Language：English   Publishing type：Research paper (scientific journal)  

The olfactory organ of tetrapods, with few exceptions, comprises the main and accessory organs: olfactory epithelium (OE) and vomeronasal organ (VNO). Unlike tetrapods, teleost fish lack a VNO. However, lungfish, a type of sarcopterygian fish closely related to tetrapods, possesses a lamellar OE similar to the OE of teleosts and a recess epithelium (RecE) resembling the amphibian VNO. The RecE has been hypothesized as a primordial VNO. Olfactory receptors in tetrapods are distinctively expressed in the OE and VNO. For instance, type 2 vomeronasal receptors (V2Rs) in Xenopus are categorized into those exclusively expressed in the OE and those solely expressed in the VNO. It remains unclear whether V2Rs are differentially expressed between the lamellar OE and RecE in lungfish. This study investigated V2R expression in the lamellar OE and RecE of the African lungfish, Protopterus annectens. P. annectens V2Rs were categorized into three groups: those exclusively expressed in the lamellar OE, those exclusively expressed in the RecE, and those expressed in both the lamellar OE and RecE. V2Rs exclusively expressed in the RecE and those expressed in both the lamellar OE and RecE formed a distinct clade in the phylogenetic tree, whereas others were solely expressed in the lamellar OE. These findings suggest that lungfish V2R expression represents an intermediate stage toward complete segregation between V2Rs expressed in the OE and those expressed in the VNO.

DOI： 10.1007/s00441-024-03918-2

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in four species, including two paedophages, which began during the 1970s–1980s, and population size rebounded during the 1990s-2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines’ disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the four species that likely experienced bottleneck, Haplochromis sp. ‘matumbi hunter,’ a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the five paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

DOI： 10.1093/molbev/msae093

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Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Baleen whales (Mysticeti) possess the necessary anatomical structures and genetic elements for olfaction. Nevertheless, the olfactory receptor gene (OR) repertoire has undergone substantial degeneration in the cetacean lineage following the divergence of the Artiodactyla and Cetacea. The functionality of highly degenerated mysticete ORs within their olfactory epithelium remains unknown. In this study, we extracted total RNA from the nasal mucosae of common minke whales (Balaenoptera acutorostrata) to investigate ORs’ localized expression. All three sections of the mucosae examined in the nasal chamber displayed comparable histological structure. However, the posterior portion of the frontoturbinal region exhibited notably high OR expression. Neither the olfactory bulb nor the external skin exhibited the expression of these genes. Although this species possesses four intact non-class-2 ORs, all the ORs expressed in the nasal mucosae belong to class-2, implying the loss of aversion to specific odorants. These anatomical and genomic analyses suggest that ORs are still responsible for olfaction within the nasal region of baleen whales, enabling them to detect desirable scents such as prey and potential mating partners.

DOI： 10.3390/ijms25073855

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.tice.2023.102255

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.acthis.2023.152078

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Abstract

The evolutionary transition of vertebrates from water to land during the Devonian period was accompanied by major changes in animal respiratory systems in terms of physiology and morphology. Indeed, the fossil record of the early tetrapods has revealed the existence of internal gills, which are vestigial fish‐like traits used underwater. However, the fossil record provides only limited data on the process of the evolutionary transition of gills from fish to early tetrapods. This study investigated the gills of Polypterus senegalus, a basal ray‐finned/amphibious fish which shows many ancestral features of stem Osteichthyes. Based on scanning electron microscopy observations and transcriptome analysis, the existence of motile cilia in the gills was revealed which may create a flow on the gill surface leading to efficient ventilation or remove particles from the surface. Interestingly, these cilia were observed to disappear after rearing in terrestrial or high CO₂ environments, which mimics the environmental changes in the Devonian period. The cilia re‐appeared after being returned to the original aquatic environment. The ability of plastic changes of gills in Polypterus revealed in this study may allow them to survive in fluctuating environments, such as shallow swamps. The ancestor of Osteichthyes is expected to have possessed such plasticity in the gills, which may be one of the driving forces behind the transition of vertebrates from water to land.

