods, including amphibians, reptiles, birds, and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes. We found that, for all clades investigated, most OR genes evolve nearly an order of magnitude faster than other protein-coding genes, with many OR genes showing signatures of diversifying selection across nearly all taxa in this study. This rapid rate of evolution suggests that chemoreceptor genes are in "evolutionary overdrive," perhaps evolving in response to the ever-changing chemical space of the environment. To obtain complementary morphological data, we stained whole fixed specimens with iodine, µCT-scanned the specimens, and digitally segmented chemosensory and nonchemosensory brain regions. We then estimated phenotypic variation within traits and among tetrapods. While we found considerable variation in chemosensory structures, they were no more diverse than nonchemosensory regions. We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space, whereas chemosensory phenotypes and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.

Keywords: chemosensation; diversifying selection; olfaction; olfactory bulb; olfactory receptor; tetrapod.

Figure 1.

Phylogeny of taxa included in this analysis with respective total intact ORs. Note this does not include all chemoreceptors, but just those within the OR Classes I and II multigene families. Numbers on the phylogeny correspond to a subset of the segmented brain and sensory regions from the soft tissue µCT-scans. Silhouettes were obtained from phylopic.org. Silhouettes and 3D reconstructions are not to scale and are enlarged for clarity. ^*Exact species for both genomic and phenotype data were not available. For Rallidae, G. okinawae was used for genomic data and P. carolina was used for the soft-tissue specimen. For Phalacrocorax, P. carbo was used for genomic data and P. auritus was used for the soft-tissue specimen. For Nothoprocta, N. pentlandii was used for morphology, and N. perdicaria was used for genomic data. Scale bars are 2 mm.

Figure 2.

(A) Simulated and observed gene tree branch lengths representing nucleotide substitutions per gene versus gene tree branch lengths representing codon substitutions per gene. For clarity, simulated values that were outside of observable data limits were removed from the plot (codon branch lengths >15 and nucleotide branch lengths >3). (B) Slopes of simulated (dashed lines) scenarios and observed scenarios (solid lines). Simulated points were removed. Slopes are plotted with observed points of Classes I and II ORs and non-OR genes. (C) Candidate genes under diversifying selection, determined from genes with codon to nucleotide branch ratios within 1 standard deviation of the mean of diversifying selection simulations. Colored red and blue points represent taxonomic group that genes belonged to, though diversifying selection was observed in all taxa. Only 2 non-OR genes fell within the cutoff. (D) Candidate genes under diversifying selection separated by gene family. Six OR subfamilies did not exhibit rates within our threshold. Note the change of axes limits from (A) and (C), zoomed in for clarity.

Figure 3.

Disparity of brain volumes through time. The mustard line is the volume of the entire brain and sensory regions, blue is the olfactory bulb scaled by total brain size, and red is the regions of the brain not associated with major primary sensory input: cerebrum, thalamus, midbrain, cerebellum, and medulla. The gray region of the figure is the confidence intervals from simulations modeling the total brain volume disparity as expected under Brownian motion and the dashed line is the mean value obtained from these simulations.