MALADAPTED GENE COMPLEXES WITHIN POPULATIONS OF THE INTERTIDAL COPEPOD TIGRIOPUS CALIFORNICUS?

The prevalence of F2 hybrid breakdown in interpopulation crosses of the marine copepod Tigriopus californicus can be explained by disruption of coadapted gene complexes. This study further dissects the nature of hybrid gene interactions, revealing that parental populations may also harbor maladapted gene complexes. Diagnostic molecular markers (14) were assayed in reciprocal F2 hybrids to test for gene interactions affecting viability. Results showed some evidence of nuclear–nuclear coadaptation. Although there were no significant examples of pairwise linkage disequilibrium between physically unlinked loci, one of the two reciprocal crosses did show an overall excess of parental double homozygotes and an overall dearth of nonparental double homozygotes. In contrast, the nuclear–cytoplasmic data showed a stronger tendency toward maladaptation within the specific inbred lines used in this study. For three out of four loci with significant frequency differences between reciprocal F2, homozygotes were favored on the wrong cytoplasmic background. A separate study of reciprocal backcross hybrids between the same two populations (but different inbred lines) revealed faster development time when the full haploid nuclear genome did not match the cytoplasm. The occurrence of such suboptimal gene complexes may be attributable to effects of genetic drift in small, isolated populations.     

Epistasis causes outbreeding depression in eucalypt hybrids

The genetic architecture underlying species differentiation is essential for understanding the mechanisms of speciation and post-zygotic reproductive barriers which exist between species. We undertook line-cross analysis of multiple hybrid (F₁, F₂ and backcrosses) and pure-species populations of two diploid eucalypt species from different subseries, Eucalyptus globulus and Eucalyptus nitens, to unravel the genetic architecture of their differentiation. The populations were replicated on two sites and monitored for growth and survival over a 14-year period. The hybrids exhibited severe outbreeding depression which increased with age. Of the composite additive, dominance and epistatic effects estimated, the additive × additive epistatic component was the most important in determining population divergence in both growth and survival. Significant dominance × dominance epistasis was also detected for survival at several ages. While favourable dominance and, in the case of survival, dominance × dominance epistasis could produce novel gene combinations which enhance hybrid fitness, at the population level, these effects were clearly overridden by adverse additive × additive epistasis which appears to be a major driver of overall outbreeding depression in the hybrid populations. The lack of model fit at older ages suggested that even high-order epistatic interactions may potentially have a significant contribution to outbreeding depression in survival. The estimated composite genetic parameters were generally stable across sites. Our results argue that the development of favourable epistasis is a key mechanism underlying the genetic divergence of eucalypt species, and epistasis is an important mechanism underlying the evolution of post-zygotic reproductive barriers.     

THE GENETICS OF CENTRAL AND MARGINAL POPULATIONS OF DROSOPHILA SERRATA. II. HYBRID BREAKDOWN IN FITNESS COMPONENTS AS A CORRELATED RESPONSE TO SELECTION FOR DESICCATION RESISTANCE

Multiple-peak epistasis is one of the four premises that underlie Wright's shifting-balance theory of evolution. A selection experiment was conducted in an attempt to push different geographic populations to different fitness peaks as a correlated response to selection for an additively controlled character (desiccation resistance). Four populations of Drosophila serrata, sampled from central and marginal areas of its distribution along a 3000-km stretch of Australia's east coast, underwent selection for desiccation resistance for 14 generations. After selection had ceased, control lines from each of the populations were crossed to determine the amount of hybrid breakdown that existed before selection and selected lines were crossed to determine the amount of hybrid breakdown after selection. Hybrid breakdown was measured in three fitness traits: developmental time, viability, and fecundity. When the individual crosses were examined, virtually no evidence was found for hybrid breakdown between these populations. However, the level of hybrid breakdown in development time in the control lines increased as the distance between the populations in the field increased. This relationship was lost in the selected lines. Therefore, selection for desiccation resistance influenced the level of hybrid breakdown in a fitness trait, although selection may need to be maintained for longer than 14 generations if a new relationship between hybrid breakdown and distance is to be formed.     