DOI： 10.1002/ece3.9964

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Lungfish are the most closely related fish to tetrapods. The olfactory organ of lungfish contains lamellae and abundant recesses at the base of lamellae. Based on the ultrastructural and histochemical characteristics, the lamellar olfactory epithelium (OE), covering the surface of lamellae, and the recess epithelium, contained in the recesses, are thought to correspond to the OE of teleosts and the vomeronasal organ (VNO) of tetrapods. With increasing body size, the recesses increase in number and distribution range in the olfactory organ. In tetrapods, the expression of olfactory receptors is different between the OE and VNO; for instance, the type 1 vomeronasal receptor (V1R) is expressed only in the OE in amphibians and mainly in the VNO in mammals. We recently reported that V1R-expressing cells are contained mainly in the lamellar OE but also rarely in the recess epithelium in the olfactory organ of lungfish of approximately 30 cm body length. However, it is unclear whether the distribution of V1R-expressing cells in the olfactory organ varies during development. In this study, we compared the expression of V1Rs in the olfactory organs between juveniles and adults of the African lungfish Protopterus aethiopicus and South American lungfish, Lepidosiren paradoxa. The density of V1R-expressing cells was higher in the lamellae than in the recesses in all specimens evaluated, and this pattern was more pronounced in juveniles than adults. In addition, the juveniles showed a higher density of V1R-expressing cells in the lamellae compared with the adults. Our results imply that differences in lifestyle between juveniles and adults are related to differences in the density of V1R-expressing cells in the lamellae of lungfish.

DOI： 10.1186/s40851-023-00202-z

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Other Link： https://link.springer.com/article/10.1186/s40851-023-00202-z/fulltext.html

Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Genetics Society of Japan  

DOI： 10.1266/ggs.23-00188

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Genetics Society of Japan  

DOI： 10.1266/ggs.23-00024

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2R repertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from “fish-type” to “tetrapod-type”, we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897 V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2R gene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both “fish-type” and “tetrapod-type”, suggesting that the common ancestor of Osteichthyes possess “tetrapod-type” V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish may provide insight into how the olfaction of osteichthyan ancestors adapt from water to land.

DOI： 10.1038/s41598-022-10428-0

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Other Link： https://www.nature.com/articles/s41598-022-10428-0

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Company of Biologists  

ABSTRACT

Fishes use olfaction to gain varied information vital for survival and communication. To understand biodiversity in fishes, it is important to identify what receptors individual fish use to detect specific chemical compounds. However, studies of fish olfactory receptors and their ligands are still limited to a few model organisms represented primarily by zebrafish. Here, we tested the c-fos expression of olfactory sensory neurons (OSNs) in an East African cichlid, the most diversified teleost lineage, by in situ hybridization with a c-fos riboprobe. We confirmed that microvillous neurons contributed the most to the detection of amino acids, as in other fishes. Conversely, we found that ciliated neurons contributed the most to the detection of conjugated steroids, known as pheromone candidates. We also found that V2Rs, the major receptor type in microvillous neurons, exhibited differential responsiveness to amino acids, and further suggest that the cichlid-specific duplication of V2R led to ligand differentiation by demonstrating a differential response to arginine. Finally, we established a non-lethal method to collect cichlid urine and showed how various OSNs, including V1R+ neurons, respond to male urine. This study provides an experimental basis for understanding how cichlids encode natural odours, which ultimately provides insight into how olfaction has contributed to the diversification of cichlids.

