Publications by authors named "Jun Kitano"

Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and the capability of organisms to utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes.

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The pituitary gland is a key endocrine gland with various physiological functions including metabolism, growth, and reproduction. It comprises several distinct cell populations that release multiple polypeptide hormones. Although the major endocrine cell types are conserved across taxa, the regulatory mechanisms of gene expression and chromatin organization in specific cell types remain poorly understood.

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In most fishes, the number of offspring increases with maternal body size. Although this size-fecundity relationship often varies among species as a result of the coevolution of life-history traits, the genetic basis of such size-fecundity relationships remains unclear. We explored the genetic basis underlying this size-fecundity relationship in two small medaka species, Oryzias latipes and O.

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Article Synopsis
  • Many animals exhibit sexual dimorphism, showing distinct phenotypic differences between males and females, particularly in certain species of insects like beetles, which have developed "weapon traits" such as large horns and mandibles.
  • Previous research has indicated that gene expression specific to sex is crucial for the development of these traits, yet the role of the Y-chromosome in this process has not been thoroughly explored.
  • In this study, using stag beetles, researchers found that males lacking a Y-chromosome can still develop male-specific traits, indicating that the Y-chromosome is not essential for the expression of these weapon traits.
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  • Cis-regulatory mutations play a key role in phenotypic evolution, but identifying their locations in non-coding regions (like promoters and enhancers) is difficult, leading to fewer known examples compared to amino acid-altering mutations.
  • The study utilized histone modification mapping and chromatin accessibility techniques (CUT&Tag and ATAC-seq) on the threespine stickleback fish to establish a link between active histone marks and high gene expression, while repressive marks correlated with lower expression levels.
  • The research found that regions with distinct histone modifications had greater nucleotide diversity and revealed specific genomic alterations (insertions and deletions) linked to different ecotypes, highlighting the utility of histone analysis for identifying regulatory elements
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  • The karyotype, which refers to the number and shape of chromosomes, is crucial for understanding evolutionary processes like speciation in eukaryotes.
  • Traditional views suggested that changes in chromosome number were mainly due to fusions and fissions, while shape changes arose from inversions; however, newer studies propose alternative mechanisms such as tandem fusions and centromere repositioning.
  • Research on medaka fishes (Oryzias species) shows significant differences in karyotypes among groups, revealing that centromere repositioning may be more influential in karyotype evolution than previously known.
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Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems.

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  • Advancements in genomic technologies are improving our understanding of speciation genetics beyond traditional model species, allowing for more diverse organisms to be studied.
  • The review highlights the history of speciation genetics, detailing insights gained from both model and non-model organisms and current trends in the field.
  • To close the gap between research on lab-based model organisms and natural non-model organisms, the authors recommend combining genetic studies with existing ecological knowledge from diverse taxa.
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  • Intrinsic postzygotic isolation results in reduced viability or fertility of hybrids due to genetic incompatibilities between different species' genomes.
  • The two main mechanisms traditionally thought to cause this isolation are Dobzhansky-Muller interactions between genes and chromosomal rearrangements affecting meiosis.
  • Recent studies indicate that intrinsic postzygotic isolation is more complex than previously understood, involving factors like overall DNA divergence and epigenetic changes, and this review examines these mechanisms across various species while addressing gaps in current knowledge.
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The analysis of otolith Sr isotope ratios (Sr/Sr) is a powerful method to study fish migration in freshwater areas. However, few studies have applied this method to study fish movement in brackish-water environments. Furthermore, despite the fact that habitat differentiation has been shown to drive genetic differentiation and reproductive isolation among stickleback fish, no studies have used the otolith Sr/Sr ratios to analyze habitat differentiation between stickleback ecotypes and species.

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AbstractSex chromosomes rapidly turn over in several taxonomic groups. Sex chromosome turnover is generally thought to start with the appearance of a new sex-determining gene on an autosome while an old sex-determining gene still exists, followed by the fixation of the new one. However, we do not know how prevalent the transient state is, where multiple sex-determining loci coexist within natural populations.

