Genetic architecture of sexual and asexual populations of the aphid Rhopalosiphum padi based on allozyme and microsatellite markers

Cyclical parthenogens, including aphids, are attractive models for comparing the genetic outcomes of sexual and asexual reproduction, which determine their respective evolutionary advantages. In this study, we examined how reproductive mode shapes genetic structure of sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) populations of the aphid Rhopalosiphum padi by comparing microsatellite and allozyme data sets. Allozymes showed little polymorphism, confirming earlier studies with these markers. In contrast, microsatellite loci were highly polymorphic and showed patterns very discordant from allozyme loci. In particular, microsatellites revealed strong heterozygote excess in asexual populations, whereas allozymes showed heterozygote deficits. Various hypotheses are explored that could account for the conflicting results of these two types of genetic markers. A strong differentiation between reproductive modes was found with both types of markers. Microsatellites indicated that sexual populations have high allelic polymorphism and heterozygote deficits (possibly because of population subdivision, inbreeding or selection). Little geographical differentiation was found among sexual populations confirming the large dispersal ability of this aphid. In contrast, asexual populations showed less allelic polymorphism but high heterozygosity at most loci. Two alternative hypotheses are proposed to explain this heterozygosity excess: allele sequence divergence during long-term asexuality or hybrid origin of asexual lineages. Clonal diversity of asexual lineages of R. padi was substantial suggesting that they could have frozen genetic diversity from the pool of sexual lineages. Several widespread asexual genotypes were found to persist through time, as already seen in other aphid species, a feature seemingly consistent with the general-purpose genotype hypothesis.     

Temporal differentiation and spatial coexistence of sexual and facultative asexual lineages of an aphid species at mating sites

Cases of coexisting sexual and asexual relatives are puzzling, as evolutionary theory predicts that competition for the same ecological niches should lead to the exclusion of one or the other population. In the cyclically parthenogenetic aphid, Rhopalosiphum padi, sexual and facultative asexual lineages are admixed in space at the time of sexual reproduction. We investigated how the interaction of reproductive mode and environment can lead to temporal niche differentiation. We demonstrated theoretically that differential sensitivity of sexual and facultatively asexual aphids to an environmental parameter (mating host suitability) shapes the two strategies: whereas the sexual lineages switch earlier to the production of sexual forms, the facultative asexual lineages delay and spread out their investment in sexual reproduction. This predicted pattern of niche specialization is in agreement with the temporal structure revealed in natura by demographic and genetic data. We propose that partial loss of sex by one pool of aphids and subsequent reduction in gene flow between lineages may favour temporal specialization through disruptive selection.     

Predominance of sexual reproduction in Romanian populations of the aphid Sitobion avenae inferred from phenotypic and genetic structure

Models of coexistence of sexual and asexual lineages in aphids assume that obligate parthenogenetic lineages predominate in areas with mild winter climate because of their high reproductive output, while sexual lineages predominate in areas with severe winter because they produce eggs resistant to frost. To validate this hypothesis in natural conditions, the reproductive mode of populations of the aphid Sitobion avenae was assessed in two very contrasting climatic situations, Romania (severe winter) and Western France (mild winter). To achieve this, reproductive modes were inferred from both (1) the population composition in sexual and asexual forms in autumn, and (2) the genetic structure of Romanian and French populations of S. avenae using microsatellite markers. Romanian populations encompassed a high proportion of sexual forms and were characterised by a very high genotypic diversity and low linkage disequilibrium. In constrast, the French population showed frequent linkage disequilibria, low genetic diversity, and high level of clonal amplification with two asexual genotypes representing over 60% of the sample. In agreement with the model's predictions, these results clearly indicate that sexual reproduction in S. avenae is predominant under the continental climate of Romania, while asexual lineages prevail under the oceanic climate of Western France.     

Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini

Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale , using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini .     