DOI： 10.1242/jeb.244737

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Other Link： https://journals.biologists.com/jeb/article-pdf/doi/10.1242/jeb.244737/2201340/jeb244737.pdf

Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cne.25416

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cne.25416

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Currently, the insertions of SINEs (and other retrotransposed elements) are regarded as one of the most reliable synapomorphies in molecular systematics. The methodological mainstream of molecular systematics is the calculation of nucleotide (or amino acid) sequence divergences under a suitable substitution model. In contrast, SINE insertion analysis does not require any complex model because SINE insertions are unidirectional and irreversible. This straightforward methodology was named the “SINE method,” which resolved various taxonomic issues that could not be settled by sequence comparison alone. The SINE method has challenged several traditional hypotheses proposed based on the fossil record and anatomy, prompting constructive discussions in the Evo/Devo era. Here, we review our pioneering SINE studies on salmon, cichlids, cetaceans, Afrotherian mammals, and birds. We emphasize the power of the SINE method in detecting incomplete lineage sorting by tracing the genealogy of specific genomic loci with minimal noise. Finally, in the context of the whole-genome era, we discuss how the SINE method can be applied to further our understanding of the tree of life.

DOI： 10.3390/genes13060989

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Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.

DOI： 10.3390/genes13050804

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Fish possess one olfactory organ called the olfactory epithelium (OE), by which various chemical substances are detected. On the other hand, tetrapods possess two independent olfactory organs called the main olfactory epithelium (MOE) and vomeronasal organ (VNO), each of which mainly detects general odorants and pheromones, respectively. Traditionally, the VNO, so-called concentrations of vomeronasal neurons, was believed to have originated in tetrapods. However, recent studies have identified a primordial VNO in lungfish, implying that the origin of the VNO was earlier than traditionally expected. In this study, we examined the presence/absence of the VNO in the olfactory organ of bichir (Polypterus senegalus), which is the most ancestral group of extant bony vertebrates. In particular, we conducted a transcriptomic evaluation of the accessory olfactory organ (AOO), which is anatomically separated from the main olfactory organ (MOO) in bichir. As a result, several landmark genes specific to the VNO and MOE in tetrapods were both expressed in the MOO and AOO, suggesting that these organs were not functionally distinct in terms of pheromone and odorant detection. Instead, differentially expressed gene (DEG) analysis showed that DEGs in AOO were enriched in genes for cilia movement, implying its additional and specific function in efficient water uptake into the nasal cavity other than chemosensing. This transcriptomic study provides novel insight into the long-standing question of AOO function in bichir and suggests that VNO originated in the lineage of lobe-finned fish during vertebrate evolution.

DOI： 10.1186/s40851-022-00189-z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Background

Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens, across different stages of fighting interactions, fighting opponents suffer from various stressors, especially from the great demand for oxygen. Using RNA sequencing, we profiled differential alternative splicing (DAS) events in the brains of fish collected before fighting, during fighting, and after fighting to study the involvement of alternative splicing (AS) in the response to stress during the fight.

Results

We found that fighting interactions induced the greatest increase in AS in the ‘during-fighting’ fish, followed by that of the ‘after-fighting’ fish. Intron retention (IR) was the most enriched type among all the basic AS events. DAS genes were mainly associated with synapse assembly, ion transport, and regulation of protein secretion. We further observed that IR events significantly differentiated between winners and losers for 19 genes, which were associated with messenger RNA biogenesis, DNA repair, and transcription machinery. These genes share many common features, including shorter intron length and higher GC content.

Conclusions

This study is the first comprehensive view of AS induced by fighting interactions in a fish species across different stages of those interactions, especially with respect to IR events in winners and losers. Together, these findings facilitate future investigations into transcriptome complexity and AS regulation in response to stress under the context of aggression in vertebrates.

DOI： 10.1186/s12864-022-08609-2

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Other Link： https://link.springer.com/article/10.1186/s12864-022-08609-2/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

Siamese fighting fish Betta splendens are notorious for their aggressiveness and males of this fish have been widely used to study aggression. However, an understanding of brain transcriptome signature associated with aggression in the context of male-male interaction in this fish remains to be understood. Herein, RNA-Seq transcriptome data from 37 brains samples collected at different fighting stages are described. These brain samples were collected before fighting (B), during fighting (D20 and D60), and after fighting (A0 and A30). The raw data were analyzed for differential gene expression using edgeR package in R. A criterion of FDR cut-off ≤ 0.05 and an absolute fold change (FC) of 0 or greater were used to identify top upregulated and downregulated genes in fighting groups (D20, D60, A0, and A30) relative to non-fighting group (B). The data presented hereafter enable fundamental studies on genes and molecular events mediating aggressive behavior in this fish and will lay a valuable foundation for future research on the aggression of vertebrates.

