POPULATION DIFFERENTIATION IN THE BEETLE TRIBOLIUM CASTANEUM. I. GENETIC ARCHITECTURE

Beyond Haldane's rule: Sex-biased hybrid dysfunction for all modes of sex determination

Haldane's rule occupies a special place in biology as one of the few 'rules' of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane's rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane's rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane's rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane's rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.

Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes)

Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.

Tribolium castaneum: A Model Insect for Fundamental and Applied Research

Tribolium castaneum has a long history as a model species in many distinct subject areas, but improved connections among the genetics, genomics, behavioral, ecological, and pest management fields are needed to fully realize this species' potential as a model. Tribolium castaneum was the first beetle whose genome was sequenced, and a new genome assembly and enhanced annotation, combined with readily available genomic research tools, have facilitated its increased use in a wide range of functional genomics research. Research into T. castaneum's sensory systems, response to pheromones and kairomones, and patterns of movement and landscape utilization has improved our understanding of behavioral and ecological processes. Tribolium castaneum has also been a model in the development of pest monitoring and management tactics, including evaluation of insecticide resistance mechanisms. Application of functional genomics approaches to behavioral, ecological, and pest management research is in its infancy but offers a powerful tool that can link mechanism with function and facilitate exploitation of these relationships to better manage this important food pest.

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.

Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs

Tribolium castaneum, the red flour beetle, is among the most well-studied eukaryotic genetic model organisms. Tribolium often serves as a comparative bridge from highly derived Drosophila traits to other organisms. Simultaneously, as a member of the most diverse order of metazoans, Coleoptera, Tribolium informs us about innovations that accompany hyper diversity. However, understanding the tempo and mode of evolutionary innovation requires well-resolved, time-calibrated phylogenies, which are not available for Tribolium. The most recent effort to understand Tribolium phylogenetics used two mitochondrial and three nuclear markers. The study concluded that the genus may be paraphyletic and reported a broad range for divergence time estimates. Here we employ recent advances in Bayesian methods to estimate the relationships and divergence times among Tribolium castaneum, T. brevicornis, T. confusum, T. freemani, and Gnatocerus cornutus using 1368 orthologs conserved across all five species and an independent substitution rate estimate. We find that the most basal split within Tribolium occurred ~86 Mya [95% HPD 85.90-87.04 Mya] and that the most recent split was between T. freemani and T. castaneum at ~14 Mya [95% HPD 13.55-14.00]. Our results are consistent with broader phylogenetic analyses of insects and suggest that Cenozoic climate changes played a role in the Tribolium diversification.

Patterns, Predictors, and Consequences of Dominance in Hybrids

AbstractCompared to those of their parents, are the traits of first-generation (F₁) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F₁ hybrids. We find that individual traits in F₁s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.

Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism and genotype by environment interactions by partitioning of mean phenotypes

Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line-cross analysis is a powerful quantitative genetics method to infer genetic architecture by analysing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line-cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulation studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses, we find that line-cross analysis has low power and high false-positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.

Genetic architecture underlying host choice differentiation in the sympatric host races of Lochmaea capreae leaf beetles

Speciation in herbivorous insects has received considerable attention during the last few decades. Much of this group's diversity originates from adaptive population divergence onto different host plants, which often involves the evolution of specialized patterns of host choice behaviour. Differences in host choice often translates directly into divergence in mating sites, and therefore positive assortative mating will be created which will act as a strong barrier to gene flow. In this study, we first explored whether host choice is a genetically determined trait in the sympatric willow and birch host races of the leaf feeding beetle Lochmaea capreae, or whether larval experience influences adult host choice. Once we had established that host choice is a genetically based trait we determined its genetic architecture. To achieve this, we employed a reciprocal transplant design in which offspring from pure willow and birch cross-types, F1, F2 and backcrosses were raised on each host plant and their preference was determined upon reaching adulthood. We then applied joint-scaling analysis to uncover the genetic architecture of host preference. Our results suggest that rearing host does not have a pronounced effect on adult's host choice; rather the segregation pattern implies the existence of genetic loci affecting host choice in these host races. The joint-scaling analysis revealed that population differences in host choice are mainly influenced by the contribution of additive genetic effects and also maternally inherited cytoplasmic effects. We explore the implications of our findings for evolutionary dynamics of sympatric host race formation and speciation.

Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae

The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because they fall between ecological niches due to their intermediate phenotypes ("extrinsic isolation"). Here, we present data from several crosses (parental crosses, F1, F2, and backcrosses) between the two host races of Lochmaea capreae on willow and birch to test for extrinsic isolation, intrinsic isolation, and environmentally dependent genetic incompatibilities. We employed a reciprocal transplant design in which offspring were raised on either host plant and their survival was recorded until adulthood. We also applied joint-scaling analysis to determine the genetic architecture of hybrid inviability. The relative fitness of the backcrosses switched between environments; furthermore, the additive genetic-environment interaction was detected as the strongest effect in our analysis. These results provide strong evidence that divergent natural selection has played a central role in the evolution of hybrid dysfunction between host races. Joint-scaling analysis detected significant negative epistatic effects that are most evident in the poor performance of F2-hybrids on willow, indicating signs of intrinsic isolation. We did not find any evidence that genetic incompatibilities are manifested independently of environmental conditions. Our findings suggest the outcome of natural hybridization between these host races is mainly affected by extrinsic isolation and a weak contribution of intrinsic isolation.

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.

Genome-wide dissection of hybrid sterility in Drosophila confirms a polygenic threshold architecture

To date, different studies about the genetic basis of hybrid male sterility (HMS), a postzygotic reproductive barrier thoroughly investigated using Drosophila species, have demonstrated that no single major gene can produce hybrid sterility without the cooperation of several genetic factors. Early work using hybrids between Drosophila koepferae (Dk) and Drosophila buzzatii (Db) was consistent with the idea that HMS requires the cooperation of several genetic factors, supporting a polygenic threshold (PT) model. Here we present a genome-wide mapping strategy to test the PT model, analyzing serially backcrossed fertile and sterile males in which the Dk genome was introgressed into the Db background. We identified 32 Dk-specific markers significantly associated with hybrid sterility. Our results demonstrate 1) a strong correlation between the number of segregated sterility markers and males' degree of sterility, 2) the exchangeability among markers, 3) their tendency to cluster into low-recombining chromosomal regions, and 4) the requirement for a minimum number (threshold) of markers to elicit sterility. Although our findings do not contradict a role for occasional major hybrid-sterility genes, they conform more to the view that HMS primarily evolves by the cumulative action of many interacting genes of minor effect in a complex PT architecture.

Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila

Based on ecological and metabolic arguments, some authors predict that adaptation to novel, harsh environments should involve alleles showing negative (diminishing return) epistasis and/or that it should be mediated in part by evolution of maternal effects. Although the first prediction has been supported in microbes, there has been little experimental support for either prediction in multicellular eukaryotes. Here we use a line-cross design to study the genetic architecture of adaptation to chronic larval malnutrition in a population of Drosophila melanogaster that evolved on an extremely nutrient-poor larval food for 84 generations. We assayed three fitness-related traits (developmental rate, adult female weight and egg-to-adult viability) under the malnutrition conditions in 14 crosses between this selected population and a nonadapted control population originally derived from the same base population. All traits showed a pattern of negative epistasis between alleles improving performance under malnutrition. Furthermore, evolutionary changes in maternal traits accounted for half of the 68% increase in viability and for the whole of 8% reduction in adult female body weight in the selected population (relative to unselected controls). These results thus support both of the above predictions and point to the importance of nonadditive effects in adaptive microevolution.

Genetic architecture of isolation between two species of Silene with sex chromosomes and Haldane's rule

Examination of the genetic architecture of hybrid breakdown can provide insight into the genetic mechanisms of commonly observed isolating phenomena such as Haldane's rule. We used line-cross analysis to dissect the genetic architecture of divergence between two plant species that exhibit Haldane's rule for male sterility and rarity, Silene latifolia and Silene diclinis. We made 15 types of crosses, including reciprocal F1, F2, backcrosses, and later-generation crosses, grew the seeds to flowering, and measured the number of viable ovules, proportion of viable pollen, and sex ratio. Typically, Haldane's rule for male rarity in XY animal hybrids is explained by interactions involving recessive X-linked alleles that are deleterious when hemizygous (dominance theory), whereas sterility is explained by rapid evolution of spermatogenesis genes (faster-male evolution). In contrast, we found that the genetic mechanisms underlying Haldane's rule between the two Silene species did not follow these conventions. Dominance theory was sufficient to explain male sterility, but male rarity likely involved faster-male evolution. We also found an effect of the neo-sex chromosomes of S. diclinis on the extreme rarity of some hybrid males. Our findings suggest that the genetic architecture of Haldane's rule in dioecious plants may differ from those commonly found in animals.

