Postzygotic Isolation Mechanisms Research Articles

Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies.

Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome vs. autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in prezygotic and postzygotic isolation mechanisms.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives.

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Meiotic Recognition of Evolutionarily Diverged Homologs: Chromosomal Hybrid Sterility Revisited.

Hybrid sterility (HS) is an early postzygotic reproductive isolation mechanism observed in all sexually reproducing species. Infertility of hybrids prevents gene flow between incipient species and leads to speciation. While Drosophila studies have focused almost exclusively on the genic control of HS, two other model species, Mus musculus and budding yeast, provided the first experimental evidence of hybrid sterility governed by the nongenic effects of DNA sequence divergence. Here, we propose that the nongenic effect of increasing DNA divergence between closely related species may impair mutual recognition of homologous chromosomes and disrupt their synapsis. Unsynapsed or mispaired homologs can induce early meiotic arrest, or their random segregation can cause aneuploidy of spermatids and sperm cells. Impaired recognition of homologs may thus act as a universal chromosomal checkpoint contributing to the complexity of genetic control of HS. Chromosomal HS controlled by the Prdm9 gene in mice and HS driven by the mismatch repair machinery in yeast are currently the most advanced examples of chromosomal homology search-based HS. More focus on the cellular and molecular phenotypes of meiosis will be needed to further validate the role of homolog recognition in hybrid sterility and speciation.

Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species

The mechanisms of reproductive isolation that cause phenotypic diversification and eventually speciation are a major topic of evolutionary research. Hybrid necrosis is a post-zygotic isolation mechanism in which cell death develops in the absence of pathogens. It is often due to the incompatibility between proteins from two parents. Here we describe a unique case of hybrid necrosis due to an incompatibility between loci on chromosomes 2 and 7 between two pollinator-isolated Petunia species. Typical immune responses as well as endoplasmic reticulum stress responses are induced in the necrotic line. The locus on chromosome 2 encodes ChiA1, a bifunctional GH18 chitinase/lysozyme. The enzymatic activity of ChiA1 is dispensable for the development of necrosis. We propose that the extremely high expression of ChiA1 involves a positive feedback loop between the loci on chromosomes 2 and 7. ChiA1 is tightly linked to major genes involved in the adaptation to different pollinators, a form of pre-zygotic isolation. This linkage of pre- and post-zygotic barriers strengthens reproductive isolation and probably contributes to rapid diversification and speciation.

Evolutionary history and diversity in the ball roller beetle Canthon cyanellus

To understand the evolutionary history of species, it is necessary to know the mechanisms for reproductive isolation, divergence-time between populations, and the relative action of the evolutionary forces (e.g., mutation, genetic drift, gene flow) within and between populations of the same, or closely related species. Although Canthon is one of the more diverse genera of neotropical beetles, insufficient research has been done to comprehend the divergent patterns that explain its speciation process. The absence of diagnostic morphological characters and the wide geographic variation of qualitative traits in Scarabaeinae obscures species delimitation, genealogical limits between populations, and its taxonomy. Canthon cyanellus is one of the best-known species in ecological and evolutionary aspects. It is a widely distributed species in the tropical forests of America. Also, the current deforestation has facilitated its incursion into open areas. Individuals from different populations have similar morphological characters but show wide variation in body color throughout their distribution, which makes it difficult to delimit the subspecies that comprise it. Recently, studies have been carried out to elucidate the pre-and postzygotic isolation mechanisms between populations and the historical biogeographical processes favoring cladogenesis events during the Pleistocene. Morphological variation of the male genitalia does not correspond to the phylogeographic structure. However, the morphological differences in one of the pieces of the endophallic sclerites have allowed a preliminary delimitation of some genetically differentiated clades. Finally, we consider that the joint analysis of traditional morphological taxonomy and phylogeography is important to understand the speciation process in the C. cyanellus complex.

Rapid Divergence of Key Spermatogenesis Genes in nasuta-Subgroup of Drosophila.