DOI： 10.1016/j.dib.2021.107448

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Research Square Platform {LLC}  

<jats:title>Abstract</jats:title>
<jats:p>The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2Rrepertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from “fish-type” to “tetrapod-type”, we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2Rgene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both “fish-type” and “tetrapod-type”, suggesting that the common ancestor of Osteichthyes possess “tetrapod-type” V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish illuminates the process of how the osteichthyan ancestors adapt from water to land.</jats:p>

DOI： 10.21203/rs.3.rs-504504/v1

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>
The cichlids of Lake Victoria are a textbook example of adaptive radiation, as &amp;gt; 500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, Haplochromis sauvagei and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.

DOI： 10.1093/molbev/msab084

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

Territorial defense involves frequent aggressive confrontations with competitors, but little is known about how brain-transcriptomic profiles change between individuals competing for territory establishment. Our previous study elucidated that when two fish Betta splendens males interact, transcriptomes across their brains synchronize in a way that reflects a mutual assessment process between them at the gene expression level. Here we aim to evaluate how the brain-transcriptomic profiles of opponents change immediately after shifting their social status (i.e., the winner/loser has emerged) and 30 min after this shift. We showed that changes in the expression of certain genes are unique to different fighting stages and the expression patterns of certain genes are transiently or persistently changed across all fighting stages. These brain transcriptomic responses are in accordance with behavioral changes across the fight. Strikingly, the specificity of the brain-transcriptomic synchronization of a pair during fighting was gradually lost after fighting ceased, leading to the emergence of a basal neurogenomic state in which the changes in gene expression were reduced to minimum and consistent across all individuals. This state shares common characteristics with the hibernation state that animals adopt to minimize their metabolic rates to save energy. Interestingly, expression changes for genes related to metabolism, autism spectrum disorder, and long-term memory still differentiated losers from winners. Together, the fighting system using male B. splendens provides a promising platform for investigating neurogenomic states of aggression in vertebrates.

DOI： 10.1016/j.gene.2021.145601

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution^1,2. Here we generate and analyse reference genomes of the platypus (<italic>Ornithorhynchus anatinus</italic>) and echidna (<italic>Tachyglossus aculeatus</italic>), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.

DOI： 10.1038/s41586-020-03039-0

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Other Link： http://www.nature.com/articles/s41586-020-03039-0

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

<title>Abstract</title>Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. In terrestrial vertebrates, the keratin genes form two major clusters, clusters 1 and 2, each of which is dominated by type I and II keratin genes. By contrast, such clusters are not observed in teleost fish. Although the diversification of keratins is believed to have made a substantial contribution to terrestrial adaptation, its evolutionary process has not been clarified. Here, we performed a comprehensive genomic survey of the keratin genes of a broad range of vertebrates. As a result, we found that ancient fish lineages such as elephant shark, reedfish, spotted gar, and coelacanth share both keratin gene clusters. We also discovered an expansion of keratin genes that form a novel subcluster in reedfish. Syntenic and phylogenetic analyses revealed that two pairs of <italic>krt18</italic>/<italic>krt8</italic> keratin genes were shared among all vertebrates, thus implying that they encode ancestral type I and II keratin protein sets. We further revealed that distinct keratin gene subclusters, which show specific expressions in the epidermis of adult amphibians, stemmed from canonical keratin genes in non-terrestrial ancestors. Molecular evolutionary analyses suggested that the selective constraints were relaxed in the adult epidermal subclusters of amphibians as well as the novel subcluster of reedfish. The results of the present study represent the process of diversification of keratins through a series of gene duplications that could have facilitated the terrestrial adaptation of vertebrates.