The genetics of floral divergence and postzygotic barriers between outcrossing and selfing populations of Arenaria uniflora (Caryophyllaceae)

The genetic architecture of floral traits involved in the evolution of self-pollination provides a window into past processes of mating system divergence. In this study, we use two generations of crosses between highly selfing and predominantly outcrossing populations of Arenaria uniflora (Caryophyllaceae) to determine the minimum number, average dominance relationships, and pleiotropic effects of genetic factors involved in floral divergence. Comparison of the F1 and F2 phenotypic means with the expectations of a completely additive model of gene action revealed a primarily additive genetic basis for floral characters associated with mating system variation. The exception was flower life span, which showed partial dominance of the outcrosser phenology. In contrast to similarly divergent species, the substantial differences in flower size between these A. uniflora populations appear to involve relatively few genes of large effect (minimum number of effective factors = 2.2 +/- 2.8 SE). In addition, correlations among traits in the F2 generation indicate that pleiotropy may be an important feature of the genetic architecture of floral evolution in A. uniflora. The evolution of selfing via major modifiers of floral morphology is consistent with other evidence for ecological selection for preemptive self-pollination in A. uniflora. Analyses of the genetic basis of autonomous selfing were complicated by hybrid breakdown in both F1 and F2 generations. Only F1 hybrids showed reductions in female fertility, but about 30% of F1 and F2 hybrids exhibited partial or complete male sterility. Male sterile flowers were characterized by short stamens, reduced petals, and a lack of protandry, as well as indehiscent anthers. This morphological breakdown mimics environmental disruptions of floral development and may result from novel genic interactions in hybrids.     

Rapid appearance of epistasis during adaptive divergence following colonization

Theory predicts that short-term adaptation within populations depends on additive (A) genetic effects, while gene-gene interactions 'epistasis (E)' are important only in long-term evolution. However, few data exist on the genetic architecture of adaptive variation, and the relative importance of A versus non-additive genetic effects continues to be a central controversy of evolutionary biology after more than 70 years of debate. To examine this issue directly, we conducted hybridization experiments between two populations of wild soapberry bugs that have strongly differentiated in 100 or fewer generations following a host plant shift. Contrary to expectation, we found that between-population E and dominance (D) have appeared quickly in the evolution of new phenotypes. Rather than thousands of generations, adaptive gene differences between populations have evolved in tens. Such complex genetic variation could underlie the seemingly extreme rates of evolution that are increasingly reported in many taxa. In the case of the soapberry bug, extraordinary ecological opportunity, rather than mortality, may have created hard selection for genetic variants. Because ultimate division of populations into genetic species depends on epistatic loss of hybrid compatibility, local adaptation based on E may accelerate macro-evolutionary diversification.     

Estimates of genetic variance in an F2 maize population

Maize (Zea mays L.) breeders have used several genetic-statistical models to study the inheritance of quantitative traits. These models provide information on the importance of additive, dominance, and epistatic genetic variance for a quantitative trait. Estimates of genetic variances are useful in understanding heterosis and determining the response to selection. The objectives of this study were to estimate additive and dominance genetic variances and the average level of dominance for an F2 population derived from the B73 x Mo17 hybrid and use weighted least squares to determine the importance of digenic epistatic variances relative to additive and dominance variances. Genetic variances were estimated using Design III and weighted least squares analyses. Both analyses determined that dominance variance was more important than additive variance for grain yield. For other traits, additive genetic variance was more important than dominance variance. The average level of dominance suggests either overdominant gene effects were present for grain yield or pseudo-overdominance because of linkage disequilibrium in the F2 population. Epistatic variances generally were not significantly different from zero and therefore were relatively less important than additive and dominance variances. For several traits estimates of additive by additive epistatic variance decreased estimates of additive genetic variance, but generally the decrease in additive genetic variance was not significant.     

Evolution of coadaptation in a two-locus epistatic system

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.     

Effect of recombination in the parent populations on the means and combining ability variances in hybrid populations of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Recombination of selected genotypes plays a key role in plant breeding for generating new base populations. We investigated the influence of recombination in two parent populations on the means and combining ability variances of their hybrid population by (1) quantitative genetic theory and (2) experiments with maize. The two parent populations were founded by four early flint and four early dent inbred lines, respectively. Each population was studied in three generations: Syn-0, the four inbred lines themselves; Syn*-1, the six intrapool single crosses (SC); and Syn*-2, the three intrapool double crosses (DC). Four interpool hybrid populations were created: (1) all 16 SC and (2) all 36 DC were produced from generations Syn-0 and Syn*-1, respectively, (3) 168 biparental progenies (BIP) of type flint x dent (female x male), and (4) 168 BIP of type dent x flint were produced according to NC-design I with randomly sampled plants of generation Syn*-2. The half-sib and full-sib families obtained in this manner were evaluated for grain yield, dry matter concentration and plant height. According to theoretical results, differences in the population means of these hybrid populations indicate the presence of various types of epistasis. Changes in combining ability variances from SC to DC reflect different levels of parental inbreeding (F = 1 vs F = 0), whereas changes from DC to BIP only reflect the effects of recombination and are attributable to covariances between additive and dominance effects caused by linkage disequilibrium in the Syn-0 generations. The experimental results showed a significant decline in yield from DC to BIP due to a loss of gene combinations with favourable epistatic effects. Estimates of sigma(2)(GCA) attributable to flint or dent lines decreased or remained unchanged from SC to DC, but generally increased in the BIP populations. The consequences of these trends for developing improved interpool hybrids are discussed.     