The crosses between closely relatedDrosophilaspecies usually produce sterile hybrid males with spermatogenesis disrupted at post-meiotic phase, especially in sperm individualization stage than the pre-meiotic stage. This is possibly due to the rapid interspecies divergence of male sex and reproduction-related genes. Here we annotated 11 key spermatogenesis genes in 35 strains of species belonging tonasuta-subgroup ofDrosophila, where many interspecies crosses produce sterile males. We characterized the divergence and polymorphism in the protein coding regions by employing gene-wide, codon-wide, and lineage-specific selection analysis to test the mode and strength of selection acting on these genes.Our analysis showed signature of positive selection at bag of marbles (bam)andbenign gonial cell neoplasma (bgcn)despite the selection constrains and the absence of endosymbiont infection which could potentially drive rapid divergence due to an arms race whileroughex (rux)showed lineage-specific rapid divergence in frontal sheen complex ofnasuta-subgroup.cookie monster (comr)showed rapid divergence consistent with the possibility of meiotic arrest observed in sterile hybrids ofDrosophilaspecies. Rapid divergence observed atdon juan (dj) and Mst98Ca-likewas consistent with fused sperm-tail abnormality observed in the hybrids ofDrosophila nasutaandDrosophila albomicans. These findings highlight the potential role of rapid nucleotide divergence in bringing about hybrid incompatibility in the form of male sterility; however, additional genetic manipulation studies can widen our understanding of hybrid incompatibilities. Furthermore, our study emphasizes the importance of young species belonging tonasuta-subgroup ofDrosophilain studying post-zygotic reproductive isolation mechanisms.

Genotype-by-environment interactions drive the maintenance of genetic variation in a Salmo trutta L. hybrid zone.

Allopatric gene pools can evolve in different directions through adaptive and nonadaptive processes and are therefore a source of intraspecific diversity. The connection of these previously isolated gene pools through human intervention can lead to intraspecific diversity loss, through extirpation of native populations or hybridization. However, the mechanisms leading to these situations are not always explicitly documented and are thus rarely used to manage intraspecific diversity. In particular, genotype‐by‐environment (GxE) interactions can drive postzygotic reproductive isolation mechanisms that may result in a mosaic of diversity patterns, depending on the local environment. We test this hypothesis using a salmonid species (Salmo trutta) in the Mediterranean (MED) area, where intensive stocking from non‐native Atlantic (ATL) origins has led to various outcomes of hybridization with the native MED lineage, going from MED resilience to total extirpation via full hybridization. We investigate patterns of offspring survival at egg stage in natural environments, based on parental genotypes in interaction with river temperature, to detect potential GxE interactions. Our results show a strong influence of maternal GxE interaction on embryonic survival, mediated by maternal effect through egg size, and a weak influence of paternal GxE interaction. In particular, when egg size is large and temperature is cold, the survival rate of offspring originating from MED females is three times higher than that of ATL females’ offspring. Because river temperatures show contrast at small scale, this cold adaptation for MED females’ offspring constitutes a potent postzygotic mechanism to explain small‐scale spatial heterogeneity in diversity observed in MED areas where ATL fish have been stocked. It also indicates that management efforts could be specifically targeted at the environments that actively favor native intraspecific diversity through eco‐evolutionary processes such as postzygotic selection.

Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes

Interspecific hybridization is a stressful condition that can lead to sterility and/or inviability through improper gene regulation in Drosophila species with a high divergence time. However, the extent of these abnormalities in hybrids of recently diverging species is not well known. Some studies have shown that in Drosophila, the mechanisms of postzygotic isolation may evolve more rapidly in males than in females and that the degree of viability and sterility is associated with the genetic distance between species. Here, we used transcriptomic comparisons between two Drosophila mojavensis subspecies and D. arizonae (repleta group, Drosophila) and identified greater differential gene expression in testes than in ovaries. We tested the hypothesis that the severity of the interspecies hybrid phenotype is associated with the degree of gene misregulation. We showed limited gene misregulation in fertile females and an increase in the amount of misregulation in males with more severe sterile phenotypes (motile vs. amotile sperm). In addition, for these hybrids, we identified candidate genes that were mostly associated with spermatogenesis dysfunction.

Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes.

Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone.

The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (Poecile carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent-including glutamate signaling, synaptic transmission, and catabolic processes-but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.