Gene flow between sexual and facultatively asexual lineages of an aphid species and the maintenance of reproductive mode variation

Many organisms considered as strictly clonal may in fact experience some rare events of sexual reproduction with their sexual relatives. However, the rate of sexual–asexual gene flow has rarely been assessed mainly because its evaluation is difficult to achieve in the field. In the cyclically parthenogenetic aphid Rhopalosiphum padi , two main sets of lineages, differing in their investment in sexual reproduction and in their genetic attributes, co-exist even at a very fine scale: the 'sexual' lineages which have a full commitment to the sexual reproduction, and the 'facultatively asexual' lineages, which allocate investment in the sexual and parthenogenetic reproduction. This system offers a unique opportunity to tackle the genetic interactions between two contrasting reproductive modes. Here, we provide evidence that gene flow occurred between sexual and facultatively asexual lineages of R. padi. We carefully examined the shuffling in phenotypic and genotypic variation following a sexual reproduction event that took place in the field. Combining genotypic data and phenotypic measurements showed that this gene mixing led to the production of a wide array of reproductive modes, including strictly asexual lineages. Finally, we discuss the central role played by facultatively asexual lineages on the maintenance of reproductive mode variation.     

Why is sex so rare in Lecane inermis (Rotifera: Monogononta) in wastewater treatment plants?

The monogonont rotifer Lecane inermis is commonly known as a facultative parthenogen. Unexpectedly, among numerous lineages we isolated from wastewater treatment plants (WWTP), only one was capable of sexual reproduction. We investigated why sex was so rare among L. inermis in WWTP. The reproductive modes of lineages derived from the sexual lineage were examined. Among all lineages, the fraction of those reproducing only asexually for 14 d was 0.39. In the subsequent round, the fraction of asexual lineages reached 0.61. The population growth rate of the parthenogenetic lineages was significantly higher than that of the sexual lineages. We simulated the fate of rotifer populations in WWTP by removing 10% of the experimental cultures each day. After 10 d of these conditions, the mean number of females was greater in parthenogenetic than in sexual lineages. After 20 d, only solitary dormant eggs remained in the sexual lineages. It therefore appears that the loss of sex may be attributed to the specific conditions of the WWTP. When there is no risk of desiccation and no need for dormancy, the fast‐growing parthenogens outcompete lineages investing in costly sex. Furthermore, even if some resting eggs were deposited, they would be washed out from the system with the excess sludge.     

Short-term consequences of reproductive mode variation on the genetic architecture of energy metabolism and life-history traits in the pea aphid

Cyclically parthenogenetic animals such as aphids are able alternating sexual and asexual reproduction during its life cycle, and represent good models for studying short-term evolutionary consequences of sex. In aphids, different morphs, whether sexual or asexual, winged or wingless, are produced in response to specific environmental cues. The production of these morphs could imply a differential energy investment between the two reproductive phases (i.e., sexual and asexual), which can also be interpreted in terms of changes in genetic variation and/or trade-offs between the associated traits. In this study we compared the G-matrices of energy metabolism, life-history traits and morph production in 10 clonal lineages (genotypes) of the pea aphid, Acyrthosiphon pisum, during both sexual and asexual phases. The heritabilities (broad-sense) were significant for almost all traits in both phases; however the only significant genetic correlation we found was a positive correlation between resting metabolic rate and production of winged parthenogenetic females during the asexual phase. These results suggest the pea aphid shows some lineage specialization in terms of energy costs, but a higher specialization in the production of the different morphs (e.g., winged parthenogenetic females). Moreover, the production of winged females during the asexual phase appears to be more costly than wingless females. Finally, the structures of genetic variance-covariance matrices differed between both phases. These differences were mainly due to the correlation between resting metabolic rate and winged parthenogenetic females in the asexual phase. This structural difference would be indicating that energy allocation rules changes between phases, emphasizing the dispersion role of asexual morphs.     

Adaptive Significance and Long-Term Survival of Asexual Lineages

Important questions remain about the long-term survival and adaptive significance of eukaryotic asexual lineages. Numerous papers dealing with sex advantages still continued to compare parthenogenetic populations versus sexual populations arguing that sex demonstrates a better fitness. Because asexual lineages do not possess any recombination mechanisms favoring rapid changes in the face of severe environmental conditions, they should be considered as an evolutionary dead-end. Nevertheless, reviewing literature dealing with asexual reproduction, it is possible to draw three stimulating conclusions. (1) Asexual reproduction in eukaryotes considerably differs from prokaryotes which experience recombination but neither meiosis nor syngamy. Recombination and meiosis would be a driving force for sexual reproduction. Eukaryotes should therefore be considered as a continuum of sexual organisms that are more or less capable (and sometimes incapable) of sexual reproduction. (2) Rather than revealing ancestral eukaryotic forms, most known lineages of asexual eukaryotes have lost sex due to a genomic conflict affecting their sexual capacity. Thus, it could be argued that hybridization is a major cause of their asexuality. Asexuality may have evolved as a reproductive mechanism reducing conflict within organisms. (3) It could be proposed that, rather than being generalists, parthenogenetic hybrid lineages could be favored when exploiting peculiar restricted ecological niches, following the “frozen niche variation” model. Although hybrid events may result in sex loss, probably caused by genomic conflict, asexual hybrids could display new original adaptive traits, and the rapid colonization of environments through clonal reproduction could favor their long-term survival, leading to evolutionary changes and hybrid speciation. Examination of the evolutionary history of asexual lineages reveals that evolutionary processes act through transitional stages in which even very small temporary benefits may be enough to counter the expected selective disadvantages.     