The quantitative genetics of fluctuating asymmetry

Fluctuating asymmetry (subtle departures from identical expression of a trait across an axis of symmetry) in many taxa is under stabilizing selection for reduced asymmetry. However, lack of reliable estimates of genetic parameters for asymmetry variation hampers our ability to predict the evolutionary outcome of this selection. Here we report on a study, based on analysis of variation within and between isofemale lines and of generation means (line-cross analysis), designed to dissect in detail the quantitative genetics of positional fluctuating asymmetry (PFA) in bristle number in natural populations of Drosophila falleni. PFA is defined as the difference between the two sides of the body in the placement or position of components of a meristic trait. Heritability (measured at 25 degrees C) of two related measures of PFA were 13% and 21%, both of which differed significantly from zero. In contrast, heritability estimates for fluctuating asymmetry in the total number of anterior (0.7%) and transverse (2.4%) sternopleural bristles were smaller, not significant, and in quantitative agreement with previously published estimates. Heritabilities for bristle number (trait size) were considerably greater than that for any asymmetry measure. The experimental design controlled for the potentially confounding effects of common familial environment, and repeated testing revealed that PFA differences between lines were genetically stable for up to 16 generations in the laboratory at 25 degrees C. We performed line cross analysis between strains at the extremes of the PFA distribution (highest and lowest values); parental strains, F1, F1r (reciprocal), F2, backcross, and backcross reciprocal generations were represented. The inheritance of PFA was described best by additive and dominance effects localized to the X-chromosomes, whereas autosomal dominance effects were also detected. Epistatic, maternal, and cytoplasmic effects were not detected. The inheritance of trait size was notably more complex and involved significant autosomal additive, dominance, and epistatic effects; maternal dominance effects; and additive and dominance effects localized to the X-chromosomes. The additive genetic correlation between PFA and its associated measure of trait size was negative (-0.049), but not statistically significant, indicating that the loci contributing additive genetic effects to these traits are probably different. It is suggested that PFA may be a sensitive measure of developmental instability because PFA taps the ability of an organism to integrate interconnected developmental pathways.     

Genomic prediction of hybrid crops allows disentangling dominance and epistasis

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dense markers in a GBLUP analysis, it is possible to split specific combining ability into dominance and across-groups epistatic deviations, and to split general combining ability (GCA) into within-line additive effects and within-line additive by additive (and higher order) epistatic deviations. We analyzed a publicly available maize data set of Dent × Flint hybrids using our new model (called GCA-model) up to additive by additive epistasis. To model higher order interactions within GCAs, we also fitted “residual genetic” line effects. Our new GCA-model was compared with another genomic model which assumes a uniquely defined effect of genes across origins. Most variation in hybrids is accounted by GCA. Variances due to dominance and epistasis have similar magnitudes. Models based on defining effects either differently or identically across heterotic groups resulted in similar predictive abilities for hybrids. The currently used model inflates the estimated additive genetic variance. This is not important for hybrid predictions but has consequences for the breeding scheme—e.g. overestimation of the genetic gain within heterotic group. Therefore, we recommend using GCA-model, which is appropriate for genomic prediction and variance component estimation in hybrid crops using genomic data, and whose results can be practically interpreted and used for breeding purposes.     

Heterosis for biomass-related traits in Arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines

Arabidopsis thaliana has emerged as a leading model species in plant genetics and functional genomics including research on the genetic causes of heterosis. We applied a triple testcross (TTC) design and a novel biometrical approach to identify and characterize quantitative trait loci (QTL) for heterosis of five biomass-related traits by (i) estimating the number, genomic positions, and genetic effects of heterotic QTL, (ii) characterizing their mode of gene action, and (iii) testing for presence of epistatic effects by a genomewide scan and marker x marker interactions. In total, 234 recombinant inbred lines (RILs) of Arabidopsis hybrid C24 x Col-0 were crossed to both parental lines and their F1 and analyzed with 110 single-nucleotide polymorphism (SNP) markers. QTL analyses were conducted using linear transformations Z1, Z2, and Z3 calculated from the adjusted entry means of TTC progenies. With Z1, we detected 12 QTL displaying augmented additive effects. With Z2, we mapped six QTL for augmented dominance effects. A one-dimensional genome scan with Z3 revealed two genomic regions with significantly negative dominance x additive epistatic effects. Two-way analyses of variance between marker pairs revealed nine digenic epistatic interactions: six reflecting dominance x dominance effects with variable sign and three reflecting additive x additive effects with positive sign. We conclude that heterosis for biomass-related traits in Arabidopsis has a polygenic basis with overdominance and/or epistasis being presumably the main types of gene action.     

Genetic architecture of differences in oviposition preference between ancestral and derived populations of the seed beetle Acanthoscelides obtectus

We investigated the additive, dominance and epistatic genetic effects underlying differentiation in oviposition preference between two populations of the seed beetle Acanthoscelides obtectus evolved in the laboratory for 102 generations on bean and chickpea seeds. We reared and tested females on each of two host legumes. The populations differed in mean oviposition preference; the preference for chickpea was stronger in population reared on the chickpea (C) than in population maintained on common bean (P). Observations in the parental populations indicated that females tend to prefer ovipositioning their eggs on the seeds they have already experienced. The patterns of the means in each of the parental populations and 12 types of hybrids (two F(1), two F(2) and eight backcrosses) indicated that population differences in oviposition preference from both rearing hosts could be explained by nonadditive genetic effects. Statistically detectable additive and dominance genetic effects were observed in the most parsimonious model only when females were reared on the chickpea. The most parsimonious models on both rearing hosts suggested a contribution of negative additive x additive epistasis to the divergence of oviposition preference between the P and C populations. This indicates a positive effect of epistasis on the performance of the second generations of hybrids.     

Genetic architecture of differences between populations of cowpea weevil (Callosobruchus maculatus) evolved in the same environment

We investigated the genetic architecture underlying differentiation in fitness-related traits between two pairs of populations of the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae). These populations had geographically distant (> 2000 km) origins but evolved in a uniform laboratory environment for 120 generations. For each pair of populations (Nigeria x Yemen and Cameroon x Uganda) we estimated the means of five fitness-related characters and a measure of fitness (net reproductive rate R0) in each of the parental populations and 12 types of hybrids (two F1 and two F2 lines and eight backcrosses). Models containing up to nine composite genetic parameters were fitted to the means of the 14 lines. The patterns of line means for all traits in the Nigeria x Yemen cross and for four traits (larval survival, developmental rate, female body weight, and fecundity) in the Cameroon x Uganda cross were best explained by models including additive, dominance, and maternal effects, but excluding epistasis. We did not find any evidence for outbreeding depression for any trait. An epistatic component of divergence was detected for egg hatching success and R0 in the Cameroon x Uganda cross, but its sign was opposite to that expected under outbreeding depression, that is, additive x additive epistasis had a positive effect on the performance of F2 hybrids. All traits except fecundity showed a pattern of heterosis. A large difference of egg-hatching success between the two reciprocal F1 lines in that cross was best explained as fertilization incompatibility between Cameroon females and sperm carrying Uganda genes. The results suggest that these populations have not converged to the same life-history phenotype and genetic architecture, despite 120 generations of uniform natural selection. However, the absence of outbreeding depression implies that they did not evolve toward different adaptive peaks.     

Generating data in models including direct and maternal dominance effects

Algorithms are presented to simulate multiple generations of animal data by a model including direct additive genetic, maternal additive genetic, direct dominance, maternal dominance and permanent environmental effects. Dominance effects were computed as parental subclasses. Testing involved five single trait models that included direct contemporary group and direct additive effects, and different combinations of maternal, permanent environmental, and dominance effects. Simulated populations included 5 generations of animals and 20 contemporary groups per generation. The base population contained 200 sires and 600 dams. Variance components were estimated by Average-Information Restricted Maximum Likelihood (AIREML). No significant bias was observed. The simulation algorithms can be used in research involving dominance models, such as evaluation of mating systems exploiting special combining abilities of prospective parents.     

Using clonal replicates to explore genetic variation in a perennial plant species

Summary An experimental design is presented for estimating genetic parameters using a family structure with clonally replicated individuals. This experimental design provides a technique to quantify genetic variation in a population, with partial separation of additive, dominance and epistatic gene action. Our method is offered as an alternative to techniques for estimating epistatic gene action that require several generations and/or inbreeding. Such methods are not particularly useful for long-lived perennials with long generation cycles. An example of the analysis is given with a forest tree species, Populus deltoides Bartr., and parameter estimates are presented for traits measured over 8 years.     

