The Evolution Of Vertebrate Chemosensory Receptor Genes

Animal chemoreception mainly contains olfaction and taste, with functions conferred by olfactory and taste systems, respectively. The olfactory system is further divided into main olfactory system (MOS) and vomeronasal organ system (VNS). In this thesis, we reconstructed the evolutionary history of chemosensory receptor genes from both VNS and taste system in marine mammals, and discussed the associated ecological significances. Furthermore, we studied the complex evolutionary history of umami/sweet receptor genes in vertebrates.The recognition and transduction of vomeronasal signals require the involvement of many proteins such as VIRs, V2Rs and TRPC2. Their essential functions and exclusive expression in VNS make their corresponding coding genes VIRs, V2Rs and Trpc2good genetic markers for evolutionary studies of vomeronasal pheromone perception in vertebrates. Among these genetic markers, Trpc2has been proved to be particularly reliable, because overwhelming evidence has demonstrated that the molecular evolution of Trpc2is in accordance with the VNS functional evolution. In other words, an intact Trpc2indicates functional vomeronasal olfaction, whereas a Trpc2pseudogene indicates nonfunctional vomeronasal olfaction. In this work, with a combination of newly sequenced and previously published Trpc2genes, we obtained9representative species of marine mammals, and conducted an evolutionary analysis on the relation between Trpc2functionality and several ecological factors. We tested three hypotheses:the vision replacement hypothesis, the hypothesis of correlation between Trpc2functionality and diet selection, the hypothesis of correlation between Trpc2functionality and copulation environment. Our results showed that the first hypothesis is not valid in this case. For example, dichromatic vision exists in West Indian manatee, polar bear and otter, Trpc2is a pseudogene in West Indian manatee and otter, but is intact in polar bear. On the relationship between feeding ecology and the functionality of Trpc2, the Trpc2functionality varies in species which have similar diet preferences, thus the second hypothesis doesn't hold. Interestingly, the third hypothesis is supported by our data. Specifically, Trpc2is pseudogenized in all the marine mammals copulating underwater while it is intact in the marine species which copulate on land. Thus, we proposed a new hypothesis stating that, the selection of mating substrates may be the driving force underlying the evolution of pheromonal olfaction functionality in marine mammals.In the study of taste perception in whales, we sequenced3umami/sweet taste and10bitter taste receptor genes in6Odontoceti and5Mysticeti species, respectively, and sequenced the taste signal transduction pathway gene Calhml from11species of cetacean representatives. Meanwhile, we analyzed three publicly available whale genome sequences to identify the genes responsible for5taste modalities and3critical genes in taste signal transduction pathway, Calhml, Trpm5and Plc?2. Our results showed that, the sweet/umami/bitter taste receptor genes examined were pseudogenized, and most of the frame-shifting mutations were shared between toothed and baleen whales, which indicated that sweet/umami/bitter taste function had been lost in the common ancestor of whales. Furthermore, we found that the sour taste gene Pkd2l1was pseudogenized while salty taste receptor genes were intact in the three whales with available genome sequences. Consistent to the massive losses of taste receptor genes, we also discovered that, Calhml and Plc?2had undergone relaxation of functional constraints in the common ancestor of whales, and Trpm5had undergone relaxation of functional constraints after the divergence of whales. Together, our data indicates that the high concentration of salt in the ocean, the feeding behavior of swallowing whole without chewing, and a dietary switch from plant to meat in the whale ancestor may account for the massive losses of taste receptor genes in whales. By contrast, the maintenance of salty taste is not unexpected. As sea-living organisms, whales are well adapted to their hyperosmotic environment; osmoregulation is required to maintain the ENaC function that regulates sodium ion fluxes and thus retains the salty taste.On the relationship between diet and the evolution of taste receptor genes, previous studies demonstrated that there was a concordance between Taslrs (the receptor genes for umami/sweet, Taslrl, Tas1r2and Tas1r3) functionality and the preference or indifference to certain foods in animals. However, this concordance between genetic and behavioral evidence has been challenged recently. To probe the generality of the consistency between Taslr functionality and feeding ecology, extensive sampling across vertebrates is required. By analyzing48currently available vertebrate genome sequences, we found the inconsistency between Taslr functionality and feeding ecology. For example, Taslr2is absent from genomes of chicken, clawed frog, horse and pig, despite distinct dietary preferences. Furthermore, nucleotide insertions or deletions were detected in a number of species, including mouse lemur, tarsier, kangaroo rat, tree shrew, pig, hyrax, tenrec, platypus, and wallaby (Taslrl); pika, tarsier, hyrax, and elephant (Taslrl); alpaca, marmoset, hyrax, and wallaby (Taslr3). Combining with published findings that argued losses of tastes in other vertebrates, we concluded that there was not a common dietary factor responsible for the loss of a specific taste. Therefore, the evolution of the Taslrs is more complex than we previously thought. For example, umami taste is absent from the piscivorous (dolphin), omnivorous (pig), herbivorous (kangaroo rat) animals. Moreover, we suggest that the sequences identified from draft genome sequences are not sufficient to conclude whether a gene is intact or pseudogenized, because numerous sequencing errors or bias could have occurred in the publicly available genome database. For example, indels of the megabat Taslrl inferred from its draft genome are quite different from those observed from newly sequencing result. In addition, gene annotations in the genome database are sometimes incorrect. For example, the dolphin Taslr2is annotated as an intact gene in Ensembl, but in fact it is a pseudogene inferred from its draft genome. All the results reported here suggest that, the evolution of Taslrs is more complex than we previously appreciated and we should be more cautious for analyzing sequences predicted from draft genome sequences.