Promoter hypermethylation of PIWI/piRNA pathway genes associated with diminished pachytene piRNA production in bovine hybrid male sterility

ABSTRACT Hybrid male sterility (HMS) is a postzygotic reproductive isolation mechanism that enforces speciation. A bovine example of HMS is the yattle (also called dzo), an interspecies hybrid of taurine cattle (Bos taurus) and yak (Bos grunniens). The molecular mechanisms underlying HMS of yattle are not well understood. Epigenetic modifications of DNA methylation and P-element induced wimpy testis (PIWI)-interacting RNA (piRNAs) are important regulators in spermatogenesis. In this study, we investigated DNA methylation patterns and piRNA expression in adult testes in hybrid infertile yattle bulls and fertile cattle and yak bulls using whole genome bisulphite-seq and small RNA-seq. Promoter hypermethylation in yattle were associated with DNA methylation involved in gamete generation, piRNA metabolic processes, spermatogenesis, and spermatid development (P < 2.6 × 10−5). Male infertility in yattle was associated with the promoter hypermethylation-associated silencing of PIWI/piRNA pathway genes including PIWIL1, DDX4, PLD6, MAEL, FKBP6, TDRD1 and TDRD5. The downstream effects of silencing these genes were diminished production of 29- to 31- nucleotide pachytene piRNAs in yattle testes. Hypermethylation events at transposable element loci (LINEs, SINEs, and LTRs) were found in yattle. LINE-derived prepachytene piRNAs increased and SINE-derived prepachytene piRNAs were reduced in yattle testes. Our data suggests that DNA methylation affects the PIWI/piRNA pathway and is involved in gene expression and pachytene piRNA production during spermatogenesis in bovine HMS. DNA hypermethylation and disruption of piRNA production contributed to unsuccessful germ cell development that may drive bovine HMS.

Speciation in Allopatric Species of the Hamster Subfamily Cricetinae (Rodentia, Cricetidae)

Abstract—According to the Dobzhansky–Muller model (Dobzhansky, 1937; Muller, 1942), in the absence of gene flow, conspecific populations can become reproductively isolated, and postzygotic isolation should increase proportionally to the square of divergence time. On the example of four pairs of allopatric species of the subfamily Cricetinae, which is characterized by different levels of divergence, the extent of the formation of reproductive barriers was established by behavioral and physiological methods. The potential prezygotic isolation was assessed by the results of behavioral experiments where female olfactory stimuli were exposed to males. A crossbreeding analysis was performed to detect postzygotic isolation. The divergence time was determined by molecular genetic methods. It was shown that complete reproductive isolation formed in a pair of allopatric species of the genus Phodopus (P. roborovskii and P. sungorus) approximately for 5 million years. The sterility of F1 males and conspecific preferences with slight differences in chromosome morphology formed in hamsters (P. sungorus and P. campbelli) in course of 0.8–1.0 million years. In the pair of species belonging to the genus Allocricetulus, which diverged only 0.3–0.4 million years ago, postzygotic isolation mechanisms and conspecific preferences for a number of traits have already partially formed on the background of differences in the structure and number of chromosomes, although in laboratory conditions it is possible to obtain fertile hybrids (F1 and F2). In the species (chromosomal forms) of the superspecies Cricetullus barabensis sensu lato, which diverged later than the pair of species of the genus Allocricetulus (0.16–0.2 million years ago), the reproductive barriers are less pronounced. Thus, the example of the closely related species of Cricetinae shows that reproductive barriers can develop in allopatry and are more pronounced in species that remain isolated for a longer time. Prezygotic barriers in allopatry can develop as rapidly as postzygotic ones, which makes the mechanism of “reinforcement,” proposed by F.G. Dobzhansky, not so relevant (in case of secondary contact zones).

Allochrony as a potential driver for reproductive isolation in adaptive radiations of European whitefish ecomorphs

AbstractIn northern Fennoscandian lakes, monophylogenetic lineages of postglacial fishes are radiating into several adaptive forms, but the speciation process is still at an incipient stage. The speciation process has received increased attention over the years, but the underlying mechanisms and drivers are still debated and poorly understood. European whitefish (Coregonus lavaretus [L.]) is the most abundant fish species in these lakes and has evolved into several ecomorphs adapted to different trophic niches and habitats. Genetic divergence has been observed among these ecomorphs, but the mechanism(s) responsible for the ongoing build‐up of reproductive isolation has still to be revealed. As these systems are young in evolutionary time (&lt;10 kyr), prezygotic and postzygotic extrinsic isolation mechanisms are thought to be more likely to contribute to the reproductive isolation than intrinsic isolation mechanisms. We determined the gonadosomatic index (GSI) of three ecomorphs in two replicated lake systems and used GSI as a proxy to investigate the prezygotic isolation mechanism, allochrony, as a driving factor of divergence in this adaptive radiation of whitefish. We found that the three ecomorphs differed in GSI values within and between lakes, suggesting different spawning times of the ecomorphs. We also show that males of one ecomorph had equal onset of maturity as another ecomorph, giving novel insights into the ongoing gene flow observed between ecomorphs. The result supports allochrony as a driver for the divergence process of whitefish ecomorphs, but more evidence is still needed to rule out that the three ecomorphs make use of different spawning grounds.