Something Old and Something New: Wedding Recombinant Inbred Lines with Traditional Line Cross Analysis Increases Power to Describe Gene Interactions

In this paper we present a novel approach to quantifying genetic architecture that combines recombinant inbred lines (RIL) with line cross analysis (LCA). LCA is a method of quantifying directional genetic effects (i.e. summed effects of all loci) that differentiate two parental lines. Directional genetic effects are thought to be critical components of genetic architecture for the long term response to selection and as a cause of inbreeding depression. LCA typically begins with two inbred parental lines that are crossed to produce several generations such as F1, F2, and backcrosses to each parent. When a RIL population (founded from the same P1 and P2 as was used to found the line cross population) is added to the LCA, the sampling variance of several nonadditive genetic effect estimates is greatly reduced. Specifically, estimates of directional dominance, additive x additive, and dominance x dominance epistatic effects are reduced by 92%, 94%, and 56% respectively. The RIL population can be simultaneously used for QTL identification, thus uncovering the effects of specific loci or genomic regions as elements of genetic architecture. LCA and QTL mapping with RIL provide two qualitatively different measures of genetic architecture with the potential to overcome weaknesses of each approach alone. This approach provides cross-validation of the estimates of additive and additive x additive effects, much smaller confidence intervals on dominance, additive x additive and dominance x dominance estimates, qualitatively different measures of genetic architecture, and the potential when used together to balance the weaknesses of LCA or RIL QTL analyses when used alone.     

Quantitative genetics of functional characters in<Emphasis Type="Italic">Drosophila melanogaster</Emphasis> populations subjected to laboratory selection

What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbredDrosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield

To understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F(10) recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most ( approximately 90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.     

The contrasting genetic architecture of wing size, viability, and development time in a rainforest species and its more widely distributed relative

Divergence among populations can occur via additive genetic effects and/or because of epistatic interactions among genes. Here we use line-cross analysis to compare the importance of epistasis in divergence among two sympatric Drosophila species from eastern Australia, one (D. serrata) distributed continuously and the other (D. birchii) confined to rainforest habitats that are often disjunct. For D. serrata, crosses indicated that development time and wing size differences were due to additive genetic effects, while for viability there were digenic epistatic effects. Crosses comparing geographically close populations as well as those involving the most geographically distant populations (including the southern species border) revealed epistatic interactions, whereas crosses at an intermediate distance showed no epistasis. In D. birchii, there was no evidence of epistasis for viability, although for development time and wing size there was epistasis in the cross between the most geographically diverged populations. Strong epistasis has not developed among the D. birchii populations, and this habitat specialist does not show stronger epistasis than D. serrata. Given that epistasis has been detected in crosses with other species from eastern Australia, including the recently introduced D. melanogaster, the results point to epistasis not being directly linked to divergence times among populations.     

Population differentiation in the beetleTribolium castaneum. I. Genetic architecture

We used joint-scaling analyses in conjunction with rearing temperature variation to investigate the contributions of additive, non-additive, and environmental effects to genetic divergence and incipient speciation among 12 populations of the red flour beetle, Tribolium castaneum, with small levels of pairwise nuclear genetic divergence (0.033 < Nei's D < 0.125). For 15 population pairs we created a full spectrum of line crosses (two parental, two reciprocal F1's, four F2's, and eight backcrosses), reared them at multiple temperatures, and analyzed the numbers and developmental defects of offspring. We assayed a total of 219,388 offspring from 5147 families. Failed crosses occurred predominately in F2's, giving evidence of F2 breakdown within this species. In all cases where a significant model could be fit to the data on offspring number, we observed at least one type of digenic epistasis. We also found maternal and cytoplasmic effects to be common components of divergence among T. castaneum populations. In some cases, the most complex model tested (additive, dominance, epistatic, maternal, and cytoplasmic effects) did not provide a significant fit to the data, suggesting that linkage or higher order epistasis is involved in differentiation between some populations. For the limb deformity data, we observed significant genotype-by-environment interaction in most crosses and pure parent crosses tended to have fewer deformities than hybrid crosses. Complexity of genetic architecture was not correlated with either geographic distance or genetic distance. Our results support the view that genetic incompatibilities responsible for postzygotic isolation, an important component of speciation, may be a natural but serendipitous consequence of nonadditive genetic effects and structured populations.