Biology subjects

Nikaido, M.

Publications and source records attributed to Nikaido, M..

10 recordsLinked to original sources

bioRxiv2026

Novel mechanisms of chemosensory adaptation to the cave environment

Smell allows animals to find food, avoid danger, and communicate through the binding of odorants to chemosensory receptors on olfactory sensory neurons. The vision-priority hypothesis predicts an antagonistic relationship between olfaction and vision, in which olfactory ability increases as visual acuity decreases along evolutionary lineages, a tradeoff that often occurs through expansion and contraction of chemosensory receptor gene families. The Mexican tetra (Astyanax mexicanus), a fish species with both sighted surface-dwelling and blind cave-dwelling populations, presents an ideal model for exploring the mechanisms underlying this tradeoff. Here we show that although cavefish can sense odorants at lower concentrations than surface fish, they do not have an expanded repertoire of chemosensory receptors, increased sensory neuron number or density, or enhanced expression of receptors compared to surface fish. Instead, cavefish have physiological adaptations to the olfactory epithelium, including more motile cilia and decreased flow rate through the olfactory pits. Pharmacological attenuation of flow rate in the olfactory pits in surface fish increased visits to the odorant source, suggesting that the reduced flow rate in cavefish is an adaptation leading to better foraging. This unexpected evolutionary path to enhanced olfaction as a compensation for loss of vision underscores the need for mechanistic understanding of comparative genomics.

evolutionary biology↗

bioRxiv2026

Evolutionary trajectories of teleost olfactory signaling genes shaped by long-term redundancy after whole-genome duplication

Whole-genome duplication (WGD) is a major evolutionary event that drives molecular and species diversification. However, few studies have traced how WGD has shaped the long-term functional evolution of individual genes. Here, we investigated the olfactory marker protein (omp) genes duplicated by the teleost-specific WGD ([~]300 million years ago) through phylogenetic, syntenic, expression, and promoter analyses. Our results suggest that the duplicated omp gene pair has retained redundancy over an extended evolutionary period, leading to both non- and sub-functionalization, thereby generating molecular diversity. Moreover, evolutionary analyses of the olfactory signal transduction cascade revealed prolonged redundancy across its components, likely constrained by gene dosage balance. These findings imply that WGD may have introduced unexpected diversity into the entire olfactory signaling machinery of teleosts through dosage-constrained functional divergence. HighlightsO_LITeleost-specific WGD generated duplicated omp genes that persisted for [~]300 million years. C_LIO_LIExtended redundancy in ompa/ompb led to both non- and sub-functionalization. C_LIO_LIOlfactory transduction genes also show long-term redundancy shaped by dosage constraints. C_LIO_LIWGD likely introduced diversification into teleost olfactory signaling via dosage constraints. C_LI

evolutionary biology↗

bioRxiv2024

Possible involvement of ghost introgressions in the striking diversity of V1R receptor genes in East African cichlids

Cichlids that have undergone adaptive radiation are genetically close but exhibit extreme ecological and morphological diversity, making them useful for understanding speciation mechanisms. Vomeronasal type 1 receptors (V1R) are highly conserved among teleost fish at the amino acid sequence level and believed to play a fundamental role in reproduction. We previously reported the surprisingly high sequence diversity of V1Rs among certain cichlid species, suggesting a possible role for V1Rs in their speciation. In this study, we investigated the process of evolutionary diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528 cichlid species, encompassing nearly all lineages. In the case of V1R2, two highly divergent alleles (1.17%: variant sites/CDS length) without recombination were preserved and shared among cichlids found in all of the East African Great Lakes. In the case of V1R6, numerous highly variable alleles that could be derived from multiple recombination events between two highly divergent alleles (1.39%: variant sites/CDS length) were found among the Lake Victoria cichlids. Additionally, we identified highly divergent alleles of V1R1 within the tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and Ectodini. Because one of the two divergent alleles of these V1Rs emerged rapidly during cichlid evolution, they are likely to have been derived from introgression. However, despite extensive investigations, we could not identify the source lineages for these introgressions, implying that they may have become extinct. This study revealed the potential role of introgression in explaining the remarkable diversity of V1Rs in East African cichlids.

evolutionary biology↗

bioRxiv2024

Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids

Cichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, "hypertrophied lip" has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.

evolutionary biology↗

bioRxiv2023

A severe bottleneck impacted the genomic structure of egg-eating cichlids

The explosive adaptive radiation of Haplochromine cichlids in Lake Victoria, East Africa, produced 500 endemic species within only 15,000 years. A paedophage or an egg-eater is considered a unique example of trophic adaptation. Many field studies reported that more than 200 cichlids have extinct due to the upsurge of Nile perch, a carnivorous species introduced to the lake in the 1950s. Especially, piscivorous cichlids like paedophages were critically damaged by Nile perch predation. Here, we performed a genome-wide evolutionary study of the paedophages in Lake Victoria to understand their past demographic events and phylogenetic relationships. We discovered evidence of a recent, short-period, and severe bottleneck in a paedophage "matumbi hunter". Interestingly, the signature of a strong bottleneck, as observed in matumbi hunter, was not detected in other species including paedophagus species. In addition, it was revealed that the population size of matumbi hunter started to decline 30 years ago and recover from 20 to 10 years ago, corresponding to the time of both disappearance and resurgence of Lake Victoria Haplochromines were reported. Although population structure analyses showed that matumbi hunter is composed of a unique genetic component, phylogenetic analyses supported its strong monophyly with other paedophagus species. These results suggest that the paedophages originated only once in Lake Victoria followed by the decline of genetic diversity in matumbi hunter. This study succeeded to demonstrate the demographic events triggered by invasive species and associated genomic consequences of the unique trophic group, promoting a holistic understanding of adaptive radiation.

evolutionary biology↗

bioRxiv2022

Plastic loss of motile cilia in the internal gills of Polypterus in response to high CO2 or terrestrial environments

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.

evolutionary biology↗

bioRxiv2021

Zebrafish pigment cells develop directly from persistent highly multipotent progenitors.