<sec><title>Highlights</title><list list-type="bullet"><list-item>Two major keratin clusters are conserved from Chondrichthyes to terrestrial vertebrates.

</list-item><list-item>Adult epidermis-specific keratins in amphibians stem from the two major clusters.

</list-item><list-item>A novel keratin gene subcluster was found in reedfish.

</list-item><list-item>Ancestral <italic>krt18</italic>/<italic>krt8</italic> gene sets were found in all vertebrates.

</list-item><list-item>Functional diversification signatures were found in reedfish and amphibian keratins.

</list-item></list></sec>

DOI： 10.1016/j.ygeno.2020.11.008

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>
The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.

DOI： 10.1093/dnares/dsaa021

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Other Link： http://academic.oup.com/dnaresearch/article-pdf/27/4/dsaa021/33860808/dsaa021.pdf

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>
The vomeronasal organ (VNO) plays a key role in sensing pheromonal cues, which elicits social and reproductive behaviors. Although the VNO is highly conserved across mammals, it has been lost in some species that have evolved alternate sensing systems during diversification. In this study, we investigate a newly identified VNO-specific gene, ancV1R, in the extant 261 species of mammals to examine the correlation between genotype (ancV1R) and phenotype (VNO). As a result, we found signatures for the relaxation of purifying selection (inactivating mutations and the elevation of dN/dS) on ancV1Rs in VNO-lacking mammals, such as catarrhine primates, cetaceans, the manatees, and several bat lineages, showing the distinct correlation between genotype and phenotype. Interestingly, we further revealed signatures for the relaxation of purifying selection on ancV1R in true seals, otters, the fossa, the owl monkey, and alcelaphine antelopes in which the existence of a functional VNO is still under debate. Our additional analyses on TRPC2, another predictive marker gene for the functional VNO, showed a relaxation of purifying selection, supporting the possibility of VNO loss in these species. The results of our present study invite more in-depth neuroanatomical investigation in mammals for which VNO function remains equivocal.

DOI： 10.1093/gbe/evaa082

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Other Link： http://academic.oup.com/gbe/article-pdf/12/6/766/33381362/evaa082.pdf

Language：English   Publishing type：Research paper (scientific journal)  

The biodiversity and taxonomy of colonial volvocine green algae are important in ancient lakes in tropical regions. However, few taxonomic studies of these algae have been conducted in African ancient lakes. Here, we describe two species of colonial volvocine green algae in cultures originating from water samples from Lake Victoria, an ancient lake in Africa. One was identified as an undescribed morphological species of Eudorina; E. compacta sp. nov. This new species can be distinguished from other Eudorina species by its compactly arranged vegetative cells that form a hollow ellipsoidal colony. The other was identified as Colemanosphaera charkowiensis. The genus Colemanosphaera is new to Africa.

DOI： 10.1371/journal.pone.0224269

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Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

The vomeronasal organ (VNO) plays a key role in sensing pheromonal cues, which elicit innate responses and induce social and sexual behaviors. The vomeronasal receptor 1 genes, V1Rs, encode members of a pheromone receptor family that are mainly expressed in the VNO. Previous studies have revealed that the V1R family shows extraordinary variety among mammalian species owing to successive gene gains and losses. Because species-specific pheromonal interaction may facilitate species-specific reproductive behaviors, understanding the evolution of V1Rs in terms of their origin, repertoire and phylogeny should provide insight into the mechanisms of animal diversification. Here I summarize recent studies about the V1R family from its initial discovery in the rat genome to extensive comparative analyses among vertebrates. I further introduce our recent findings for V1Rs in a broad range of vertebrates, which reveal unexpected diversity as well as shared features common among lineages.

DOI： 10.1266/ggs.19-00009

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Language：English   Publishing type：Research paper (scientific journal)  

BACKGROUND: The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. RESULTS: Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. CONCLUSIONS: These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.

