Understanding how genetic differentiation is maintained between closely related species with overlapping habitats is a central question in evolutionary biology. The sticklebacks Gasterosteus aculeatus and Gasterosteus nipponicus occur in sympatry with reproductive isolation on the Pacific coast of Hokkaido Island. However, their distributions and hybridization patterns in more northern regions remain largely elusive. Here, we...

Hybridization and introgression frequently occur even between distantly related species. A central question in speciation research is which genomic regions act as barriers to gene flow and how genome‐wide differentiation persists despite hybridization between species. Ecological divergence is well known to promote genomic differentiation, especially during the early stages of speciation. However, the extent to which ecological...

DNA within the nucleus is organised into a well‐regulated three‐dimensional (3D) structure. However, how such 3D genome structures influence speciation processes remains largely elusive. Recent studies have shown that 3D genome structures influence mutation rates, including the occurrence of chromosomal rearrangement. For example, breakpoints of chromosomal rearrangements tend to be located at topologically associating domain...

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...

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 n...

Charrs ( Salvelinus ) reach their southernmost distribution in Japan, and are uniquely adapted to the short, steep streams of this island archipelago. Southern Asian Dolly Varden ( Salvelinus curilus ) occur only in Hokkaido Island, whereas white-spotted charr ( Salvelinus leucomaenis ) range to southern Honshu. Both species diverged from an ancestral lineage during the late Pliocene/early Pleistocene, when lowered sea levels...

Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called “pelvic‐fin brooding,” wherein females carry externally fe...

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega‐3 long‐chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n‐3) and docosahexaenoic acid (DHA; 22:6n‐3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty ac...

Elucidation of the genetic mechanisms of convergent evolution, the evolution of similar or the same phenotypes in phylogenetically independent lineages, helps predict how populations will respond to the same selective pressures. Convergent evolution can be caused by either the fixation of identical‐by‐descent alleles, independent mutations at the same gene, or mutations in different genes controlling the same trait. To what ex...

Intragenomic conflict, the conflict of interest between different genomic regions within an individual, is proposed as a mechanism driving both the rapid evolution of heterochromatin‐related proteins and the establishment of intrinsic genomic incompatibility between species. Although molecular studies of laboratory model organisms have demonstrated the link between heterochromatin evolution and hybrid abnormalities, we know li...

Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback ( Gasterosteus aculeatus ) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate gene...

Predator‐ and prey‐induced phenotypic plasticity is widely observed among amphibian species. Although ecological factors inducing diverse phenotypic responses have been extensively characterized, we know little about the molecular bases of variation in phenotypic plasticity. Larvae of the Hokkaido salamander, Hynobius retardatus , exhibit two distinct morphs: the presence of their prey, Rana pirica tadpoles, induces a broad‐he...

Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived fro...

Closely related species of fish often exhibit different migration patterns. Even within species, anadromous and resident populations can be found in a diverse number of taxa. Although several environmental factors that regulate behavioral and physiological changes associated with fish migration have been identified, the genetic mechanisms underlying the variation in the ability to respond to these environmental cues in fishes...