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The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is, changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of O. latipes, O. javanicus, and O. celebensis, we found that repositioning of centromere‐associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated. [ABSTRACT FROM AUTHOR]

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. sakaizumii. Our findings showed that O. sakaizumii has a higher fecundity than O. latipes, and quantitative trait locus analysis using interspecific F2 hybrids showed that chromosome 23 is linked to the size‐fecundity relationship. In particular, the genes igf1 and lep‐b in this region are known to be associated with life‐history traits, including somatic growth, gonad maturation, and progeny numbers in various taxa. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that the relatively high fecundity observed in O. sakaizumii is an adaptation to high latitudes. We also discuss the potential ecological ramifications associated with the evolution of increased fecundity in this species. [ABSTRACT FROM AUTHOR]

Background: Rainbowfish is a clade of colorful freshwater fish. Melanotaenia praecox is a small rainbowfish species with biological characteristics that make it potentially useful as an experimental model species. We anticipate that M. praecox could become a new model used in various fields, such as ecology, evolution, and developmental biology. However, few previous studies have described experimental set‐ups needed to understand the molecular and genetic mechanisms within this species. Results: We describe detailed procedures for genetic engineering in the rainbowfish M. praecox. By using these procedures, we successfully demonstrated CRISPR/Cas‐mediated knockout and Tol2 transposon‐mediated transgenesis in this species. Regarding the CRISPR/Cas system, we disrupted the tyrosinase gene and then showed that injected embryos lacked pigmentation over much of their body. We also demonstrated that a Tol2 construct, including a GFP gene driven by a ubiquitous promoter, was efficiently integrated into the genome of M. praecox embryos. Conclusions: The establishment of procedures for genetic engineering in M. praecox enables investigation of the genetic mechanisms behind a broad range of biological phenomena in this species. Thus, we suggest that M. praecox can be used as a new model species in various experimental biology fields. Key Findings: We describe detailed procedures for genetic engineering in the rainbowfish Melanotaenia praecox.We successfully demonstrated CRISPR/Cas‐ediated knockout and Tol2 transposon‐mediated transgenesis in this species.The establishment of procedures for genetic engineering in M. praecox enables investigation of the genetic mechanisms behind a broad range of biological phenomena in this species. [ABSTRACT FROM AUTHOR]

Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of 'ghost introgression' in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthys in Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population‐genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorus and A. poptae, but the large time‐lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted. [ABSTRACT FROM AUTHOR]