Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents

ヤマアラシ亜目における嗅覚・フェロモン・味覚受容体遺伝子の同調的進化～グルメな動物は鼻も良い！？～.京都大学プレスリリース. 2024-04-23.Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively

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

Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers

Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (∼ 4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser’s (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage

セキツイ ドウブツ ノ キュウカク ジュヨウ ニ カンスル イデンシ ノ シンカ ノ ケンキュウ : スイセイ テキオウ ノ ブンシ キバン ニ カンスル ヒトツ ノ コウサツ

京都大学0048新制・課程博士博士(理学)甲第13474号理博第3217号新制||理||1476(附属図書館)UT51-2007-T850京都大学大学院理学研究科生物科学専攻(主査)准教授 久保田 信, 教授 今福 道夫, 教授 白山 義久学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDA

Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene.

Odontocetes and mysticetes are two extant suborders of cetaceans. It is reported that the former have no sense of olfaction, while the latter can smell in air. To explain the ecological reason why mysticetes still retain their sense of smell, two hypotheses have been proposed - the echolocation-priority hypothesis, which assumes that the acquisition of echolocation causes the reduction of the importance of olfaction, and the filter-feeder hypothesis, which assumes that olfactory ability is important for filter-feeders to locate their prey because clouds of plankton give off a peculiar odor. The olfactory marker protein (OMP) is almost exclusively expressed in vertebrate olfactory receptor neurons, and is considered to play important roles in olfactory systems. In this study, full-length open reading frames of OMP genes were identified in 6 cetacean species and we analyzed the nonsynonymous to synonymous substitution rate ratio based on the maximum likelihood method. The evolutionary changes of the selective pressures on OMP genes did fit better to the filter-feeder hypothesis than to the echolocation-priority hypothesis. In addition, no pseudogenization mutations are found in all five odontocetes OMP genes investigated in this study. It may suggest that OMP retains some function even in 'anosmic' odontocetes

Supplementary Information for "Organization and distribution of glomeruli in the bowhead whale olfactory bulb"

<p>A STL-formatted image of the 3D bowhead whale olfactory bulb</p

Pairwise comparison of orthologous olfactory receptor genes between two sympatric sibling sea kraits of the genus Laticauda in Vanuatu.

Olfaction-based reproductive isolation is widely observed in animals, but little is known about the genetic basis of such isolation mechanisms. Two species of sibling amphibious sea snakes, Laticauda colubrina and L. frontalis live in Vanuatu sympatrically and syntopically, but no natural hybrids have been reported. Adult females of both taxa possess distinctive lipids in the skin, and male L. frontalis distinguishes conspecific females based on olfactory cues. To shed light on the molecular basis of the evolution of olfaction-based isolation mechanisms, olfactory receptor (OR) gene repertoires of both taxa were identified using pyrosequencing-based technology, and orthologous OR gene sets were identified. Few species-specific gene duplications or species-specific gene losses were found. However, the nonsynonymous-to-synonymous substitution rate ratio was relatively higher between orthologous OR genes of L. frontalis and L. colubrina, indicating that L. frontalis and L. colubrina have evolved to possess different olfactory senses. We suggest that L. frontalis and L. colubrina have evolved allopatrically, and this may be a byproduct of the allopatric evolution, and that this dissimilarity may function as a premating isolation barrier, since L. frontalis has returned to the ancestral range (Vanuatu)

Aquatic adaptation and the evolution of smell and taste in whales

鯨類の化学感覚能力の一端を解明. 京都大学プレスリリース. 2015-03-05.[Introduction]While olfaction is one of the most important senses in most terrestrial mammals, it is absent in modern toothed whales (Odontoceti, Cetacea). Furthermore, behavioral evidence suggests that gustation is very limited. In contrast, their aquatic sistergroup, baleen whales (Mysticeti) retain small but functional olfactory organs, and nothing is known about their gustation. It is difficult to investigate mysticete chemosensory abilities because experiments in a controlled setting are impossible. [Results]Here, we use the functional regionalization of the olfactory bulb (OB) to identify the loss of specific olfactory functions in mysticetes. We provide the whole-genome sequence of a mysticete and show that mysticetes lack the dorsal domain of the OB, an area known to induce innate avoidance behavior against odors of predators and spoiled foods. Genomic and fossil data suggest that mysticetes lost the dorsal domain of the OB before the Odontoceti-Mysticeti split. Furthermore, we found that all modern cetaceans are revealed to have lost the functional taste receptors. [Conclusion]These results strongly indicate that profound changes in the chemosensory capabilities had occurred in the cetacean lineage during the period when ancestral whales migrated from land to water

Animal cellulases with a focus on aquatic invertebrates

Cellulose is utilized as a nutritional source by various organisms. For a long time it was believed that only protozoa, bacteria, and fungi, in addition to plants and photosynthetic bacteria, are able to synthesize cellulases encoded by their own genes. However, the widespread distribution of cellulases throughout the animal kingdom has recently been recognized. Conventionally, animals digest cellulose utilizing cellulases derived from symbiotic bacteria in the digestive organs. However, recent molecular biological studies have shown that some cellulase genes are actually encoded on animal chromosomes. In addition, the homologous primary structure of cellulases obtained from various invertebrate phyla indicates the possible vertical transfer of the cellulase gene from ancient organisms that are now extinct. The results of studies on cellulases with unique enzymatic properties are expected to be applied to bioethanol production and aquaculture. In the present review, we describe cellulases, focusing primarily on aquatic invertebrates in which both endogenous and exogenous cellulases are involved in the breakdown of cellulose in the digestive organs