VIABILITY OF RAZORBACK-FLANNELMOUTH SUCKER HYBRIDS

Razorback sucker (Xyrauchen texanus) and flannelmouth sucker (Catostomus latipinnis) live in sympatry in the Colorado River basin. Although morphological intermediates have been described since 1889, hybrids were seemingly rare. Rarity of hybrids was likely attributed to razorback suckers' ability to find conspecific mates throughout the basin. Dams have segmented the Colorado River, altering habitat and isolating native fish populations. As a result, razorback suckers became endangered. Razorback suckers are uncommon in the Colorado River and hybridization could increase because of limited conspecific mates. To understand the impacts of hybridization on recovery of the razorback sucker, information on hybrid viability is needed. We compared hatch success and larval survival of artificially spawned razorback sucker, flannelmouth sucker, and their hybrids. We were able to successfully spawn and rear all combinations, implying that there are limited pre- and postzygotic isolation mechanisms, and hybrids are likely to survive in the wild.

Intraspecific chromosome polymorphisms can lead to reproductive isolation and speciation: an example in red brocket deer (Mazama americana).

The red brocket (Mazama americana) is a South American deer with a wide geographical distribution that presents different chromosomal variants depending on their location. At least six different cytotypes belonging to two distinct evolutionary lineages have been described. This study aimed to verify the existence of postzygotic reproductive isolation between cytotypes of M. americana by comparative evaluation of pure and hybrid males. Seven 18-month-old bucks were submitted to seminal collection and evaluation and testicle histological evaluations. The pure males showed normal parameters for sperm quality and testicular histology. Hybrids from the same evolutionary lineage (≤3 chromosomes different from the progenitors) showed similar results to pure males, except for the reduced ratio of round spermatids to pachytene spermatocytes. Hybrids between cytotypes of different evolutionary lineages (≥10 chromosomes different from progenitors) presented azoospermia and evidence of testicular degeneration. Despite the striking morphological similarities, we can conclude that populations with more distinct karyotypes possess an effective reproductive barrier; moreover, there is evidence that reproductive isolation mechanisms exist between some closer karyotypes, corroborating the hypothesis that M. americana is best characterized as a superspecies. Thus, the future description of several new species for this taxon is expected, since the tendency is to establish efficient mechanisms of postzygotic reproductive isolation, preventing the introgression and fusion of genomes from different populations through chromosome variation.

Components of reproductive isolation between the closely related grasshopper species Chorthippus biguttulus and C. mollis

The formation and maintenance of species in nature is accomplished by the evolution of reproductive isolating mechanisms. To understand patterns of speciation and coexistence between species, it is crucial to obtain a complete synopsis of reproductive isolating barriers. We identified multiple reproductive isolation barriers between two closely related species, Chorthippus biguttulus and Chorthippus mollis, and quantified their respective contributions to isolation. To this end, we produced hybrids and backcrosses in the laboratory to examine reproductive isolation at multiple stages in the life history. The prezygotic barriers, based on chemical and acoustic cues, are currently the strongest impediments to gene flow between C. biguttulus and C. mollis. This indicates an important role for sexual selection in the maintenance of species isolation. However, extrinsic and intrinsic postzygotic isolation barriers also contributed to reproductive isolation. The virtual sterility of F1 hybrid males was based on both the dysfunctionality of their testes and intermediate behavioral mating traits (behavioral sterility). This study demonstrates that a cascade of reproductive isolating mechanisms reduces the gene flow between C. biguttulus and C. mollis. Our results further demonstrate that the courtship display in these species consists of multimodal signals and indicates a key role of chemical cues in reproductive isolation and speciation in grasshoppers. The identification of species isolating mechanisms is essential for understanding the processes that drive speciation. A profound understanding of reproductive isolating mechanisms and their fitness consequences in a system is required to predict a specific speciation scenario. Members of the grasshopper subfamily Gomphocerinae show an enormous diversity and complexity in courtship behavior, especially in acoustic displays. Here, we demonstrate that non-acoustic and postzygotic isolation mechanisms also strongly contribute to reproductive isolation between the closely related grasshopper species, C. biguttulus and C. mollis. In addition, our results suggest that ongoing gene flow between this species pair is unlikely and that sexual selection plays an important role in the maintenance of species isolation.