Functional rare males in diploid parthenogenetic Artemia

Functional males that are produced occasionally in some asexual taxa – called ‘rare males’ – raise considerable evolutionary interest, as they might be involved in the origin of new parthenogenetic lineages. Diploid parthenogenetic Artemia produce rare males, which may retain the ability to mate with females of related sexual lineages. Here, we (i) describe the frequency of male progeny in populations of diploid parthenogenetic Artemia, (ii) characterize rare males morphologically, (iii) assess their reproductive role, using cross‐mating experiments with sexual females of related species from Central Asia and characterize the F1 hybrid offspring viability and (iv) confirm genetically both the identity and functionality of rare males using DNA barcoding and microsatellite loci. Our result suggests that these males may have an evolutionary role through genetic exchange with related sexual species and that diploid parthenogenetic Artemia is a good model system to investigate the evolutionary transitions between sexual species and parthenogenetic strains.     

Admixed sexual and facultatively asexual aphid lineages at mating sites

Cyclically parthenogenetic organisms may have facultative asexual counterparts. Such organisms, including aphids, are therefore interesting models for the study of ecological and genetic interactions between lineages differing in reproductive mode. Earlier studies on aphids have revealed major differences in the genetic outcomes of populations that are possibly resulting mostly either from sexual or from asexual reproduction. Besides, notable gene flow between sexual and asexual derivatives has been suspected, which could lead to the emergence of new asexual lineages. The present study examines the interplay between these lineages and is based on analyses of population structure of individuals that may contribute to the pool of sexual reproductive forms in the host alternating aphid Rhopalosiphum padi. Using a Bayesian assignment method, we first show that the sexual forms of R. padi on mating sites encompass two genetically distinct clusters of individuals in the western part of France. The first cluster included unique genotypes of sexual lineages, while the second cluster included facultatively asexual lineages in numerous copies, the reproductive mode of the two clusters being confirmed by reference clones. Sexual reproductive forms produced by sexual and facultatively asexual lineages are thus admixed at mating sites which gives a large opportunity for the two clusters to mate with each other. Nevertheless, this study also highlights, as previously demonstrated, that the two clusters retained high genetic differentiation. Possible explanations for the inferred limited genetic exchanges are advanced in the discussion, but further dedicated investigations are required to solve this paradox.     

Spatial and temporal genetic variability in French populations of the peach-potato aphid,Myzus persicae

The peach-potato aphid, Myzus persicae (Sulzer), has a complex reproductive mode in which some lineages reproduce by continuous parthenogenesis, whereas others reproduce sexually once a year. The climate is thought to act directly on the reproductive mode, because sexual eggs are the only form that can resist frost in cold regions. Sexual reproduction necessitates an obligatory host alternation that may result in long-distance dispersal. Here, we examined the genetic variability at seven microsatellite loci of populations of M. persicae in France, where both reproductive modes occur. We provide clear genetic evidence that the breeding system affects genotypic variability, as cyclically parthenogenetic aphids are far more variable than their obligately parthenogenetic counterparts. A temporal decrease in genetic variability and a temporal genetic differentiation effect suggest the existence of selective factors that play an important role in shaping the genetic structure of M. persicae populations. Lastly, differences in the population structure between reproductive modes suggest that the migration associated with the change of host during sexual reproduction lowers the level of population differentiation.     