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Intrinsic hybrid incompatibility is one of the important isolating barriers between species. In organisms with sex chromosomes, intrinsic hybrid incompatibility often follows two rules: Haldane's rule and large-X effects. One explanation for these two rules is that sex chromosomes are hotspots for meiotic drivers that can cause intrinsic hybrid incompatibility between geographically isolated populations.

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Adaptation to similar environments can lead to the evolution of similar phenotypes in phylogenetically independent lineages. However, the extent of parallel evolution often varies. Because such variations can be due to environmental heterogeneity among seemingly similar habitats, identification of the environmental factors that cause non-parallel patterns can provide valuable insight into the ecological factors associated with phenotypic diversification.

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  • Repeated colonization and hybridization on Muna Island contribute to increased biodiversity among the Oryzias woworae fish species group, indicating a complex evolutionary history.
  • Phylogenetic analyses show that while all populations on Muna Island are related, multiple distinct lineages exist, and there were multiple colonization events with introgressive hybridization occurring primarily in one local population.
  • The study suggests these colonizations happened during the Quaternary period, facilitated by land bridges due to decreased sea levels, leading to rich and varied genetic diversity in the fish species of this region.
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Freshwater halfbeaks of the genus (Zenarchopteridae) uniquely diversified on Sulawesi Island, where tectonic movements have been very active since the Pliocene. Most species of this genus have quite limited distributions, which indicates that geographic isolations have contributed to their diversification. In this study, we demonstrated that secondary contacts and resultant admixtures between long-isolated species/populations may have also been important.

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Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, which diversified during the last 4.

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  • * Phylogenomic analysis shows that pelvic-fin brooders have evolved independently at least twice within the Adrianichthyidae family, highlighting the complexity of evolutionary genetics behind this trait.
  • * Investigations into the physical traits and genetic mapping reveal that specific characteristics supporting this reproductive method are controlled by different genetic regions, indicating that independent genetic mutations may drive the repeated evolution of pelvic-fin brooding.
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Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and -regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments.

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Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations.

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Article Synopsis
  • The article explores fundamental questions in evolutionary biology, such as whether evolution occurs in small gradual steps or significant leaps, and how predictable and constrained the process is.
  • Advances in genome sequencing and editing technologies are key to investigating the genetic factors driving phenotypic diversity and speciation in natural populations.
  • The discussion emphasizes how these new tools can help identify causative genes and mutations, contributing to our understanding of biodiversity and its future responses to environmental changes.*
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  • Local adaptation may lead to a concentrated genetic architecture, where key alleles for traits are found close together on chromosomes, as seen in the evolution of threespine stickleback fish adapting to marine versus freshwater habitats.
  • The study examined genomic rearrangements to understand how these "genomic islands" formed, using comparative analysis with the closely related tubesnout and other species.
  • Findings showed that smaller rearrangements and lineage-specific genes are more common near these adaptive loci, suggesting that selection pressures on certain genes may have led to their clustering through genomic changes.
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It is still difficult to construct the genomes of higher organisms as their genome sequences must be extended to the length of the chromosome by linkage analysis. In this study, we attempted to provide an innovative alternative to conventional linkage analysis by devising a method to genotype sperm using 10× Genomics single-cell genome sequencing libraries to generate a linkage map without interbreeding individuals. A genome was assembled using sperm from the Japanese stickleback , with single-cell genotyping yielding 1 864 430 very dense hetero-SNPs and an average coverage per sperm cell of 0.

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An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea.

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Fitness of aquatic animals can be limited by the scarcity of nutrients such as long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). DHA availability from diet varies among aquatic habitats, imposing different selective pressures on resident animals to optimize DHA acquisition and synthesis. For example, DHA is generally poor in freshwater ecosystems compared to marine ecosystems.

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The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better.

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