Hybridization and divergence in multi-species oak (Quercus) communities

Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post-zygotic isolation mechanisms, such as ecologically dependent selection on a ...

Separation in flowering time contributes to the maintenance of sympatric cryptic plant lineages

Sympatric cryptic lineages are a challenge for the understanding of species coexistence and lineage diversification as well as for management, conservation, and utilization of plant genetic resources. In higher plants studies providing insights into the mechanisms creating and maintaining sympatric cryptic lineages are rare. Here, using microsatellites and chloroplast sequence data, morphometric analyses, and phenological observations, we ask whether sympatrically coexisting lineages in the common wetland plant Juncus effusus are ecologically differentiated and reproductively isolated. Our results show two genetically highly differentiated, homoploid lineages within J. effusus that are morphologically cryptic and have similar preference for soil moisture content. However, flowering time differed significantly between the lineages contributing to reproductive isolation and the maintenance of these lineages. Furthermore, the later flowering lineage suffered less from predispersal seed predation by a Coleophora moth species. Still, we detected viable and reproducing hybrids between both lineages and the earlier flowering lineage and J. conglomeratus, a coexisting close relative. Flowering time differentiation between the lineages can be explained by neutral divergence alone and together with a lack of postzygotic isolation mechanisms; the sympatric coexistence of these lineages is most likely the result of an allopatric origin with secondary contact.

Assessing postzygotic isolation using zygotic disequilibria in natural hybrid zones.

Hybrid zones as windows on evolutionary processes provide a natural laboratory for studying the genetic basis and mechanisms of postzygotic isolation. One resultant pattern in hybrid zones is the Hardy-Weinberg disequilibrium (HWD) for a single locus or the linkage disequilibrium (LD) for multiple loci produced by natural selection against hybrids. However, HWD and the commonly used low-order gametic or composite digenic LD cannot fully reflect the pattern of the high-order genotypic interactions. Here we propose the use of zygotic LD to elucidate the selection mechanisms of postzygotic isolation, and its calculation is based on genotypic frequencies only, irrespective of the type of mating system. We numerically and analytically show that the maximum composite digenic LD is always greater than the maximum absolute zygotic LD under the linear-additive selection, but is comparable to or smaller than the maximum absolute zygotic LD under the strong epistatic selection. Selection mechanisms can be inferred by testing such differences. We analyze a previously reported mouse hybrid zone assayed with genome-wide SNPs, and confirm that the composite digenic LD cannot appropriately indicate all possible significant genotypic interactions for a given SNP pair. A large proportion of significant zygotic LDs, ∼75% in general in the mouse hybrid zone, cannot be revealed from the composite digenic LD analysis. Statistical tests indicate that epistatic selection occurred among multiple loci in the mouse hybrid zone. The results highlight that the joint patterns of the composite digenic and zygotic LDs can help to elucidate the selection mechanism that is potentially involved in postzygotic isolation.

Genetic mechanisms of postzygotic reproductive isolation: An epistatic network in rice

Products of interspecific crosses often show abnormal phenotypes such as sterility, weakness and inviability. These phenomena play an important role in speciation as mechanisms of postzygotic reproductive isolation (RI). During the past two decades, genetics studies in rice have characterized a number of gene loci responsible for postzygotic RI. I have identified 10 loci including three sets of epistatic networks in a single inter-subspecific cross (Oryza sativa ssp. indica × japonica). These results suggest that RI genes cause developmental dysfunction of vegetative and/or reproductive organs through a variety of molecular pathways. The latest molecular studies demonstrated that hybrid incompatibility is mainly due to deleterious interactions caused by species-specific mutations of two or more genes, mediated by proteins acting within the same molecular pathway. Because genetic interactions provide a perspective on gene function, epistatic networks are a key to the understanding of the molecular basis of postzygotic RI. In this review, I focus on recent progress in postzygotic RI studies in rice and discuss the evolutionary significance as well as implications for improving rice productivity.