Genetic Control of Contagious Asexuality in the Pea Aphid

Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally interbreed because some asexual lineages maintain a residual production of males potentially able to mate with the females produced by sexual lineages. Hence, this species is an ideal model to study the genetic basis of the loss of sexual reproduction with quantitative genetic and population genomic approaches. Our analysis of the co-segregation of ∼300 molecular markers and reproductive phenotype in experimental crosses pinpointed an X-linked region controlling obligate asexuality, this state of character being recessive. A population genetic analysis (>400-marker genome scan) on wild sexual and asexual genotypes from geographically distant populations under divergent selection for reproductive strategies detected a strong signature of divergent selection in the genomic region identified by the experimental crosses. These population genetic data confirm the implication of the candidate region in the control of reproductive mode in wild populations originating from 700 km apart. Patterns of genetic differentiation along chromosomes suggest bidirectional gene flow between populations with distinct reproductive modes, supporting contagious asexuality as a prevailing route to permanent parthenogenesis in pea aphids. This genetic system provides new insights into the mechanisms of coexistence of sexual and asexual aphid lineages.     

High mutation rates in the mitochondrial genomes of Daphnia pulex

Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10(-7) and 1.73 × 10(-7) per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.     

Fitness and sexual response to population density in Daphnia pulex

1. The switch between asexual and sexual reproduction is an important fitness component in cyclically parthenogenetic populations as it is the key to persistence in unstable habitats and because it influences population genetic characteristics such as linkage disequilibrium and population genetic structure.
2. Genetic variation for sexual and asexual reproductive rate ( R _C) was examined, under varying population density, in Daphnia pulex sampled from a rockpool system and two other distinct European localities.
3. Density affected the switch to sexual behaviour, as found in other studies and reduced R _c. Production of males was not correlated with sexual reproduction, promoting outcrossing.
4. Genetic variation was found for the response to density, both within and between populations. There was substantial variation within the rockpools despite their demographic instability, indicating rapid recovery of life-history variation or maintenance during bottlenecks.     

Population genetics and ecology of Artemia: Insights into parthenogenetic reproduction

The relative advantages of sexual and parthenogenetic reproduction have long interested biologists and remain a central issue in ecological and evolutionary studies. Recent data on brine shrimp (Artemia) indicate that extensive ecological and genetic divergence occurs in an obligately parthenogenetic lineage. This challenges the belief that parthenogenetic lineages are evolutionary 'dead ends' and that extensive divergence is necessarily linked to recent recruitment from sexual ancestors. The molecular evidence suggests that parthenogenesis in Artemia is relatively ancient, with a single asexual lineage branching from an Old World sexual ancestor approximately five million years ago. Automictic recombination (which can occur in diploid but not polyploid parthenogenetic brine shrimp) appears to play a central role in the long-term maintenance of the parthenogenetic lineage.     

POLYPHYLETIC ORIGINS OF ASEXUALITY IN DAPHNIA PULEX. I. BREEDING-SYSTEM VARIATION AND LEVELS OF CLONAL DIVERSITY

There is growing evidence that transitions from sexual to asexual reproduction are often provoked by internal genetic factors rather than extrinsic selection pressures. In the cladoceran crustacean Daphnia pulex, the shift to asexuality has been linked to sex-limited meiosis suppression. Most populations of this species reproduce by obligate parthenogenesis, but cyclically parthenogenetic populations persist in the southern portion of its range. The meiosis-suppressor model predicts that asexuality in D. pulex has polyphyletic origins and that the coexistence of cyclically parthenogenetic lines with male-producing obligately asexual clones should be unstable. For the present study, we examined the genotypic structure of D. pulex populations from a region in which there is an abrupt microgeographical shift in breeding system. Populations in Michigan largely reproduce by cyclic parthenogenesis, while those in Ontario are obligately asexual. Allozyme studies on 77 populations from this area revealed 50 obligately asexual clones, divisible into two groups: one derived from a single parent species and the other derived via interspecific hybridization. Although nearly 50% of the clones retained male production, there was, as predicted, no evidence of coexistence between cyclically parthenogenetic populations and male-producing obligately asexual clones. The survey did, however, reveal a low incidence of cyclically parthenogenetic populations in Ontario. The high genotypic diversity of these populations suggests that they are not only resistant to meiosis suppression, but able to rework genetic variation gained from asexual clones into a sexual breeding system.     