Developmental trajectories and breakdown in F1 interpopulation hybrids of Tribolium castaneum

When hybrid inviability is an indirect by-product of local adaptation, we expect its degree of severity between pairs of populations to vary and to be sensitive to the environment. While complete reciprocal hybrid inviability is the outcome of the gradual process of local adaptation, it is not representative of the process of accumulation of incompatibility. In the flour beetle, Tribolium castaneum, some pairs of populations exhibit complete, reciprocal F1 hybrid incompatibility while other pairs are fully or partially compatible. We characterize this naturally occurring variation in the degree and timing of expression of the hybrid incompatible phenotype to better understand the number of genes or developmental processes contributing to speciation. We assessed the morphological and developmental variation in four Tribolium castaneum populations and their 12 possible F1 hybrids at each life-history stage from egg to adult. We find that the rate of hybrid larval development is affected in all interpopulation crosses, including those eventually producing viable, fertile adults. Hybrid incompatibility manifests early in development as changes in the duration of instars and diminished success in the transition between instars are relative to the parent populations. Parent populations with similar developmental profiles may produce hybrids with disrupted development. The degree and timing of expression of hybrid inviability depends upon populations crossed, direction of the cross, and environment in which hybrids are raised. Our findings suggest that the coordinated expression of genes involved in transitional periods of development is the underlying cause of hybrid incompatibility in this species.

Hybrid breakdown weakens under thermal stress in population crosses of the copepod Tigriopus californicus

The outcome of hybridization can be impacted by environmental conditions, which themselves can contribute to reproductive isolation between taxa. In crosses of genetically divergent populations, hybridization can have both negative and positive impacts on fitness, the balance between which might be tipped by changes in the environment. Genetically divergent populations of the intertidal copepod Tigriopus californicus have been shown to differ in thermal tolerance at high temperatures along a latitudinal gradient. In this study, a series of crosses were made between pairs of genetically divergent populations of T. californicus, and the thermal tolerance of these hybrids was tested. In most cases, the first-generation hybrids had relatively high thermal tolerance and the second-generation hybrids were not generally reduced below the less-tolerant parental population for high temperature tolerance. This pattern contrasts with previous studies from crosses of genetically divergent populations of this copepod, which often shows hybrid breakdown in these second-generation hybrids for other measures of fitness. These results suggest that high temperature stress could either increase the positive impacts of hybridization or decrease the negative impacts of hybridization resulting in lowered hybrid breakdown in these population crosses.

An unusual barrier to gene flow: perpetually immature larvae from inter-population crosses in the flour beetle, Tribolium castaneum

We genetically characterize an unusual hybrid incompatibility phenotype manifest in F(1) offspring of crosses between two populations of Tribolium castaneum. Hybrid larvae cease development at the third larval instar, persisting as 'perpetually immature larvae' thereafter. Although unable to produce viable adult hybrid offspring with one another, each population produces abundant, fertile hybrids with other populations, indicating a recent origin of the incompatibility and facilitating genetic studies. We mapped the paternal component of the hybrid phenotype to a single region, which exhibits two characteristics common to hybrid incompatibility: marker transmission ratio distortion within crosses and elevated genetic divergence between populations. The incompatible variation and an elevation in between-population genetic divergence is associated with a region containing the T. castaneum ecdysone receptor homologue, a major regulatory switch, controlling larval moults, pupation and metamorphosis. This contributes to understanding the genetics of speciation in the Coleoptera, one of the most speciose of all arthropod taxa.

Interactions among flower-size QTL of Mimulus guttatus are abundant but highly variable in nature

The frequency and character of interactions among genes influencing complex traits remain unknown. Our ignorance is most acute for segregating variation within natural populations, the epistasis most relevant for quantitative trait evolution. Here, we report a comprehensive survey of interactions among a defined set of flower-size QTL: loci polymorphic within a single natural population of yellow monkeyflower (Mimulus guttatus). We find that epistasis is typical. Observed phenotypes routinely differ from those predicted on the basis of direct allelic affects in the isogenic background, although the direction of deviations is highly variable. Across QTL pairs, there are significantly positive and negative interactions for every trait. Across traits, specific locus pairs routinely exhibit both positive and negative interactions. There was a tendency for negative epistasis to accompany positive direct effects and vice versa for the trait of corolla width, which may be due, at least in part, to the fact that QTL were identified from their direct effects on this trait.