DOI： 10.1186/s12862-019-1387-2

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Pheromones are crucial for eliciting social and sexual behaviors in diverse animal species. The vomeronasal receptor type-1 (V1R) genes, encoding members of a pheromone receptor family, are highly variable in number and repertoire among mammals due to extensive gene gain and loss. Here, we report a novel pheromone receptor gene belonging to the V1R family, named ancient V1R (ancV1R), which is shared among most Osteichthyes (bony vertebrates) from the basal lineage of ray-finned fishes to mammals. Phylogenetic and syntenic analyses of ancV1R using 115 vertebrate genomes revealed that it represents an orthologous gene conserved for >400 My of vertebrate evolution. Interestingly, the loss of ancV1R in some tetrapods is coincident with the degeneration of the vomeronasal organ in higher primates, cetaceans, and some reptiles including birds and crocodilians. In addition, ancV1R is expressed in most mature vomeronasal sensory neurons in contrast with canonical V1Rs, which are sparsely expressed in a manner that is consistent with the "one neuron-one receptor" rule. Our results imply that a previously undescribed V1R gene inherited from an ancient Silurian ancestor may have played an important functional role in the evolution of vertebrate vomeronasal organ.

DOI： 10.1093/molbev/msy186

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Pheromones are crucial for eliciting innate responses and inducing social and sexual behaviors in mammals. The vomeronasal receptor 1 genes, V1Rs, encode members of a pheromone receptor family that are mainly expressed in the vomeronasal organ (VNO). The V1R family shows extraordinary variety in gene number among vertebrates owing to successive gene gains and losses during evolution. Such diversity is believed to reflect a degree of dependence on the VNO. We investigated V1R evolution in primate lineages closely related to humans because these VNOs show a trend toward degeneration. We performed extensive phylogenetic analyses for V1Rs from a broad range of primate species. Although the decline of intact genes was evident in anthropoids (hominoids, Old World monkeys and New World monkeys), we found that a certain number of intact genes persist in New World monkeys. In one New World monkey species, the common marmoset (Callithrix jacchus), we examined seven putatively functional V1Rs using in situ hybridization and reverse transcription-PCR. Based on their mRNA expression patterns in the VNO and other organs, two types of V1Rs emerged: the canonical class with VNO-specific expression, and a second group having more ubiquitous expression in various organs as well as VNO. Furthermore, phylogenetic analysis revealed that the class with the more widespread expression had been retained longer in evolution than the VNO-specific type. We propose that the acquisition of a novel non-VNO-related function(s) may have led to the survival of a small but persistent number of V1Rs in anthropoid primates.

DOI： 10.1016/j.gene.2017.11.048

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DOI： 10.1111/1755-0998.12690

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DOI： 10.1186/s12862-015-0530-y

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DOI： 10.1016/j.gene.2015.01.057

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DOI： 10.1038/nature13726

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/gbe/evu086

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DOI： 10.1016/j.ympev.2013.06.007

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DOI： 10.1101/gr.158105.113

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DOI： 10.1093/gbe/evt041

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DOI： 10.1016/j.gene.2012.05.047

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DOI： 10.1016/j.gene.2012.03.002

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DOI： 10.1073/pnas.1115675108

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DOI： 10.1016/j.gene.2009.11.005

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DOI： 10.1093/molbev/msp252

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DOI： 10.1016/j.gene.2009.10.002

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DOI： 10.1186/1471-2148-9-233

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DOI： 10.1016/j.gene.2009.01.014

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DOI： 10.1016/j.gene.2006.12.040

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DOI： 10.1016/j.ympev.2006.08.005

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DOI： 10.1007/s00335-007-9000-1

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DOI： 10.1016/j.ympev.2006.03.032

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DOI： 10.1016/j.gene.2006.05.003

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DOI： 10.1266/ggs.81.181

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DOI： 10.1093/molbev/msj071

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DOI： 10.1016/j.ympev.2005.10.018

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DOI： 10.1016/j.gene.2005.09.042

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DOI： 10.1080/10635150590905939