Neural crest cells (NCCs) are highly multipotent stem cells. A long-standing controversy exists over the mechanism of NCC fate specification, specifically regarding the presence and potency of intermediate progenitors. The direct fate restriction (DFR) model, based on early in vivo clonal studies, hypothesised that intermediates are absent and that migrating cells maintain full multipotency1-6. However, most authors favour progressive fate restriction (PFR) models, with fully multipotent early NCCs (ENCCs) transitioning to partially-restricted intermediates before committing to individual fates7-12. Here, single cell transcriptional profiling of zebrafish pigment cell development leads to us proposing a Cyclical Fate Restriction mechanism of NCC development that reconciles the DFR and PFR models. Our clustering of single NCC Nanostring transcriptional profiles identifies only broadly multipotent intermediate states between ENCCs and differentiated melanocytes and iridophores. Leukocyte tyrosine kinase (Ltk) marks the multipotent progenitor and iridophores, consistent with biphasic ltk expression13-15. Ltk inhibitor and constitutive activation studies support expression at an early multipotent stage, whilst lineage-tracing of ltk-expressing cells reveals their multipotency extends beyond pigment cell-types to neural fates. We conclude that pigment cell development does not involve a conventional PFR mechanism, but instead occurs directly and more dynamically from a broadly multipotent intermediate state.

developmental biology↗

bioRxiv2021

Neural activation in the olfactory epithelium of East African cichlid in response to odorant exposure

Fishes use olfaction to gain various 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 neural activation of olfactory sensory neurons (OSNs) in East African cichlids, 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 detection of conjugated steroids, known as pheromone candidates. We also found that V2Rs, the major expressed receptor in microvillous neurons exhibited differential responsiveness to amino acids, and further suggested that the cichlid-specific duplication of V2R led to ligand differentiation in cichlids by demonstrating a differential response to arginine. Finally, we established a nonlethal 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 odors and illuminates how olfaction has contributed to the diversification of cichlids by combining with phylogenetic studies of olfactory receptors gene evolutions.

neuroscience↗

bioRxiv2020

A unique neurogenomic state emerges after aggressive confrontations in males of the fish Betta splendens

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 brain-transcriptomic synchronization occurs in a pair-specific manner between two males of the fish Betta splendens during fighting, reflecting a mutual assessment process between them at the level of gene expression. Here we evaluated 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 unique and carryover hypotheses can be adapted to this system, in which changes in the expression of certain genes are unique to different fighting stages and in which the expression patterns of certain genes are transiently or persistently changed across all fighting stages. Interestingly, the specificity of the brain-transcriptomic synchronization of a pair during fighting was gradually lost after fighting ceased, because of the decrease in the variance in gene expression across all individuals, leading to the emergence of a basal neurogenomic state. Strikingly, this unique state was more basal than the state that existed in the before-fighting group and resulted in the reduced and consistent expression of genes across all individuals. In spite of the consistent and basal overall gene expression in each individual in this state, expression changes for genes related to metabolism, learning and memory, and autism still differentiated losers from winners. The fighting system using male B. splendens thus provides a promising platform for investigating neurogenomic states of aggression in vertebrates. Author summaryCompetitive interactions involve complex decision-making tasks that are shaped by mutual feedback between participants. When two animals interact, transcriptomes across their brains synchronize in a way that reflects how they assess and predict the others fighting ability and react to each others decisions. Here, we elucidated the gradual loss of brain-transcriptomic synchrony between interacting opponents after their interaction ceased, leading to the emergence of a basal neurogenomic state, in which the variations in gene expression were reduced to a minimum among all individuals. This basal neurogenomic state shares common characteristics with the hibernation state, which animals adopt to minimize their metabolic rates to cope with harsh environmental conditions. We demonstrated that this unique neurogenomic state, which is newly characterized in the present study, is composed of the expression of a unique set of genes, each of which was presumably minimally required for survival, providing a hypothesis that this state represents the smallest unit of neurogenomic activity for sustaining an active life.

molecular biology↗

bioRxiv2020

Conserved Keratin Gene Clusters in Ancient Fish: an Evolutionary Seed for Terrestrial Adaptation

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 krt18/krt8 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. HighlightsO_LITwo major keratin clusters are conserved from sharks to terrestrial vertebrates. C_LIO_LIAdult epidermis-specific keratins in amphibians stem from the two major clusters. C_LIO_LIA novel keratin gene subcluster was found in reedfish. C_LIO_LIAncestral krt18/krt8 gene sets were found in all vertebrates. C_LIO_LIFunctional diversification signatures were found in reedfish and amphibian keratins. C_LI

evolutionary biology↗