Phylogenetic evidence for hybrid origins of asexual lineages in an aphid species

Understanding the mode of origin of asexuality is central to ongoing debates concerning the evolution and maintenance of sexual reproduction in eukaryotes. This is because it has profound consequences for patterns of genetic diversity and ecological adaptability of asexual lineages, hence on the outcome of competition with sexual relatives both in short and longer terms. Among the possible routes to asexuality, hybridization is a very common mechanism in animals and plants. Aphids present frequent transitions from their ancestral reproductive mode (cyclical parthenogenesis) to permanent asexuality, but the mode of origin of asexual lineages is generally not known because it has never been thoroughly investigated with appropriate molecular tools. Rhopalosiphum padi is an aphid species with coexisting sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages that are genetically distinct. Previous studies have shown that asexual lineages of R. padi are heterozygous at most nuclear loci, suggesting either that they have undergone long-term asexuality (under which heterozygosity tends to increase) or that they have hybrid origins. To discriminate between these alternatives, we conducted an extensive molecular survey combining the sequence analysis of alleles of two nuclear DNA markers and mitochondrial DNA haplotypes in sexual and asexual lineages of R. padi. Both nuclear and cytoplasmic markers clearly showed that many asexual lineages have hybrid origins, the first such demonstration in aphids. Our results also indicated that asexuals result from multiple events of hybridization between R. padi and an unknown sibling species, and are of recent origin (contradicting previous estimates that asexual R. padi lineages were of moderate longevity). This study constitutes another example that putatively ancient asexual lineages are actually of much more recent origin than previously thought. It also presents a robust approach for testing whether hybrid origin of asexuality is also a common phenomenon in aphids.     

Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.     

The eco-evolutionary importance of reproductive system variation in the macroalgae: Freshwater reds as a case study

The relative frequency of sexual versus asexual reproduction governs the distribution of genetic diversity within and among populations. Most studies on the consequences of reproductive variation focus on the mating system (i.e., selfing vs. outcrossing) of diploid-dominant taxa (e.g., angiosperms), often ignoring asexual reproduction. Although reproductive systems are hypothesized to be correlated with life-cycle types, variation in the relative rates of sexual and asexual reproduction remains poorly characterized across eukaryotes. This is particularly true among the three major lineages of macroalgae (green, brown, and red). The Rhodophyta are particularly interesting, as many taxa have complex haploid–diploid life cycles that influence genetic structure. Though most marine reds have separate sexes, we show that freshwater red macroalgae exhibit patterns of switching between monoicy and dioicy in sister taxa that rival those recently shown in brown macroalgae and in angiosperms. We advocate for the investigation of reproductive system evolution using freshwater reds, as this will expand the life-cycle types for which these data exist, enabling comparative analyses broadly across eukaryotes. Unlike their marine cousins, species in the Batrachospermales have macroscopic gametophytes attached to filamentous, often microscopic sporophytes. While asexual reproduction through monospores may occur in all freshwater reds, the Compsopogonales are thought to be exclusively asexual. Understanding the evolutionary consequences of selfing and asexual reproduction will aid in our understanding of the evolutionary ecology of all algae and of eukaryotic evolution generally.     

EVOLUTION OF TRADE-OFFS BETWEEN SEXUAL AND ASEXUAL PHASES AND THE ROLE OF REPRODUCTIVE PLASTICITY IN THE GENETIC ARCHITECTURE OF APHID LIFE HISTORIES

Life‐history theory postulates that evolution is constrained by trade‐offs (i.e., negative genetic correlations) among traits that contribute to fitness. However, in organisms with complex life cycles, trade‐offs may drastically differ between phases, putatively leading to different evolutionary trajectories. Here, we tested this possibility by examining changes in life‐history traits in an aphid species that alternates asexual and sexual reproduction in its life cycle. The quantitative genetics of reproductive and dispersal traits was studied in 23 lineages (genotypes) of the bird cherry‐oat aphid Rhopalosiphum padi, during both the sexual and asexual phases, which were induced experimentally under specific environmental conditions. We found large and significant heritabilities (broad‐sense) for all traits and several negative genetic correlations between traits (trade‐offs), which are related to reproduction (i.e., numbers of the various sexual or asexual morphs) or dispersal (i.e., numbers of winged or wingless morphs). These results suggest that R. padi exhibits lineage specialization both in reproductive and dispersal strategies. In addition, we found important differences in the structure of genetic variance–covariance matrices ( G ) between phases. These differences were due to two large, negative genetic correlations detected during the asexual phase only: (1) between fecundity and age at maturity and (2) between the production of wingless and winged parthenogenetic females. We propose that this differential expression in genetic architecture results from a reallocation scheme during the asexual phase, when sexual morphs are not produced. We also found significant G × E interaction and nonsignificant genetic correlations across phases, indicating that genotypes could respond independently to selection in each phase. Our results reveal a rather unique situation in which the same population and even the same genotypes express different genetic (co)variation under different environmental conditions, driven by optimal resource allocation criteria.