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DOI： 10.1093/molbev/msh069

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DOI： 10.1385/1-59259-755-6:189

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DOI： 10.1093/molbev/msg187

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DOI： 10.1016/S1055-7903(03)00120-9

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DOI： 10.1016/S1055-7903(03)00035-6

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DOI： 10.1016/S1055-7903(03)00121-0

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DOI： 10.1266/ggs.78.107

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DOI： 10.1007/s00239-002-2326-0

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DOI： 10.1007/s002390010241

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DOI： 10.1007/s0033501-1015-4

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DOI： 10.1093/oxfordjournals.molbev.a026242

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DOI： 10.1093/oxfordjournals.molbev.a026194

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DOI： 10.1093/oxfordjournals.molbev.a025997

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J-GLOBAL

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J-GLOBAL

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Language：English   Publishing type：Research paper, summary (international conference)  

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Language：Japanese  

CiNii Books

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Language：Japanese   Publisher：エヌ・ティー・エス  

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Language：Japanese   Publisher：エヌ・ティー・エス  

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Language：English   Publishing type：Research paper, summary (international conference)  

DOI： 10.1016/j.neures.2009.09.1170

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DOI： 10.1016/j.gene.2007.10.008

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DOI： 10.1016/j.gene.2007.06.003

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DOI： 10.1093/molbev/msi179

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Language：Japanese   Publisher：Palaeontological Society of Japan  

Baleen whales (suborder Mysticeti) comprise eleven extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships still remain confusing. SINE (short interspersed repetitive element) insertion data are now regarded as almost ideal shared derived characters at the molecular level, and we have applied this method to this problem. Here, we successfully reconstruct the phylogenetic relationships of these whales by characterizing 40 informative SINE loci. One of the intriguing conclusions is that balaenopterids and eschrichtiids radiated very rapidly during a very short evolutionary period. During this period, when newly inserted SINE loci retained ancestral polymorphisms, speciation occurred and these SINEs were sorted incompletely into each lineage, thus resulting in inconsistencies regarding the presence or absence of the SINE. This is in sharp contrast to the phylogeny of toothed whales, for which no SINE inconsistencies have been found. Furthermore, we found monophyletic groupings between humpback and fin whales, and also between (sei + Bryde's) and blue whales, both of which have not previously been recognized. The comprehensive SINE insertion data, together with the mitochondrial DNA phylogeny that was recently completed, provide a nearly complete picture of the evolutionary history of baleen whales.

DOI： 10.14825/kaseki.77.0_22

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DOI： 10.1016/j.ympev.2003.09.005

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DOI： 10.1093/molbev/msg052

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DOI： 10.1016/S0378-1119(00)00427-3

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Language：Japanese   Publisher：岩波書店  

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Venue：中央大学  

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Venue：東京工業大学  

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Venue：盛岡市  

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Venue：東京慈恵会医科大学  

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Venue：箱根市  

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Venue：箱根市  

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Venue：高槻・現代劇場，高槻市  

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Venue：高槻・現代劇場，高槻市  

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Venue：筑波大学  

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Venue：慶応大学  

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Venue：生命の星・地球博物館、小田原市  

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Venue：東京工業大学  

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Venue：首都大学東京  

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Venue：東京工業大学  

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Venue：東京工業大学  

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Venue：東京工業大学  

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Venue：東京大学  

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Venue：東京慈恵会医科大学  

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Venue：北九州市立自然史・歴史博物館  

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Language：Japanese   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Symposium, workshop panel (nominated)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

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Language：Japanese   Presentation type：Symposium, workshop panel (nominated)  

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Language：Japanese   Presentation type：Poster presentation  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Venue：基礎生物学研究所，岡崎市  

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Language：Japanese   Presentation type：Poster presentation  

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Venue：東京慈恵会医科大学  

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Venue：東京大学  

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Venue：東京大学  

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Venue：東京大学  

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Language：Japanese   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Venue：富山県民会館  

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Venue：神戸国際会議場，神戸市  

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