Mitonuclear match: optimizing fitness and fertility over generations drives ageing within generations

Many conserved eukaryotic traits, including apoptosis, two sexes, speciation and ageing, can be causally linked to a bioenergetic requirement for mitochondrial genes. Mitochondrial genes encode proteins involved in cell respiration, which interact closely with proteins encoded by nuclear genes. Functional respiration requires the coadaptation of mitochondrial and nuclear genes, despite divergent tempi and modes of evolution. Free-radical signals emerge directly from the biophysics of mosaic respiratory chains encoded by two genomes prone to mismatch, with apoptosis being the default penalty for compromised respiration. Selection for genomic matching is facilitated by two sexes, and optimizes fitness, adaptability and fertility in youth. Mismatches cause infertility, low fitness, hybrid breakdown, and potentially speciation. The dynamics of selection for mitonuclear function optimize fitness over generations, but the same selective processes also operate within generations, driving ageing and age-related diseases. This coherent view of eukaryotic energetics offers striking insights into infertility and age-related diseases.

Complex deleterious interactions associated with malic enzyme may contribute to reproductive isolation in the copepod Tigriopus californicus

Dobzhansky-Muller incompatibilities can result from the interactions of more than a single pair of interacting genes and there are several different models of how such complex interactions can be structured. Previous empirical work has identified complex conspecific epistasis as a form of complex interaction that has contributed to postzygotic reproductive isolation between taxa, but other forms of complexity are also possible. Here, I probe the genetic basis of reproductive isolation in crosses of the intertidal copepod Tigriopus californicus by looking at the impact of markers in genes encoding metabolic enzymes in F₂ hybrids. The region of the genome associated with the locus ME2 is shown to have strong, repeatable impacts on the fitness of hybrids in crosses and epistatic interactions with another chromosomal region marked by the GOT2 locus in one set of crosses. In a cross between one of these populations and a third population, these two regions do not appear to interact despite the continuation of a large effect of the ME2 region itself in both crosses. The combined results suggest that the ME2 chromosomal region is involved in incompatibilities with several unique partners. If these deleterious interactions all stem from the same factor in this region, that would suggest a different form of complexity from complex conspecific epistasis, namely, multiple independent deleterious interactions stemming from the same factor. Confirmation of this idea will require more fine-scale mapping of the interactions of the ME2 region of the genome.

Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation

Ecological selection against hybrids between populations occupying different habitats might be an important component of reproductive isolation during the initial stages of speciation. The strength and directionality of this barrier to gene flow depends on the genetic architecture underlying divergence in ecologically relevant phenotypes. We here present line cross analyses of inheritance for two key foraging-related morphological traits involved in adaptive divergence between stickleback ecotypes residing parapatrically in lake and stream habitats within the Misty Lake watershed (Vancouver Island, Canada). One main finding is the striking genetic dominance of the lake phenotype for body depth. Selection associated with this phenotype against first- and later-generation hybrids should therefore be asymmetric, hindering introgression from the lake to the stream population but not vice versa. Another main finding is that divergence in gill raker number is inherited additively and should therefore contribute symmetrically to reproductive isolation. Our study suggests that traits involved in adaptation might contribute to reproductive isolation qualitatively differently, depending on their mode of inheritance.

The nature of interactions that contribute to postzygotic reproductive isolation in hybrid copepods

Deleterious interactions within the genome of hybrids can lower fitness and result in postzygotic reproductive isolation. Understanding the genetic basis of these deleterious interactions, known as Dobzhansky-Muller incompatibilities, is the subject of intense current study that seeks to elucidate the nature of these deleterious interactions. Hybrids from crosses of individuals from genetically divergent populations of the intertidal copepod Tigriopus californicus provide a useful model in which to study Dobzhansky-Muller incompatibilities. Studies of the basis of postzygotic reproductive isolation in this species have revealed a number of patterns. First, there is evidence for a breakdown in genomic coadaptation between mtDNA-encoded and nuclear-encoded proteins that can result in a reduction in hybrid fitness in some crosses. It appears from studies of the individual genes involved in these interactions that although this coadaptation could lead to asymmetries between crosses, patterns of genotypic viabilities are not often consistent with simple models of genomic coadaptation. Second, there is a large impact of environmental factors on these deleterious interactions suggesting that they are not strictly intrinsic in nature. Temperature in particular appears to play an important role in determining the nature of these interactions. Finally, deleterious interactions in these hybrid copepods appear to be complex in terms of the number of genetic factors that interact to lead to reductions in hybrid fitness. This complexity may stem from three or more factors that all interact to cause a single incompatibility or the same factor interacting with multiple other factors independently leading to multiple incompatibilities.

