Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes

Abstract

Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully aquatic and amphibious sea snakes and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of the olfactory receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number of OR genes has decreased in sea snakes, and fully aquatic species lost MOS which is responsible for detecting airborne odours. By contrast, sea snakes including fully aquatic species retain a number of V2R genes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully aquatic species, but their residual olfactory capability is distinct from that of other fully aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully aquatic snakes, implying their importance in understanding the process of aquatic adaptation.

Keywords: OR; TAAR; V1R; V2R; amphibious; fully aquatic.

Figure 1.

A schematic view of the evolution of terrestrial adaptation of vertebrates and three major groups of extant fully aquatic amniotes. Branch colour indicates representative lifestyle in each branch (brown, terrestrial; purple, amphibious; blue, fully aquatic), and circles in ancestral nodes represent lifestyles at these points in evolution. Extinct amphibious species are also shown for cetaceans (Amburocetus [3]) and sirenians (Pezosiren [4]). (Online version in colour.)

Figure 2.

Phylogenetic relationship of squamates analysed in this study, and the numbers of olfactory GPCR genes identified in the genome assemblies of these species. Red, pink, and grey bars indicate the numbers of intact genes, truncated genes, and pseudogenes, respectively. Approximate divergence time follows Sanders et al. [–8] and Kim et al. [35]. *Only the third exon of the V2R genes was identified and analysed. **The OR gene repertoire of a green anole is taken from Vandewege et al. [36]. (Online version in colour.)

Figure 3.

Evolution of the gain and loss of OR and V2R genes in snakes. Evolutionary changes in the number of intact OR (a) and V2R (b) genes are estimated using the reconciled tree method [37]. Python intact ORs identified by Vandewege et al. [36] were included in the dataset for this calculation. (Online version in colour.)

Figure 4.

Expression levels of the OR and V2R genes in the three potential olfactory organs and the liver. Each dot represents a single OR/V2R gene identified in this study, and the y-axis shows normalized gene expression levels in FPKM values. Red, pink, and black dots represent intact genes, truncated genes, and pseudogenes, respectively. The mean FPKM values of intact, truncated, and pseudogenes in each organ are shown as bars in the background. Difference of the mean FPKM values of intact OR/V2R genes between each chemosensory organ and a control (liver) is calculated, and chemosensory organs with obviously (greater than 1) and significantly (p < 0.01, paired t-test) larger FPKM values compared to the control are shown with asterisks (see electronic supplementary material, table S5 for details). Arrows indicate an intact OR gene expressed in the tongue. Approximate position of each organ in a fully aquatic hydrophiin (H. melanocephalus) is also shown. (Online version in colour.)