Genetic variation and co-variation for fitness between intra-population and inter-population backgrounds in the red flour beetle, Tribolium castaneum

Hybrids from crosses between populations of the flour beetle, Tribolium castaneum, express varying degrees of inviability and morphological abnormalities. The proportion of allopatric population hybrids exhibiting these negative hybrid phenotypes varies widely, from 3% to 100%, depending upon the pair of populations crossed. We crossed three populations and measured two fitness components, fertility and adult offspring numbers from successful crosses, to determine how genes segregating within populations interact in inter-population hybrids to cause the negative phenotypes. With data from crosses of 40 sires from each of three populations to groups of five dams from their own and two divergent populations, we estimated the genetic variance and covariance for breeding value of fitness between the intra- and inter-population backgrounds and the sire × dam population interaction variance. The latter component of the variance in breeding values estimates the change in genic effects between backgrounds owing to epistasis. Interacting genes with a positive effect, prior to fixation, in the sympatric background but a negative effect in the hybrid background cause reproductive incompatibility in the Dobzhansky-Muller speciation model. Thus, the sire × dam population interaction provides a way to measure the progress towards speciation of genetically differentiating populations on a trait by trait basis using inter-population hybrids.

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.

Genetic architecture and postzygotic reproductive isolation: evolution of Bateson-Dobzhansky-Muller incompatibilities in a polygenic model

The Bateson-Dobzhansky-Muller model predicts that postzygotic isolation evolves due to the accumulation of incompatible epistatic interactions, but few studies have quantified the relationship between genetic architecture and patterns of reproductive divergence. We examined how the direction and magnitude of epistatic interactions in a polygenic trait under stabilizing selection influenced the evolution of hybrid incompatibilities. We found that populations evolving independently under stabilizing selection experienced suites of compensatory allelic changes that resulted in genetic divergence between populations despite the maintenance of a stable, high-fitness phenotype. A small number of loci were then incompatible with multiple alleles in the genetic background of the hybrid and the identity of these incompatibility loci changed over the evolution of the populations. For F(1) hybrids, reduced fitness evolved in a window of intermediate strengths of epistatic interactions, but F(2) and backcross hybrids evolved reduced fitness across weak and moderate strengths of epistasis due to segregation variance. Strong epistatic interactions constrained the allelic divergence of parental populations and prevented the development of reproductive isolation. Because many traits with varying genetic architectures must be under stabilizing selection, our results indicate that polygenetic drift is a plausible hypothesis for the evolution of postzygotic reproductive isolation.

Genetic differentiation among wild populations of Tribolium castaneum estimated using microsatellite markers

We report our characterization of the genetic variation within and differentiation among wild-collected populations of the red flour beetle, Tribolium castaneum, using microsatellite loci identified from its genome sequence. We find that global differentiation, estimated as the average F(ST) across all loci and between all population pairs, is 0.180 (95% confidence intervals of 0.142 and 0.218). A majority of our pairwise population comparisons (>70%) were significant even though this species is considered an excellent colonizer by virtue of its pest status. Regional genetic variation between Tribolium populations is 2-3 times that observed in the fruit fly, Drosophila melanogaster. There was a weak positive correlation between genetic distance [F(ST)/(1 - F(ST))] and geographic distance [ln(km)]; pairs of populations with the highest degree of genetic differentiation (F(ST) > 0.29) have been shown to exhibit significant postzygotic reproductive isolation when crossed in previous studies. We discuss the possibility that local extinction and kin-structured colonization have increased the level of genetic differentiation between Tribolium populations.

The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology

Tribolium castaneum is a small, low-maintenance beetle that has emerged as a sophisticated model system for studying the evolution of development and that complements (in some cases, even rivals) Drosophila for functional genetic analysis of basic biological questions. Although Tribolium and Drosophila are both holometabolous insects, they differ fundamentally in larval and adult morphology. Even generally conserved developmental features, such as body segmentation, are achieved by quite different means. Thus, comparison of developmental mechanisms between these two insects can address many interesting questions concerning the evolution of morphology and other characters. Genetic tools available for Tribolium include genetic maps for visible and molecular markers, chromosomal rearrangements that enable lethal mutations to be balanced in true-breeding stocks, transposon-based transformation systems, a completed and annotated genome sequence, and systemic RNA interference (RNAi), which makes it possible to knock down any given gene and even particular splice variants in the offspring or in any tissue of the injected animal. Inactivating gene functions at various developmental stages provides new opportunities to investigate post-embryonic development, as well as larval and adult physiology, including hormonal control, host-parasite interactions, and pesticide resistance.

Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum

Microbotryum violaceum, the anther-smut fungus, forms a complex of sibling species which specialize on different plants. Previous studies have shown the presence of partial ecological isolation and F1 inviability, but did not detect assortative mating apart from a high selfing rate. We investigated other post-mating barriers and show that F1 hybrid sterility, the inability of gametes to mate, increased gradually with the increasing genetic distance between the parents. F2 hybrids showed a reduced ability to infect the plants that was also correlated with the genetic distance. The host on which the F2 hybrids were passaged caused a selection for alleles derived from the pathogen species originally isolated from that host, but this effect was not detectable for the most closely related species. The post-mating barriers thus remain weak among the closest species pairs, suggesting that premating barriers are sufficient to initiate divergence in this system.

Host genetic architecture in single and multiple infections

Hosts are often target to multiple simultaneous infections by genetically diverse parasite strains. The interaction among these strains and the interaction of each strain with the host was shown to have profound effects on the evolution of parasite traits. Host factors like genetic architecture of resistance have so far been largely neglected. To see whether genetic architecture differs between different kinds of infections we used joint scaling analysis to compare the genetic components of resistance in the red flour beetle Tribolium castaneum exposed to single and multiple strains of the microsporidian Nosema whitei. Our results indicate that additive, dominance and epistatic components were more important in single infections whereas maternal components play a decisive role in multiple infections. In detail, parameter estimates of additive, dominance and epistatic components correlated positively between single and multiple infections, whereas maternal components correlated negatively. These findings may suggest that specificity of host-parasite interactions are mediated by genetic and especially epistatic components whereas maternal effects constitute a more general form of resistance.

Genetic architecture of hybrid male sterility in Drosophila: analysis of intraspecies variation for interspecies isolation

BACKGROUND

The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete.

METHODOLOGY/PRINCIPAL FINDINGS

Isofemale strains of D. mojavensis vary significantly in their production of sterile F(1) sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F(1) hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F(1) is complex, involving multiple QTL, epistasis, and cytoplasmic effects.

CONCLUSIONS/SIGNIFICANCE

The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation.

Nonadditive genetic components in resistance of the red flour beetle Tribolium castanaeum against parasite infection

Genetically coupled antagonistic coevolution between host and parasites can select for the maintenance of recombination in the host. Mechanistically, maintenance of recombination relies on epistatic interactions between resistance genes creating linkage disequilibria (LD). The role of epistasis in host resistance traits is however only partly understood. Therefore, we applied the joint scaling principle to assess epistasis and other nonadditive genetic components of two resistance traits, survival, and parasite spore load, in population crosses of the red flour beetle Tribolium castanaeum under infections with the microsporidian Nosema whitei. We found nonadditive components only in infected populations but not in control populations. The genetic architecture underlying survival under parasite infection was more complex than that of spore load. Accordingly, the observed negative correlation between survival and spore load was mainly based on a correlation between shared additive components. Breakdown of resistance was especially strong in F2 crosses between resistant lines indicating that multiple epistatic routes can lead to the same adaptation. In general, the wide range of nonoverlapping genetic components between crosses indicated that parasite resistance in T. castanaeum can be understood as a multi peaked fitness landscape with epistasis contributing substantially to phenotypic differentiation in resistance.

Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers

Model species often provide initial hypotheses and tools for studies of development, genetics and molecular evolution in closely related species. Flour beetles of the genus Tribolium Macleay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful developmental genetic system. The convenience with which congeneric and other species of tenebrionid flour beetles can be reared in the laboratory makes this group attractive for comparative studies on a small phylogenetic scale. Here we present the results of phylogenetic analyses of relationships among the major pest species of Tribolium based on two mitochondrial and three nuclear markers (cytochrome oxidase 1, 16S ribosomal DNA, wingless, 28S ribosomal DNA and histone H3). The utility of partitioning the dataset in a manner informed by biological structure and function is demonstrated by comparing various partitioning strategies. In parsimony and partitioned Bayesian analyses of the combined dataset, the castaneum and confusum species groups are supported as monophyletic and as each other's closest relatives. However, a sister group relationship between this clade and Tribolium brevicornis (Leconte 1859) is not supported. The inferred phylogeny provides an evolutionary framework for comparative studies using flour beetles.